DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of the FAD3 gene in claim 94 and SEQ ID NO: 43 in claim 95 & SEQ ID NO: 46 in claim 91 in the reply filed on 11/25/2025 is acknowledged.
Claims 10, 86 & 87 are rejoined based on Applicant’s amendment. The species of LOX-3 in claim 94 is rejoined based on art.
Claim 73, drawn to an oil, remains withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 11/25/2025.
The election/restriction requirement is made FINAL.
Applicant “maintains traversal” of the restriction of claim 73 in Remarks filed 7/11/2025 in response to the Office Action mailed 2/11/2025 on the grounds that amended claim 73 requires the mutated gene or gene fragment of the plant or plant part from which the oil was produced (Remarks, 11, paragraph 4). This argument is unpersuasive, because a fragment of a mutated gene may be identical to other DNA polynucleotides, both naturally occurring and mutated, and thus an oil identical to the oil of claim 73 can still be produced without the plant or plant part of the instant invention. The restriction was already made FINAL in the Office Action mailed 2/11/2025 and is maintained.
Status of Claims
Claims 1, 3, 10, 16, 25, 30, 36, 37, 83-89, 91, 93-95 are under examination on the merits.
Claim 73 is withdrawn.
The objections to the specification are withdrawn in light of Applicant’s amendments.
The objection to claim 1 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 3, 16, 36, 37, 85, 88-90, 92 & 93 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, for Written Description, is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 3, 16, 36, 37, 85, 88-90, 92 & 93 under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, for Scope of Enablement, is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 3, 36, 37, 85, 88-89, & 93 under 35 U.S.C. 102(a)(1) and 102(a)(2) over Hildebrand et al US 5,017,386, taken with the evidence of Kitamura (1984) Agric. BioI. Chem., 48 (9),2339-2346 and Wang et al (1994) Proc. Natl. Acad. Sci. 91:5828-5832 and Du et al (2021) Food Chemistry. 335, 127582 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 3, 36, 37, 83, 85, 88-89, & 92 under 35 U.S.C. 102(a)(1) as being anticipated by Shin et al (2010) Theor Appl Genet. 124:613–622, taken with the evidence of Kim et al (1998). Korean J. Food Sci. Technol. 30(4):751-758 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1, 3, 30, 36, 37, 85, 88-93 under 35 U.S.C. 102(a)(1) as being anticipated by Forster et al (1999) Plant Molecular Biology 39: 1209–1220, taken with the evidence of Forster et al (1994) Plant Physiol. 106: 1227-1228 and GenBank accession X78580.1 is withdrawn in light of Applicant’s amendments.
The provisional rejection of claim 37 on the ground of nonstatutory double patenting as being unpatentable over claim 36 of copending Application No. 18/853,521 is withdrawn in light of Applicant’s amendments.
Claim Interpretation
In claims 84, 86-87, which recite that the amount of a fatty acid has decreased or increased by a percentage, “the amount” is interpreted as the content expressed as percent of total fatty acids. This is in keeping with the specification page 76 (lines 1-8 and line 30-page 77 line 2).
Claim Objections
Claims 16, 30 and 95 are objected to because of the following informalities:
Claim 16 (lines 2 and line 6): " in one more genes" should read either --in one or more genes-- or --in one more gene--.
Claims 30 (line 4) and 95 (lines 4, 8, 13, 16): "and retains" should read --and retaining-- or --that retains--.
Appropriate correction is required.
Claim 25 objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Claim Rejections - 35 USC § 112
Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 16, 91 & 95 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Based on Applicant’s amendments of the claims, this rejection is modified from the rejection set forth in the Office action mailed 2/11/2025, as applied to claims 1, 3, 16, 36, 37, 83-85, 88-90 & 92-93. Applicant' s arguments filed 7/23/2025 have been fully considered but they are not persuasive.
The term “FAD3C activity” in claim 95 (line 13) and “functional FAD3C protein” in claim 91 (lines 17-18) is indefinite because FAD3C activity or function is not defined by the claim or the specification. FAD3 genes within a species may be labeled FAD3C when more than one FAD3 gene is present; however, species with a single FAD3 gene may not have a “FAD3C” gene at all (Blume et al (2024) BMC Biotechnology 24:107, hereafter Blume, published after the filing of the instant Application: table 4). Thus, it is indefinite which FAD3 genes, encoding proteins of different structures across species, are encompassed by having “FAD3C activity” or being a “functional FAD3C” protein.
The term “exon 4” in claim 16 (line 4), “exon 2” in claim 16 (line 8) and “exon 3” in line 9 is a relative term which renders the claim indefinite. LOX genes in different plant species are numbered according to different standards; thus, it is indefinite which LOX genes, encoding proteins of different structures that participate in different pathways, are encompassed in the term LOX-2. Likewise, FAD2 and FAD3 proteins in different species may or may not comprise a single exon, or may have intron/exon boundaries at different locations in the gene (Blume, page 6, left column, paragraph 1 & page 8, right column, paragraph 3 & figure 2C), so it is indefinite which exons in FAD3 proteins that are not pea FAD3C and pea FAD3D proteins are encompassed by the number in claim 16.
Claim 86 recites “the amount of linolenic acid plus linoleic acid is reduced by at least 4%” in lines 2-3. It is unclear if this requirement means that the percentage of linolenic acid and the percentage of linoleic acid are summed and then reduced by 4% or if the percentage of linolenic acid and the percentage of linoleic acid both must be reduced by at least 4%. More than one possible interpretation renders the claim indefinite.
Claim 16 recites the limitation "said one or more insertions, substitutions, or deletions in one more genes selected from the group consisting of LOX-2 and LOX-3" in lines 2-3. There is insufficient antecedent basis for this limitation in the claim. Claim 94 recites a mutated LOX-3, and claim 1 recites a mutated LOX-2 gene (lines 4-5), but neither claim recites insertions, substitutions, or deletions in one more genes selected from the group consisting of LOX-2 and LOX3.
Claim 16 also recites the limitation "said one or more insertions, substitutions, or deletions in one more genes selected from the group consisting of FAD2 and FAD3" in lines 6-7. There is insufficient antecedent basis for this limitation in the claim. Claim 94 recites a mutated FAD2 gene or a mutated FAD3 gene comprising one or more insertions, substitutions, or deletion (lines 5-6) but does not recite insertions, substitutions, or deletions in one more genes selected from the group consisting of FAD2 or FAD3.
Claim 84 recites the limitation “said polyunsaturated lipid” in line 2. There is insufficient antecedent basis for this limitation in the claim.
Applicant urges that amended claims requiring at least 90% identity to SEQ ID NO: 10, which is pea Lox-2 and has a known number of exons, overcome the original indefiniteness rejection (Remarks page 15, paragraph 6-page 16, paragraph 1).
This argument is unpersuasive, because the amended and new claims require a FAD3C gene which has the same indefiniteness issues outlined for the Lox-2 protein.
Improper Dependency
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 36 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
The rejection is modified from the rejection as set forth in the Office action mailed 2/11/2025, as applied to claims 3, 85, & 88-89. Applicant' s arguments filed 7/23/2025 have been fully considered but they are not persuasive.
Claim 36 depends on amended claim 1 which requires a plant comprising a mutated LOX-gene comprising a nucleic acid sequence having at least 90% sequence identity to SEQ ID NO: 10. However, nucleic acid sequences of at least 90% sequence identity to SEQ ID NO: 10 are not know in the art outside of pea. See alignments in the Scope of Enablement rejection part D below. Because claim 36 encompasses species that would not comprise an endogenous lox-2 gene within the limitations of claim 1, claim 36 fails to include all the limitations of claim 1.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Applicant urges that some plants with reduced LOX activity may not necessarily have the recited phenotypes of claims 3, 85 & 88-89, because LOX activity can refer to the ability to catalyze co-oxidation of a substrate, including to produce 6-carbon aldehydes, or LOX activity may refer to ability to catalyze co-oxidation of pigments and proteins that influences post-harvest quality. Applicant urges that whether reduced LOX activity results in reduced hexanal, hexanol, and/or linolenic acid depends on extent of reduction of LOX activity and other factors, such as substrate availability, presence of other enzymes with related activity, and environment (Remarks, page 12, paragraph 8-page 13, paragraph 2). Applicant urges that because desirable characteristics may not be linked to one another in plants, some plants with reduced LOX activity may have reduced yield and/or total protein content (Remarks page 13, paragraph 3).
This argument is persuasive with regard to claims 3, 85 & 88-89 because claim 1 encompasses nucleic acids that vary from SEQ ID NO: 10 and might have LOX activity that differs from that of SEQ ID NO: 10. However, Applicant’s arguments are not applicable to the rejection of claim 36.
Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
A. Claims 1, 10, 16, 84, 86-87, 91, 93-95 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims require a plant or plant part comprising decreased fatty acid desaturase activity and a mutated FAD3 gene comprising one or more insertions, substitutions or deletions. Claim 16 further recites one or more insertions, substitutions, or deletions in one more genes selected from FAD3 located at least partially in the nucleotide region corresponding to exon 2 of the FAD3C gene. Claim 91 further requires a protein encoded by SEQ ID NO: 46 or a functional FAD3C protein with at least 90% sequence identity to SEQ ID NO: 46. Claim 95 further requires a gene encoding for a protein comprising SEQ ID NO: 43 or a sequence having 90% sequence identity to SEQ ID NO: 43 and FAD3C activity.
The claims require a gene from the genus of plant genes named FAD3C. The specification teaches two examples of FAD3 genes, FAD3C (SEQ ID NO: 46, encoding SEQ ID NO: 43) and FAD3D (SEQ ID NO: 56, encoding SEQ ID NO: 53). The specification describes that FAD3 catalyzes the insertion of a double bond into linoleic acid to form linolenic acid (page 2, lines 2-4). Thus, the claims are broad and read on a mutation in any FAD3C gene.
FAD3 genes are known in the art. A sequence of a predicted FAD in pea Lathyrus oleraceus (NCBI Reference Sequence XM_051025045.1, available 8/25/2025 after the filing of the instant invention) that has 100% identity to just 41% of the sequence of SEQ ID NO: 46. See piecewise alignments below.
Range 1: 116 to 435
Alignment statistics for match #1
Score
Expect
Identities
Gaps
Strand
592 bits(320)
2e-172
320/320(100%)
0/320(0%)
Plus/Plus
Query 1 ATGGTTGTTCAAGAACCTCAAAATCTGCTACATGTTGGTAATGGTGATGTTCTTGTTGAT 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 116 ATGGTTGTTCAAGAACCTCAAAATCTGCTACATGTTGGTAATGGTGATGTTCTTGTTGAT 175
Query 61 GATGaaaaaaaaCACCACCATACAAGTTTTGATCCAAGTGCTCCTCCACCATTTAAGATT 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 176 GATGAAAAAAAACACCACCATACAAGTTTTGATCCAAGTGCTCCTCCACCATTTAAGATT 235
Query 121 GCAGAGGTTCGTGCCGCGATTCCGAAACACTGTTGGGTTAAGAATCCATGGATTTCTCTT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 236 GCAGAGGTTCGTGCCGCGATTCCGAAACACTGTTGGGTTAAGAATCCATGGATTTCTCTT 295
Query 181 AGTTATCTTCTTAGAGACATTTTCATTGTCACTGCATTGGTAGCTGCTGCAATTCATTTC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 296 AGTTATCTTCTTAGAGACATTTTCATTGTCACTGCATTGGTAGCTGCTGCAATTCATTTC 355
Query 241 AATAATTGGATCTTTTGGCCAATTTATTGGATTTCTCAAGGAACTATGTTTTGGGCTCTT 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 356 AATAATTGGATCTTTTGGCCAATTTATTGGATTTCTCAAGGAACTATGTTTTGGGCTCTT 415
Query 301 TTTGTTCTTGGACATGATTG 320
||||||||||||||||||||
Sbjct 416 TTTGTTCTTGGACATGATTG 435
Range 2: 1090 to 1282
Alignment statistics for match #2
Score
Expect
Identities
Gaps
Strand
357 bits(193)
1e-101
193/193(100%)
0/193(0%)
Plus/Plus
Query 2712 GACAGAAGCAGCAAAGCCAGTGCTAGGAAAATATTATCGTGAGCCAGAGAAATCTGGGGC 2771
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1090 GACAGAAGCAGCAAAGCCAGTGCTAGGAAAATATTATCGTGAGCCAGAGAAATCTGGGGC 1149
Query 2772 AGTCCCATTCCATCTCTTTAAGTACTTTCTACACAGCATGAATCAGGACCACTTCGTCAG 2831
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1150 AGTCCCATTCCATCTCTTTAAGTACTTTCTACACAGCATGAATCAGGACCACTTCGTCAG 1209
Query 2832 TGATTCTGGAGACATTGTTTTCTACCAAACAGACCCTAAGCTCCATAATAATTCTTGGAC 2891
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1210 TGATTCTGGAGACATTGTTTTCTACCAAACAGACCCTAAGCTCCATAATAATTCTTGGAC 1269
Query 2892 CAAGTCTGAGTAA 2904
|||||||||||||
Sbjct 1270 CAAGTCTGAGTAA 1282
Range 3: 685 to 871
Alignment statistics for match #3
Score
Expect
Identities
Gaps
Strand
346 bits(187)
2e-98
187/187(100%)
0/187(0%)
Plus/Plus
Query 1059 GTGGAACAGAAGTCCTGGTAAAGAAGGTTCACATTTCAATCCATATAGCAAATTGTTCAC 1118
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 685 GTGGAACAGAAGTCCTGGTAAAGAAGGTTCACATTTCAATCCATATAGCAAATTGTTCAC 744
Query 1119 ACCAAGTGAGAGAAAAGATGTGTTAACTTCAACATTTTGTTGGGGTATCATGTTTTGTGG 1178
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 745 ACCAAGTGAGAGAAAAGATGTGTTAACTTCAACATTTTGTTGGGGTATCATGTTTTGTGG 804
Query 1179 GCTTGTTTATTTATCCTTAATAAAGGGTCCtttttttATGCTCAAAATCTATGGAGTTCC 1238
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 805 GCTTGTTTATTTATCCTTAATAAAGGGTCCTTTTTTTATGCTCAAAATCTATGGAGTTCC 864
Query 1239 ttattgg 1245
|||||||
Sbjct 865 TTATTGG 871
Range 4: 951 to 1090
Alignment statistics for match #4
Score
Expect
Identities
Gaps
Strand
259 bits(140)
3e-72
140/140(100%)
0/140(0%)
Plus/Plus
Query 1824 AGGAATGGGACTATCTAAGAGGTGGTTTAACGACCGTGGATCGTGACTATGGTTGGGTTA 1883
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 951 AGGAATGGGACTATCTAAGAGGTGGTTTAACGACCGTGGATCGTGACTATGGTTGGGTTA 1010
Query 1884 ACAACATTCACCATGACATTGGCACACATGTTATTCATCATCTTTTTCCTCAAATTCCAC 1943
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1011 ACAACATTCACCATGACATTGGCACACATGTTATTCATCATCTTTTTCCTCAAATTCCAC 1070
Query 1944 ATTATCATTTGATTGAAGCG 1963
||||||||||||||||||||
Sbjct 1071 ATTATCATTTGATTGAAGCG 1090
Range 5: 593 to 685
Alignment statistics for match #5
Score
Expect
Identities
Gaps
Strand
172 bits(93)
4e-46
93/93(100%)
0/93(0%)
Plus/Plus
Query 860 TTGACAGAGAAGATGTACAAGAGTTTAGACAACATGACAAAAACAATGAGATTTACTTTT 919
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 593 TTGACAGAGAAGATGTACAAGAGTTTAGACAACATGACAAAAACAATGAGATTTACTTTT 652
Query 920 CCTTTTCCAATCTTTGCATACCCTTTTTATTTG 952
|||||||||||||||||||||||||||||||||
Sbjct 653 CCTTTTCCAATCTTTGCATACCCTTTTTATTTG 685
Range 6: 435 to 526
Alignment statistics for match #6
Score
Expect
Identities
Gaps
Strand
171 bits(92)
1e-45
92/92(100%)
0/92(0%)
Plus/Plus
Query 424 GTGGCCATGGAAGCTTTTCAAATAGTGTTAAGCTGAATAGTTTTGTGGGCCATATCTTGC 483
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 435 GTGGCCATGGAAGCTTTTCAAATAGTGTTAAGCTGAATAGTTTTGTGGGCCATATCTTGC 494
Query 484 ATTCTTCGATTCTTGTTCCATATCATGGATGG 515
||||||||||||||||||||||||||||||||
Sbjct 495 ATTCTTCGATTCTTGTTCCATATCATGGATGG 526
Range 7: 871 to 956
Alignment statistics for match #7
Score
Expect
Identities
Gaps
Strand
154 bits(83)
1e-40
86/87(99%)
1/87(1%)
Plus/Plus
Query 1341 GATCTTTATCATGTGGTTGGACTTTGTCACATATATGCATCACCATGGTTACTCTCAGAA 1400
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 871 GATCTTTATCATGTGGTTGGACTTTGTCACATATATGCATCACCATGGTTACTCTCAGAA 930
Query 1401 ACTACCTTGGTATCGTGGCAAGGTAAT 1427
||||||||||||||||||||||| |||
Sbjct 931 ACTACCTTGGTATCGTGGCAAGG-AAT 956
Range 8: 525 to 592
Alignment statistics for match #8
Score
Expect
Identities
Gaps
Strand
126 bits(68)
3e-32
68/68(100%)
0/68(0%)
Plus/Plus
Query 619 GGAGAATCAGCCATAGAACTCATCATCAAAATCATGGTCATGTTGAGAAAGATGAATCCT 678
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 525 GGAGAATCAGCCATAGAACTCATCATCAAAATCATGGTCATGTTGAGAAAGATGAATCCT 584
Query 679 GGGTTCCT 686
||||||||
Sbjct 585 GGGTTCCT 592
In other species, sequences with at least 90% identity to the full sequence of instant SEQ ID NO: 46 are not known. The nearest sequence known in another species, Lathyrus linifolius, has only 82% similarity and 63.7% match (GenBank OZ206517.1 from nucleotide 286,759,569 to 286,762,568, available 12/1/2024, after the filing of the instant application) . See alignment below.
OZ206517s24
LOCUS OZ206517s24 12010020 bp DNA linear PLN 01-DEC-2024
COMMENT segment of length 12010020: from 276000001 to 288010020
DEFINITION Lathyrus linifolius genome assembly, chromosome: 3.
ACCESSION OZ206517
VERSION OZ206517.1
DBLINK BioProject: PRJEB82905
BioSample: SAMEA7522408
Sequence Read Archive: ERR13245272, ERR13245273, ERR13245274,
ERR13245275, ERR13245276, ERR13245277, ERR13245278, ERR13245279,
ERR13245280, ERR13248951
KEYWORDS .
SOURCE Lathyrus linifolius
ORGANISM Lathyrus linifolius
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50
kb inversion clade; NPAAA clade; Hologalegina; IRL clade; Fabeae;
Lathyrus.
REFERENCE 1
CONSRTM Wellcome Sanger Tree of Life Programme
TITLE Direct Submission
JOURNAL Submitted (27-NOV-2024) WELLCOME SANGER INSTITUTE, Tree of Life,
Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
COMMENT The assembly drLatLini1.hap1.1 is based on 25x PacBio data and
Arima2 Hi-C data generated by the Darwin Tree of Life Project
(https://www.darwintreeoflife.org/). The assembly process included
the following sequence of steps: initial PacBio assembly generation
with Hifiasm in Hi-C integrated assembly mode, and Hi-C based
scaffolding with YaHS. The mitochondrial and chloroplast genomes
were assembled using OATK. Finally, each haplotype assembly was
analysed and manually improved using TreeVal. Chromosome-scale
scaffolds confirmed by the Hi-C data have been named in order of
size.
FEATURES Location/Qualifiers
source 1..726504577
/organism="Lathyrus linifolius"
/mol_type="genomic DNA"
/db_xref="taxon:313096"
/chromosome="3"
/geo_loc_name="United Kingdom:Surrey | RBG Kew | rock
garden. Origin, UNITED KINGDOM | within Mardale Mountain
Meadow sheep exclosure below Harter Fell | S of RSPB
Haweswater | 400 m"
/collection_date="2020-09-03"
assembly_gap 4899641..4899840
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 13200474..13200673
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 16034903..16035102
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 16127804..16128003
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 18225795..18225994
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 20991322..20991521
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 26508108..26508307
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 33684510..33684709
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 42345744..42345943
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 48981864..48982063
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 49984996..49985195
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 59018196..59018395
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 60013396..60013595
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 76052968..76053167
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 77189646..77189845
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 79061760..79061959
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 79551874..79552073
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 100007658..100007857
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 106238138..106238337
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 109362786..109362985
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 121290969..121291168
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 133410198..133410397
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 133498885..133499084
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 133598721..133598920
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 134037302..134037501
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 137543036..137543235
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 149980816..149981015
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 150238329..150238528
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 156821393..156821592
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 157335877..157336076
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 157778049..157778248
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 157988222..157988421
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 160183422..160183621
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 167870413..167870612
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 170536028..170536227
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 171439416..171439615
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 174432278..174432477
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 175238734..175238933
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 176160329..176160528
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
Query Match 63.7%; Score 1849.4; Length 12010020;
Best Local Similarity 82.0%;
Matches 2524; Conservative 0; Mismatches 301; Indels 254; Gaps 24;
Qy 1 ATGGTTGTTCAAGAACCTCAAAATCTGCTACATGTTGGTAATGGTGATGTTCTTGTTGAT 60
|||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
Db 10762567 ATGGTTGTTCAAGAACCTCAAACTCTGCTACATGTTGGTAATGGTGATGTTCTTGTTGAT 10762508
Qy 61 GATGAAAAAAAACACCACC---ATACAAGTTTTGATCCAAGTGCTCCTCCACCATTTAAG 117
|||||||||||||| |||| ||||||||||||||||||||||||||||||||||||||
Db 10762507 GATGAAAAAAAACAACACCATGATACAAGTTTTGATCCAAGTGCTCCTCCACCATTTAAG 10762448
Qy 118 ATTGCAGAGGTTCGTGCCGCGATTCCGAAACACTGTTGGGTTAAGAATCCATGGATTTCT 177
|||||||||||||| ||||||||||||||||| |||||||||||||||||||||||||||
Db 10762447 ATTGCAGAGGTTCGCGCCGCGATTCCGAAACATTGTTGGGTTAAGAATCCATGGATTTCT 10762388
Qy 178 CTTAGTTATCTTCTTAGAGACATTTTCATTGTCACTGCATTGGTAGCTGCTGCAATTCAT 237
|||||||||||||||||||| ||||||||||||| |||||| |||||||||||||||||
Db 10762387 CTTAGTTATCTTCTTAGAGATGTTTTCATTGTCACCGCATTGATAGCTGCTGCAATTCAT 10762328
Qy 238 TTCAATAATTGGATCTTTTGGCCAATTTATTGGATTTCTCAAGGAACTATGTTTTGGGCT 297
|||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||
Db 10762327 TTCAATAATTGGATCTTTTGGCCAATTTATTGGATTTCTCAAGGGACTATGTTTTGGGCT 10762268
Qy 298 CTTTTTGTTCTTGGACATGATTGGTATTCTTTTTT--TTCATTCATTTTTTAATTTCAAT 355
|||||||||||||||||||||||||||| ||||| |||||| |||||| | || |
Db 10762267 CTTTTTGTTCTTGGACATGATTGGTATTAATTTTTAATTCATTTTTTTTTTTAATTTCAA 10762208
Qy 356 AATTTTTTTATGTTAATTTAACTCATAGATTTGTTTTTTTTTTGGTATCTGTGTGTTTGA 415
| |||||||||||||||||||||| || |||||||||| |||||||||||
Db 10762207 TAATTTTTTATGTTAATTTAACTCACGAGATTTGTTTTTTTTTG-----TGTGTGTTTGA 10762153
Qy 416 TTTGAACAGTGGCCATGGAAGCTTTTCAAATAGTGTTAAGCTGAATAGTTTTGTGGGCCA 475
||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 10762152 TTTGAGCAGTGGCCATGGAAGCTTTTCAAATAGTGTTAAGCTGAATAGTTTTGTGGGCCA 10762093
Qy 476 TATCTTGCATTCTTCGATTCTTGTTCCATATCATGGATGGTTTGTTCTTTTTTTTAATAT 535
||||||||||||||| ||||||||||||||||||||||||||||||||||||||||
Db 10762092 TATCTTGCATTCTTCAATTCTTGTTCCATATCATGGATGGTTTGTTCTTTTTTTTATATG 10762033
Qy 536 GATTCTTTTTAAGATGCTTTTCTGTTCATTTTATTCTGTTTAAGATTCTTTTTTCTTTT- 594
| |||| | |||||||||||||||||||| |||||||||||||| | ||||
Db 10762032 ATTCTTTTTAAGATGTTTTTTCTGTTCATTTTATTCTCTTTAAGATTCTTTTATATTTTT 10761973
Qy 595 ----------------TTTTGAATCTGATTTATTTTTGCAGGAGAATCAGCCATAGAACT 638
|||| ||||||||||||||||||||||||||||| |||||||||
Db 10761972 TTATTATCAATTTTTATTTTAAATCTGATTTATTTTTGCAGGAGAATCAGTCATAGAACT 10761913
Qy 639 CATCATCAAAATCATGGTCATGTTGAGAAAGATGAATCCTGGGTTCCTGTATATAACTTT 698
|||||||||||||||||||||||||||||||||||||| ||||||||||||| || |||
Db 10761912 CATCATCAAAATCATGGTCATGTTGAGAAAGATGAATCATGGGTTCCTGTATGTATTTTT 10761853
Qy 699 TTCTTTCTTTTC---------ATTTACCATGAAATTTACACAATTACCGTAACAAAATTA 749
||| |||||||| ||||||| ||| ||||||| ||| ||||||| |||||||
Db 10761852 TTCCTTCTTTTCACATTCAAGATTTACCGTGAGATTTACATAATCACCGTAATAAAATTA 10761793
Qy 750 CGATGATTGTGTCTATTTCACGGTATAATCTTAATTTGTCTAAAATGGTGAAAATCTTTG 809
|||||||| |||| |||||| | |||| ||||||||| || || | | | | |
Db 10761792 CGATGATTCTGTCAATTTCATGATATAGTCTTAATTTATCCAATAATTTCTCATTAT--- 10761736
Qy 810 TTAATTGTTTATGATATCATGTTTTTGTGTTTGTATGTTGAATGTCTCAGTTGACAGAGA 869
||| ||| ||| | |||||| |||||||||||| |||||||
Db 10761735 -------------------TGTGTTTATGTATTTATGTTTAATGTCTCAGTTAACAGAGA 10761695
Qy 870 AGATGTACAAGAGTTTAGACAACATGACAAAAACAATGAGATTTACTTTTCCTTTTCCAA 929
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 10761694 AGATGTACAAGAGTTTAGACAACATGACAAAAACAATGAGATTTACTTTTCCTTTTCCAA 10761635
Qy 930 TCTTTGCATACCCTTTTTATTTGGTGAGTGATTCCCTTACAACATTGTTTGTTTTGTTTT 989
||||||||||||| |||||||||||||| ||||| ||||||||| || |||||||||
Db 10761634 TCTTTGCATACCCATTTTATTTGGTGAGAGATTCTCTTACAACA----TTTTTTTGTTTT 10761579
Qy 990 GTTTTGTTACATTATAATTATAAATAATAATTTCTAACAATTTTTTTTATTTATGTAAAC 1049
||||||| ||||||||||| ||||||||||||||||||||||| |||||||||||
Db 10761578 ATTTTGTTCCATTATAATTAAAAATAATAATTTCTAACAATTTT-----TTTATGTAAAC 10761524
Qy 1050 CACA-TTTCAGTGGAACAGAAGTCCTGGTAAAGAAGGTTCACATTTCAATCCATATAGCA 1108
|||| ||||||||||||||||||||||| |||||||||||||||||||||||||||||||
Db 10761523 CACATTTTCAGTGGAACAGAAGTCCTGGAAAAGAAGGTTCACATTTCAATCCATATAGCA 10761464
Qy 1109 AATTGTTCACACCAAGTGAGAGAAAAGATGTGTTAACTTCAACATTTTGTTGGGGTATCA 1168
||||||||||||||| ||||||||||||||||||||||||| ||||||||||||||||||
Db 10761463 AATTGTTCACACCAAATGAGAGAAAAGATGTGTTAACTTCATCATTTTGTTGGGGTATCA 10761404
Qy 1169 TGTTTTGTGGGCTTGTTTATTTATCCTTAATAAAGGGTCCTTTTTTTATGCTCAAAATCT 1228
||||||||| ||||||||||||||||||||||||||||||||| ||||||||||||||||
Db 10761403 TGTTTTGTGTGCTTGTTTATTTATCCTTAATAAAGGGTCCTTTCTTTATGCTCAAAATCT 10761344
Qy 1229 ATGGAGTTCCTTATTGGGTAA-TATTATTATTATTATTTAATATTTATTTCACATTTTCT 1287
||||||||||||||||||||| |||||||| |||||||||||||| ||| | |||||||
Db 10761343 ATGGAGTTCCTTATTGGGTAATTATTATTACTATTATTTAATATTAGTTTGAAATTTTCT 10761284
Qy 1288 TTTATGTTTAAAATTAGTGTAAAAGATTTACTTTTTTTTTCTTCTGATATGTAGATCTTT 1347
|||||||||||||||||||||| |||||||||| ||| |||||| ||||||||||||
Db 10761283 TTTATGTTTAAAATTAGTGTAACAGATTTACTTATTT----TTCTGAAATGTAGATCTTT 10761228
Qy 1348 ATCATGTGGTTGGACTTTGTCACATATATGCATCACCATGGTTACTCTCAGAAACTACCT 1407
|||||||||||||||||||||||||||||||||||||||||||| |||| |||||||||
Db 10761227 ATCATGTGGTTGGACTTTGTCACATATATGCATCACCATGGTTATGCTCAAAAACTACCT 10761168
Qy 1408 TGGTATCGTGGCAAGGTAATATAAAAATA-------------TTATTATTCAAAAAAATT 1454
||||||||||| ||||||||||||||||| || |||||||| ||
Db 10761167 TGGTATCGTGGAAAGGTAATATAAAAATATTTTTATTTTTATTTTTTATTCAATTTTTTT 10761108
Qy 1455 TGTCTCTGTTTTCTTGGCTGTTATTCGGTGAAAGAGAATCTCTAAAAGCTAAGGAATTGG 1514
|||| ||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||
Db 10761107 TGTCACTGTTTTCTTGGCTGTTATGCGGTGAAATAGAATCTCTAAAAGCTAAGGAATAGG 10761048
Qy 1515 ACTTTAGTTTCAGATTTCTTTTTCTTTTTAAATTCCTTTATTAAATATATATTTATATTA 1574
||||||||| ||||||||||||||||||| |||||||||||||||| |||||||||||||
Db 10761047 ACTTTAGTTACAGATTTCTTTTTCTTTTTTAATTCCTTTATTAAATTTATATTTATATTA 10760988
Qy 1575 TTAACCAAGATATTTTGAAGGTGAAATAATATAATTATAAGCAATTCTGT-GTACATGAA 1633
|||||||||||||||||||||||||||||||||||||||||||||| ||| |||||||||
Db 10760987 TTAACCAAGATATTTTGAAGGTGAAATAATATAATTATAAGCAATTTTGTCGTACATGAA 10760928
Qy 1634 AAGTATTTAGGAATTTGTTCTAAGAAAACATGTTGGATGTAAGTTTTTAAATAAGGGTCG 1693
||||||||||||| ||||||| |||||||| | | || | | | ||
Db 10760927 AAGTATTTAGGAACTTGTTCTGAGAAAACACGCATAAAAACTTTTATGATTTCGATTTC- 10760869
Qy 1694 CACATTGATATAAATAGTATAGATATTATGATGCTGATTATGGTAATGTGAAATAAATAA 1753
|| || ||||||||||| ||| || | || | ||
Db 10760868 -----------AATTAATATAGATATTACGATATTGGT--------------ATCAGTAT 10760834
Qy 1754 TAATTTGTTCTTTTATATAAAAACGGTGAATAATGATATCAGTGTCGTAATAATATTTTG 1813
| || ||| ||| | || | | ||||| || ||||||||||
Db 10760833 CTGCATTTTTTTTGATACCGTATCGATTATTAATGGGAT----------GTAATATTTTG 10760784
Qy 1814 ATAATTGGACAGGAATGGGACTATCTAAGAGGTGGTTTAACGACCGTGGATCGTGACTAT 1873
||| | |||||||||||||||||||||| |||||||||||||| |||||||||||||||
Db 10760783 GTAAATTGACAGGAATGGGACTATCTAAGGGGTGGTTTAACGACAGTGGATCGTGACTAT 10760724
Qy 1874 GGTTGGGTTAACAACATTCACCATGACATTGGCACACATGTTATTCATCATCTTTTTCCT 1933
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 10760723 GGTTGGGTTAACAACATTCACCATGACATTGGCACACATGTTATTCATCATCTTTTTCCT 10760664
Qy 1934 CAAATTCCACATTATCATTTGATTGAAGCGGTACATTCTCTTTCTTTCACTCTTTTTGTT 1993
||||||||||||||||||||| ||||||||||||||||||||||||| ||||| ||| ||
Db 10760663 CAAATTCCACATTATCATTTGGTTGAAGCGGTACATTCTCTTTCTTTAACTCTCTTT-TT 10760605
Qy 1994 TTTTTACTTTCTCAATAACAAAGGAATAAAGGCCCCAAACAATAAAGAAAAAGGCCCACA 2053
|||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
Db 10760604 TTTTTACTTTCTCAATAACAAAAGAATAAAGGCCCCAAACAATAAAGAAAAAGGCCCACA 10760545
Qy 2054 ATTCAACTTGCATAGTTACCTTTGAAGTGGAGTGTGACAACACAAGGACTTTGTCTTTAA 2113
||||||||||||||||| |||| |||||||||||||||||||||||||||||||||||||
Db 10760544 ATTCAACTTGCATAGTTGCCTTAGAAGTGGAGTGTGACAACACAAGGACTTTGTCTTTAA 10760485
Qy 2114 TGTTAGGGTTCATACACTAGACTTAACTCCACTTGCATGTTTGTTTAATTTCCATTGAAA 2173
||||||||||||||||||||| ||||||||||||| ||||||||||||||||||||||||
Db 10760484 TGTTAGGGTTCATACACTAGAGTTAACTCCACTTGTATGTTTGTTTAATTTCCATTGAAA 10760425
Qy 2174 GCAAACAAAAAAACCCTCAAAATTTGTCATTGTTGCATTTTTACCAGATTTTACAATATA 2233
|| || |||||||| ||||||||| |||||||||||||| ||||||| | ||||
Db 10760424 GCCAAAAAAAAAACATAAAAAATTTGTTGATGTTGCATTTTTACGTGATTTTAGAGTATA 10760365
Qy 2234 GCCAATCTCAACCATTTATTTTATATCTAACTATTCAG-AATTAAATTCACTCTCAT--- 2289
| ||||||||||||||||||| | ||| ||| || | | || |||||||||||||
Db 10760364 GTCAATCTCAACCATTTATTTAAAATCGAACGGTTATGTATTTTAATTCACTCTCATGCG 10760305
Qy 2290 -----------CATGGTAAAATGAATCCGACCCATTATACATATATATTTTGTCTGTATT 2338
|||||||| || |||| || | ||| || | ||||||||| |||
Db 10760304 ATAAAATTAAAGGTGGTAAAACAAACTCGACTCACAAAACAAATCTGTTTTGTCTGCATT 10760245
Qy 2339 CTTTACGGGATAAATTAAAGTTTAAGAGCTGTATCCTCTCTATATCATTCTCGCAACGT- 2397
|||| |||||| ||||| |||||||| || || | |||||| |||||||| |
Db 10760244 TTTTATGGGATAGATTAAGATTTAAGAGTTGCATTC-CTCTATGTCATTCTCATTTTTTT 10760186
Qy 2398 ------------------------------------------------------------ 2397
Db 10760185 TCAGATAATTTCTGCGAACGTTTTCATTAATATAAATTTTTACAACTTTTAAGTTTTAGA 10760126
Qy 2398 --------------------------------------TTTTTCTAAAGACAGATTGATA 2419
||||| |||||||| | |||
Db 10760125 AGTTAAGGGTCTGTTAGACCTACCCCAATCCATTCTACTTTTTTGAAAGACAGTCTAATA 10760066
Qy 2420 TTTTAGACTCACATTCTCTAATATGATAATTTTATTCCACCCCCATTATTTTTAGAAACT 2479
||||| |||| ||| || ||||| ||| || | ||||| |||||||||||||||||| |
Db 10760065 TTTTAAACTCGCATCCTATAATACGATCGTTCTTTTCCA-CCCCATTATTTTTAGAAATT 10760007
Qy 2480 TTGCA-------------CGGGTTTGGCACAATGTTAGTTGCATGTTTGAAAGAAATAAT 2526
|| || | | || |||||||| ||||||||||||| |
Db 10760006 TTACAAGACGAACATGATCATTTGCCATTGTATCTTAGTTGCTGGTTTGAAAGAAATGAC 10759947
Qy 2527 GATAAAATATAAGATGCATTACCATATTACTTTTATTAAGG-GAAGAAAAAATGAATGAG 2585
|||||||||| | || ||| ||||||| ||||||||| ||||| ||||||||||||
Db 10759946 GATAAAATATTGGTTGTATTTTCATATTAGTTTTATTAAATAGAAGAGAAAATGAATGAG 10759887
Qy 2586 AAAGTGTGGGGTGTATTACCAAAAGAGGAGGTGTGAATAGTTACCGAATATAGAATCAGA 2645
||| |||||||||||| |||||| |||||||||||||||||||| | |||||||
Db 10759886 AAAACGTGGGGTGTATTGCCAAAACAGGAGGTGTGAATAGTTACCAATTATAGAAATCAG 10759827
Qy 2646 AACAAACAGTGTCATTGAATCGTACAATAAAACATGTTTGTGTTTGTTTTTTCCTGTGTG 2705
|| || | ||||| |||||||||||||||||||||||||||||||||| ||||
Db 10759826 AAAGAAACATTGTCATGAATTGTACAATAAAACATGTTTGTGTTTGTTTTTTCCTCTGTG 10759767
Qy 2706 ATTTCAGACAGAAGCAGCAAAGCCAGTGCTAGGAAAATATTATCGTGAGCCAGAGAAATC 2765
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 10759766 ATTTCAGACAGAAGCAGCAAAGCCAGTGCTAGGAAAATATTATCGTGAGCCAGAGAAATC 10759707
Qy 2766 TGGGGCAGTCCCATTCCATCTCTTTAAGTACTTTCTACACAGCATGAATCAGGACCACTT 2825
||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||
Db 10759706 TGGGGCAGTCCCATTTCATCTGTTTAAGTACTTTCTACACAGCATGAATCAGGACCACTT 10759647
Qy 2826 CGTCAGTGATTCTGGAGACATTGTTTTCTACCAAACAGACCCTAAGCTCCATAATAATTC 2885
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 10759646 CGTCAGTGATTCTGGAGACATTGTTTTCTACCAAACAGACCCTAAGCTCCATAATAATTC 10759587
Qy 2886 TTGGACCAAGTCTGAGTAA 2904
|||||||||||||||||||
Db 10759586 TTGGACCAAGTCTGAGTAA 10759568
Proteins with 90% sequence identity to SEQ ID NO: 43 are described in the art; however, no putative FAD proteins with as little as 90% sequence identity to SEQ ID NO: 43 are found in species other than pea. For example, UniProt record A0A072UYW9_MEDTR (first available 10/1/2014) teaches a Medicago truncatula FAD sequence with 89.9% sequence similarity to instant SEQ ID NO: 43. See alignment below. No pea FAD3 are described with 90% sequence identity to SEQ ID NO: 43.
A0A072UYW9_MEDTR
ID A0A072UYW9_MEDTR Unreviewed; 385 AA.
AC A0A072UYW9;
DT 01-OCT-2014, integrated into UniProtKB/TrEMBL.
DT 01-OCT-2014, sequence version 1.
DT 08-OCT-2025, entry version 50.
DE SubName: Full=Microsomal omega-3 fatty acid desaturase {ECO:0000313|EMBL:KEH34298.1};
DE SubName: Full=Putative fatty acid desaturase domain-containing protein {ECO:0000313|EMBL:RHN67670.1};
GN Name=25490906 {ECO:0000313|EnsemblPlants:KEH34298};
GN OrderedLocusNames=MTR_3g464330 {ECO:0000313|EMBL:KEH34298.1};
GN ORFNames=MtrunA17_Chr3g0105171 {ECO:0000313|EMBL:RHN67670.1};
OS Medicago truncatula (Barrel medic) (Medicago tribuloides).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; Hologalegina; IRL clade; Trifolieae; Medicago.
OX NCBI_TaxID=3880 {ECO:0000313|EMBL:KEH34298.1, ECO:0000313|Proteomes:UP000002051};
RN [1] {ECO:0000313|EMBL:KEH34298.1, ECO:0000313|EnsemblPlants:KEH34298}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=A17 {ECO:0000313|EMBL:KEH34298.1}, and cv. Jemalong A17
RC {ECO:0000313|EnsemblPlants:KEH34298};
RX PubMed=22089132; DOI=10.1038/nature10625;
RA Young N.D., Debelle F., Oldroyd G.E., Geurts R., Cannon S.B., Udvardi M.K.,
RA Benedito V.A., Mayer K.F., Gouzy J., Schoof H., Van de Peer Y., Proost S.,
RA Cook D.R., Meyers B.C., Spannagl M., Cheung F., De Mita S.,
RA Krishnakumar V., Gundlach H., Zhou S., Mudge J., Bharti A.K., Murray J.D.,
RA Naoumkina M.A., Rosen B., Silverstein K.A., Tang H., Rombauts S.,
RA Zhao P.X., Zhou P., Barbe V., Bardou P., Bechner M., Bellec A., Berger A.,
RA Berges H., Bidwell S., Bisseling T., Choisne N., Couloux A., Denny R.,
RA Deshpande S., Dai X., Doyle J.J., Dudez A.M., Farmer A.D., Fouteau S.,
RA Franken C., Gibelin C., Gish J., Goldstein S., Gonzalez A.J., Green P.J.,
RA Hallab A., Hartog M., Hua A., Humphray S.J., Jeong D.H., Jing Y.,
RA Jocker A., Kenton S.M., Kim D.J., Klee K., Lai H., Lang C., Lin S.,
RA Macmil S.L., Magdelenat G., Matthews L., McCorrison J., Monaghan E.L.,
RA Mun J.H., Najar F.Z., Nicholson C., Noirot C., O'Bleness M., Paule C.R.,
RA Poulain J., Prion F., Qin B., Qu C., Retzel E.F., Riddle C., Sallet E.,
RA Samain S., Samson N., Sanders I., Saurat O., Scarpelli C., Schiex T.,
RA Segurens B., Severin A.J., Sherrier D.J., Shi R., Sims S., Singer S.R.,
RA Sinharoy S., Sterck L., Viollet A., Wang B.B., Wang K., Wang M., Wang X.,
RA Warfsmann J., Weissenbach J., White D.D., White J.D., Wiley G.B.,
RA Wincker P., Xing Y., Yang L., Yao Z., Ying F., Zhai J., Zhou L., Zuber A.,
RA Denarie J., Dixon R.A., May G.D., Schwartz D.C., Rogers J., Quetier F.,
RA Town C.D., Roe B.A.;
RT "The Medicago genome provides insight into the evolution of rhizobial
RT symbioses.";
RL Nature 480:520-524(2011).
RN [2] {ECO:0000313|EMBL:KEH34298.1, ECO:0000313|EnsemblPlants:KEH34298}
RP GENOME REANNOTATION.
RC STRAIN=A17 {ECO:0000313|EMBL:KEH34298.1}, and cv. Jemalong A17
RC {ECO:0000313|EnsemblPlants:KEH34298};
RX PubMed=24767513; DOI=10.1186/1471-2164-15-312;
RA Tang H., Krishnakumar V., Bidwell S., Rosen B., Chan A., Zhou S.,
RA Gentzbittel L., Childs K.L., Yandell M., Gundlach H., Mayer K.F.,
RA Schwartz D.C., Town C.D.;
RT "An improved genome release (version Mt4.0) for the model legume Medicago
RT truncatula.";
RL BMC Genomics 15:312-312(2014).
RN [3] {ECO:0000313|EnsemblPlants:KEH34298}
RP IDENTIFICATION.
RC STRAIN=cv. Jemalong A17 {ECO:0000313|EnsemblPlants:KEH34298};
RG EnsemblPlants;
RL Submitted (APR-2015) to UniProtKB.
RN [4] {ECO:0000313|Proteomes:UP000265566}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Jemalong A17 {ECO:0000313|Proteomes:UP000265566};
RX PubMed=30397259; DOI=10.1038/s41477-018-0286-7;
RA Pecrix Y., Staton S.E., Sallet E., Lelandais-Briere C., Moreau S.,
RA Carrere S., Blein T., Jardinaud M.F., Latrasse D., Zouine M., Zahm M.,
RA Kreplak J., Mayjonade B., Satge C., Perez M., Cauet S., Marande W.,
RA Chantry-Darmon C., Lopez-Roques C., Bouchez O., Berard A., Debelle F.,
RA Munos S., Bendahmane A., Berges H., Niebel A., Buitink J., Frugier F.,
RA Benhamed M., Crespi M., Gouzy J., Gamas P.;
RT "Whole-genome landscape of Medicago truncatula symbiotic genes.";
RL Nat. Plants 4:1017-1025(2018).
RN [5] {ECO:0000313|EMBL:RHN67670.1}
RP NUCLEOTIDE SEQUENCE.
RC TISSUE=Leaves {ECO:0000313|EMBL:RHN67670.1};
RA Pecrix Y., Gamas P., Carrere S.;
RT "Whole-genome landscape of Medicago truncatula symbiotic genes.";
RL Nat. Plants 0:0-0(2018).
CC -!- PATHWAY: Lipid metabolism. {ECO:0000256|ARBA:ARBA00005189}.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000256|ARBA:ARBA00004370}.
CC -!- SIMILARITY: Belongs to the fatty acid desaturase type 1 family.
CC {ECO:0000256|ARBA:ARBA00009295}.
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DR EMBL; CM001219; KEH34298.1; -; Genomic_DNA.
DR EMBL; PSQE01000003; RHN67670.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A072UYW9; -.
DR STRING; 3880.A0A072UYW9; -.
DR EnsemblPlants; KEH34298; KEH34298; MTR_3g464330.
DR Gramene; rna15879; RHN67670.1; gene15879.
DR KEGG; mtr:25490906; -.
DR HOGENOM; CLU_033094_1_0_1; -.
DR OrthoDB; 1461976at2759; -.
DR Proteomes; UP000002051; Chromosome 3.
DR Proteomes; UP000265566; Chromosome 3.
DR ExpressionAtlas; A0A072UYW9; differential.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0042389; F:omega-3 fatty acid desaturase activity; IBA:GO_Central.
DR GO; GO:0016717; F:oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water; IEA:InterPro.
DR GO; GO:0006636; P:unsaturated fatty acid biosynthetic process; IBA:GO_Central.
DR CDD; cd03507; Delta12-FADS-like; 1.
DR InterPro; IPR005804; FA_desaturase_dom.
DR InterPro; IPR021863; FAS_N.
DR InterPro; IPR012171; Fatty_acid_desaturase.
DR PANTHER; PTHR32100; OMEGA-6 FATTY ACID DESATURASE, CHLOROPLASTIC; 1.
DR Pfam; PF11960; DUF3474; 1.
DR Pfam; PF00487; FA_desaturase; 1.
PE 3: Inferred from homology;
KW Fatty acid biosynthesis {ECO:0000256|ARBA:ARBA00023160};
KW Fatty acid metabolism {ECO:0000256|ARBA:ARBA00022832};
KW Lipid biosynthesis {ECO:0000256|ARBA:ARBA00022516};
KW Lipid metabolism {ECO:0000256|ARBA:ARBA00023098};
KW Membrane {ECO:0000256|ARBA:ARBA00023136, ECO:0000256|SAM:Phobius};
KW Oxidoreductase {ECO:0000256|ARBA:ARBA00023002};
KW Reference proteome {ECO:0000313|Proteomes:UP000002051};
KW Transmembrane {ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|SAM:Phobius}.
FT TRANSMEM 54..75
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 81..100
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 214..234
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT TRANSMEM 246..263
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 18..72
FT /note="Fatty acid desaturase N-terminal"
FT /evidence="ECO:0000259|Pfam:PF11960"
FT DOMAIN 80..334
FT /note="Fatty acid desaturase"
FT /evidence="ECO:0000259|Pfam:PF00487"
SQ SEQUENCE 385 AA; 44918 MW; 07E8403BEA93C17B CRC64;
Query Match 90.0%; Score 1979.5; Length 385;
Best Local Similarity 89.9%;
Matches 349; Conservative 13; Mismatches 23; Indels 3; Gaps 2;
Qy 1 MVVQEPQNLLHVGNGDVLVDDEKKHHHTSFDPSAPPPFKIAEVRAAIPKHCWVKNPWISL 60
| |:||| | |||||||: | ||| :|||||||||||||:||||||||||||| |||
Db 1 MAVKEPQTLQHVGNGDVV--DAKKHQQ-NFDPSAPPPFKIAEIRAAIPKHCWVKNPLISL 57
Qy 61 SYLLRDIFIVTALVAAAIHFNNWIFWPIYWISQGTMFWALFVLGHDCGHGSFSNSVKLNS 120
|:|||:||| ||:||||||||||||||||||||||||||||||||||||||||| |||
Db 58 GYVLRDLFIVIALIAAAIHFNNWIFWPIYWISQGTMFWALFVLGHDCGHGSFSNSSLLNS 117
Qy 121 FVGHILHSSILVPYHGWRISHRTHHQNHGHVEKDESWVPLTEKMYKSLDNMTKTMRFTFP 180
||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 118 LVGHFLHSSILVPYHGWRISHRTHHQNHGHVEKDESWVPLTEKMYKSLDNMTKTMRFTFP 177
Qy 181 FPIFAYPFYLWNRSPGKEGSHFNPYSKLFTPSERKDVLTSTFCWGIMFCGLVYLSLIKGP 240
|||||||||||||||||||||||||||||||||||||:||| || |||| | ||||||||
Db 178 FPIFAYPFYLWNRSPGKEGSHFNPYSKLFTPSERKDVITSTVCWSIMFCLLTYLSLIKGP 237
Qy 241 FFMLKIYGVPYWIFIMWLDFVTYMHHHGYSQKLPWYRGKEWDYLRGGLTTVDRDYGWVNN 300
|||:||||||||||||||||||||||||||||||||:|||||||||||||||||||||
Db 238 IVMLKLYGVPYWIFIMWLDFVTYMHHHGYSQKLPWYRGQEWDYLRGGLTTVDRDYGWVNN 297
Qy 301 IHHDIGTHVIHHLFPQIPHYHLIEATEAAKPVLGKYYREPEKSGAVPFHLFKYFLHSMNQ 360
||||||||||||||||||||||:||||||||||||||||||||| || ||||||||||:|
Db 298 IHHDIGTHVIHHLFPQIPHYHLVEATEAAKPVLGKYYREPEKSGPVPHHLFKYFLHSMSQ 357
Qy 361 DHFVSDSGDIVFYQTDPKLHNNSWTKSE 388
|||||||||||||| |||| ||:|||||
Db 358 DHFVSDSGDIVFYQADPKLQNNTWTKSE 385
Fatty acid desaturases (FAD) belong to a large genus of proteins. FAD genes are named according to orthology with Arabidopsis genes (Xiao et al (2022) Molecular Biology Reports. 49:9997–10011 (published 7/11/2022, hereafter Xiao); page 9998, left column, paragraph 3). Duplications of genes encoding FAD have diversified functions in plant species, allowing for different catalytic abilities and the synthesis of new fatty acids and derivatives and affecting qualities such as seed oil and abiotic and biotic stress resistance (Xiao page 9998, right column, paragraph 2 & table 1).
Because different numbers of FAD3 genes are present within plant species, some plant species with only a single FAD3 gene may lack a “FAD3C” gene (Blume et al (2024) BMC Biotechnology. 24:107, published 12/18/2024 after the filing of the instant application. Hereafter, Blume. Table 4). In Camelina sativa, where FAD3 genes have high sequence conservancy, subfunctionalization of homologs is based on expressional differences, and FAD3 promoter regions have different cis-acting elements (Blume page 8, paragraphs 4-5).
The instant specification has not described the necessary features of a FAD3 protein that confers FAD3C functional activity or that differentiates FAD3C functional activity from the activity of another FAD3 gene. The instant specification has also not described any structural features of the promoter or other regulatory regions of a FAD3 protein that differentiates FAD3C function from another FAD3 gene.
Since the disclosure fails to describe the common attributes that identify members of the genus of FAD3C proteins, and because the genera are highly variant, SEQ ID NOs: 43 & 46 are insufficient to describe the claimed genera.
Hence, Applicant has not, in fact, described FAD3C proteins over the full scope of the claims, and the specification fails to provide an adequate written description of the claimed invention. Therefore, given the lack of written description in the specification with regard to the structural and functional characteristics of the claimed compositions, Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
B. Claims 1, 10, 16, 84, 86-87, 91, 93-95 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims require a plant or plant part comprising a mutated lox-3 gene comprising one or more insertions, substitutions or deletions. Claim 16 further recites one or more insertions, substitutions, or deletions located at least partially in the nucleotide region corresponding to exon 4 of the lox-2 or lox-3 gene. Claim 91 further requires a protein encoded by SEQ ID NO: 27 or a functional LOX-3 protein encoded by a sequence with at least 90% sequence identity to SEQ ID NO: 27. Claim 95 further requires a gene encoding for a protein comprising at least 90% sequence identity to SEQ ID NO: 25.
The claims require a gene from the genus of plant genes named LOX-3. The specification provides examples of lipoxygenase activity to catalyze co-oxidation of a substrate (page 17, lines 14-17) but does not specifically define the activity of LOX-3. The species of LOX-3 genes described in the specification are the pea LOX-3 gene (instant SEQ ID NO: 27). Thus, the specification does not describe species over the full scope of claimed genes. The species of LOX-3 proteins described in the specification include the amino acid sequences of SEQ ID NO: 25 and 26 (page 34, lines 31-32).
LOX genes are known in the art, including a LOX gene in pea with greater than 99% sequence identity to instant SEQ ID NO: 27 (GenBank sequence X78581.1, available 11/14/2006). See alignment below.
Score
Expect
Identities
Gaps
Strand
6035 bits(3268)
0.0
3326/3354(99%)
3/3354(0%)
Plus/Plus
Query 1 ATGTTTTCAGGCGTGACTGGTATTCTGAATAGAGGCCATAAAATAAAAGGGACAGTGGTG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 5974 ATGTTTTCAGGCGTGACTGGTATTCTGAATAGAGGCCATAAAATAAAAGGGACAGTGGTG 6033
Query 61 TTGATGAGAAAGAATGTGTTGGATATAAACAGCTTAACCACTGTTGGTGGTGTTATCGGT 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6034 TTGATGAGAAAGAATGTGTTGGATATAAACAGCTTAACCACTGTTGGTGGTGTTATCGGT 6093
Query 121 CAAGGCTTCGACATTCTCGGTTCCACGGTTGATAATCTCACTGCTTTCTTAGGCCGTTCT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6094 CAAGGCTTCGACATTCTCGGTTCCACGGTTGATAATCTCACTGCTTTCTTAGGCCGTTCT 6153
Query 181 GTTTCTCTTCAGTTGATCAGTGCAACAAAACCTGATGGTACAGTTTCTATAACattttga 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6154 GTTTCTCTTCAGTTGATCAGTGCAACAAAACCTGATGGTACAGTTTCTATAACATTTTGA 6213
Query 241 gcttttgaaaatgaattttgattctgtatttaattgtttttatttgtattttgtTAGCGA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6214 GCTTTTGAAAATGAATTTTGATTCTGTATTTAATTGTTTTTATTTGTATTTTGTTAGCGA 6273
Query 301 CTGGGAAAGGGAAGCTTGGAAAAGCTACTTTTCTGGAAGGTATAATTTCTTCATTACCAA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6274 CTGGGAAAGGGAAGCTTGGAAAAGCTACTTTTCTGGAAGGTATAATTTCTTCATTACCAA 6333
Query 361 CTTTGGGAGCTGGACAATCTGCTTTTAAGATTCACTTTGAATGGGATGATGATATGGGAA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6334 CTTTGGGAGCTGGACAATCTGCTTTTAAGATTCACTTTGAATGGGATGATGATATGGGAA 6393
Query 421 TTCCTGGTGCATTTTATATTAAAAACTTTATGCAAACTGAGTTTTTTCTTGTGAGTTTGA 480
||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||
Sbjct 6394 TTCCTGGCGCATTTTATATCAAAAACTTTATGCAAACTGAGTTTTTTCTTGTGAGTTTGA 6453
Query 481 CTCTTGATGACATTCCAAATCACGGAAGTATCTACTTTGTATGCAACTCTTGGATATATA 540
|||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
Sbjct 6454 CTCTTGATGACATTCCAAATCATGGAAGTATCTACTTTGTATGCAACTCTTGGATATATA 6513
Query 541 ATGCCAAACACCACAAAATCGATCGCATTTTCTTTGCGAATCAGGTATATATATGTTTAT 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6514 ATGCCAAACACCACAAAATCGATCGCATTTTCTTTGCGAATCAGGTATATATATGTTTAT 6573
Query 601 ATTTGTATATTTGTTTTCAACTTTAAGGCTTATGAGGAAGATAATCGAAGAATTGTGTTG 660
||||||||||| |||| ||||||||||||||||||||||||||| ||||||||||||||
Sbjct 6574 GTTTGTATATTTCTTTTGAACTTTAAGGCTTATGAGGAAGATAATAGAAGAATTGTGTTG 6633
Query 661 CAGACGTATCTTCCGAGTGAAACTCCGGCTCCATTAGTCCATTATAGAGAAGAAGAATTG 720
|||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||
Sbjct 6634 CAGACGTATCTTCCGAGTGAGACTCCGGCTCCATTAGTCCATTATAGAGAAGAAGAATTG 6693
Query 721 AATAATTTAAGAGGAGACGGAACAGGAGAGCGCAAAGAATGGGAAAGGATCTATGATTAC 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6694 AATAATTTAAGAGGAGACGGAACAGGAGAGCGCAAAGAATGGGAAAGGATCTATGATTAC 6753
Query 781 GATGTCTATAATGATTTAGGAAATCCAGATTCGGGTGAGAACCATGCTCGTCCGGTTCTT 840
|||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct 6754 GATGTCTATAATGATTTAGGAAATCCGGATTCGGGTGAGAACCATGCTCGTCCGGTTCTT 6813
Query 841 GGAGGGTCTGAAACCTATCCTTATCCGCGTAGGGGGAGAACCGGTCGAAAACCAACCAGA 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6814 GGAGGGTCTGAAACCTATCCTTATCCGCGTAGGGGGAGAACCGGTCGAAAACCAACCAGA 6873
Query 901 AAAGGTTTAACTTCTATTACATTGAGTATGAATAATGTTTTATCAGTTATCACTATACAA 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6874 AAAGGTTTAACTTCTATTACATTGAGTATGAATAATGTTTTATCAGTTATCACTATACAA 6933
Query 961 TATCATTTCAACTATTTTATTGCTATTAAGCAGATCCTAATAGTGAGAGTAGAAGTGATT 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6934 TATCATTTCAACTATTTTATTGCTATTAAGCAGATCCTAATAGTGAGAGTAGAAGTGATT 6993
Query 1021 ATGTGTATCTTCCAAGAGATGAAGCTTTTGGTCACTTGAAGTCATCAGATTTTCTCACTT 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 6994 ATGTGTATCTTCCAAGAGATGAAGCTTTTGGTCACTTGAAGTCATCAGATTTTCTCACTT 7053
Query 1081 ATGGATTAAAAGCTGTGTCTCAAAACGTGGTTCCTGCATTAGAATCTGTGTTCTTTGATT 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 7054 ATGGATTAAAAGCTGTGTCTCAAAACGTGGTTCCTGCATTAGAATCTGTGTTCTTTGATT 7113
Query 1141 TGAATTTCACGCCAAATGAGTTTGATAGCTTTGATGAAGTTCATGGATTGTATGAGGGTG 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 7114 TGAATTTCACGCCAAATGAGTTTGATAGCTTTGATGAAGTTCATGGATTGTATGAGGGTG 7173
Query 1201 GAATTAAGCTGCCAACAAATATACTTAGCCAGATAAGCCCGTTACCCGTGCTTAAGGAGA 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 7174 GAATTAAGCTGCCAACAAATATACTTAGCCAGATAAGCCCGTTACCCGTGCTTAAGGAGA 7233
Query 1261 TCTTTCGAACCGATGGTGAAAATACCCTTAAATATCCACCACCTAAAGTAATTCAAGGTA 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 7234 TCTTTCGAACCGATGGTGAAAATACCCTTAAATATCCACCACCTAAAGTAATTCAAGGTA 7293
Query 1321 TTTCATTTTCATACCTTAAAAATACTCATGCCTAAAATCGCCATGATAAGCGCTTATACT 1380
|||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct 7294 TTTCATTTTCATACCTTAAAAATATTCATGCCTAAAATCGCCATGATAAGCGCTTATACT 7353
Query 1381 ATAAGCTGCAAAAAGTATTTTTATGTAAACATGATCTTACTAGTCTATATTATTGATTGA 1440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 7354 ATAAGCTGCAAAAAGTATTTTTATGTAAACATGATCTTACTAGTCTATATTATTGATTGA 7413
Query 1441 ACAGTAAGTAGGTCTGGATGGATGACTGATGAAGAATTCGCAAGAGAAATGCTTGCTGGA 1500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 7414 ACAGTAAGTAGGTCTGGATGGATGACTGATGAAGAATTCGCAAGAGAAATGCTTGCTGGA 7473
Query 1501 GTAAATCCAAATGTGATATGCTGTCTTCAGGTAGACGTAGATACAATTGGCCGAGCATTG 1560
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 7474 GTAAATCCAAATGTGATATGCTGTCTTCAGGTAGACGTAGATACAATTGGCCGAGCATTG 7533
Query 1561 TTACTAAATATCGCGttttttttGTTTCTTTATTCTTTTGAACCGGATTGTTGGTCTGAC 1620
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 7534 TTACTAAATATCGCGTTTTTTTTGTTTCTTTATTCTTTTGAACCGGATTGTTGGTCTGAC 7593
Query 1621 AGACGACCTAATGAAGGATCGTTGTTTGATTCTTGCAGGAGTTTCCTCCGCGAAGCAAGC 1680
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 7594 AGACGACCTAATGAAGGATCGTTGTTTGATTCTTGCAGGAGTTTCCTCCGCGAAGCAAGC 7653
Query 1681 TTGACAGTCAAATCTATGGTGATCACACTAGTAAAATAAGCAAAGAGCACCTAGAGCCTA 1740
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 7654 TTGACAGTCAAATCTATGGTGATCACACTAGTAAAATAAGCAAAGAGCACCTAGAGCCTA 7713
Query 1741 ATTTAGAAGGACTCACAGTAGAAGAGGTACACTTTTGCTTGATGAGTTCTATTATTTTCT 1800
||||||||||||||||||||||||||||||| ||||||||||||| ||||||||||||||
Sbjct 7714 ATTTAGAAGGACTCACAGTAGAAGAGGTACAATTTTGCTTGATGAATTCTATTATTTTCT 7773
Query 1801 ATGCTTTGTTAAGTTTTATTATTATGATTAACAATGAGAATTGTATTTGATTACTGCTGT 1860
||||||||||||||||||||||||||||||||||||||||||||||||||||| | | |
Sbjct 7774 ATGCTTTGTTAAGTTTTATTATTATGATTAACAATGAGAATTGTATTTGATTA-T--TCT 7830
Query 1861 AAAGGCAATTCAAAACAAGAAATTGTTCCTACTAGATCATCATGACTCAATTATGCCATA 1920
|||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct 7831 AAAGGCAATTCAAAACAAGAAATTGTTCCTGCTAGATCATCATGACTCAATTATGCCATA 7890
Query 1921 CTTAAGGAGAATAAACTCAACTTCCACAAAGGCTTATGCTACCAGAACAATCCTTTTCTT 1980
|||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Sbjct 7891 CTTAAGGAGAATAAACTCAACTTCCACAAAGGCTTATGCTACTAGAACAATCCTTTTCTT 7950
Query 1981 GAACAATAACCAAAATTTGAAGCCCCTGGCTATAGAGTTGAGTTTGCCACACCCTCAAGG 2040
|||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||
Sbjct 7951 GAACAATAACCAAAATTTGAAGCCACTGGCTATAGAGTTGAGTTTACCACACCCTCAAGG 8010
Query 2041 AGATGAACACGGCGCTGTTAGTTATGTTTATCAACCTGCGCTAGAAGGCGTTGAAAGTAA 2100
|||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8011 AGATGAACACGGTGCTGTTAGTTATGTTTATCAACCTGCGCTAGAAGGCGTTGAAAGTTC 8070
Query 2101 CATTTGGTTATTGGCTAAAGCTTATGTGATTGTGAATGATTCCTGCTACCATCAACTTGT 2160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8071 CATTTGGTTATTGGCTAAAGCTTATGTGATTGTGAATGATTCCTGCTACCATCAACTTGT 8130
Query 2161 TAGCCATTGGtatatattttgtcgataaattatataaattataacttttgatatgtatat 2220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8131 TAGCCATTGGTATATATTTTGTCGATAAATTATATAAATTATAACTTTTGATATGTATAT 8190
Query 2221 atatCGATGAATTGATTCGCGATTCTTGATGATAATAGGTTGAATACTCACGCAGTTGTT 2280
|||||||||||||||||| ||||| |||||||||||||||||||||||||||||||||||
Sbjct 8191 ATATCGATGAATTGATTCACGATTTTTGATGATAATAGGTTGAATACTCACGCAGTTGTT 8250
Query 2281 GAGCCGTTTGTCATAGCAACTAACAGGCATCTGAGTTGTCTTCACCCGATTTATAAACTT 2340
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8251 GAGCCGTTTGTCATAGCAACTAACAGGCATCTGAGTTGTCTTCACCCGATTTATAAACTT 8310
Query 2341 TTGTATCCTCACTATCGCGATACAATGAATATAAACTCTCTCGCTCGACTTTCCCTCGTC 2400
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8311 TTGTATCCTCACTATCGCGATACAATGAATATAAACTCTCTCGCTCGACTTTCCCTCGTC 8370
Query 2401 AACGACGGAGGTATCATCGAGAAAACTTTTTTGTGGGGAAGATATTCTATGGAAATGTCT 2460
|||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8371 AACGACGGCGGTATCATCGAGAAAACTTTTTTGTGGGGAAGATATTCTATGGAAATGTCT 8430
Query 2461 TCTAAAGTTTACAAGAATTGGGTTTTCACAGAGCAAGCATTGCCTGCTGATCTTATAAAA 2520
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8431 TCTAAAGTTTACAAGAATTGGGTTTTCACAGAGCAAGCATTGCCTGCTGATCTTATAAAA 8490
Query 2521 AGGTAACATTTTTACACAAACATAAGACATAAACTTAAAGAACTTTCTATGTTGATTATA 2580
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8491 AGGTAACATTTTTACACAAACATAAGACATAAACTTAAAGAACTTTCTATGTTGATTATA 8550
Query 2581 ATGTGAAATTGTTGTTTTAGAGGAATGGCTATTGAGGATCCATCTTCTCCATGTGGTGTT 2640
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8551 ATGTGAAATTGTTGTTTTAGAGGAATGGCTATTGAGGATCCATCTTCTCCATGTGGTGTT 8610
Query 2641 AAGCTTGTGGTAGAGGATTATCCTTATGCTGTTGATGGATTAGAGATATGGGCTATAATA 2700
||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Sbjct 8611 AAGCTTGTGGTAGAGGATTATCCTTATGCTGTTGATGGATTGGAGATATGGGCTATAATA 8670
Query 2701 AAGACATGGGTTCAAGACTATGTCTCCTTGTACTATACCTCAGATGAAAAACTTAGGCAA 2760
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8671 AAGACATGGGTTCAAGACTATGTCTCCTTGTACTATACCTCAGATGAAAAACTTAGGCAA 8730
Query 2761 GATTCTGAACTTCAAGCTTGGTGGAAAGAGCTCGTGGAGGTCGGTCATGGTGACAAGAAA 2820
||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Sbjct 8731 GATTCTGAACTTCAAGCTTGGTGGAAAGAGCTCGTGGAGGTCGGTCACGGTGACAAGAAA 8790
Query 2821 AACGAGCCGTGGTGGCCTAAGATGCAAACTCGAGAAGACTTAATTGAAGTTTGCAGTATT 2880
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8791 AACGAGCCGTGGTGGCCTAAGATGCAAACTCGAGAAGACTTAATTGAAGTTTGCAGTATT 8850
Query 2881 GTCATATGGACTGCTTCAGCTCTTCACGCAGCTGTTAATTTCGGGCAATATTCCTACGGA 2940
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8851 GTCATATGGACTGCTTCAGCTCTTCACGCAGCTGTTAATTTCGGGCAATATTCCTACGGA 8910
Query 2941 GGTTTAATCTTAAACCGTCCAACTCTTAGTAGACGATTCATGCCTGAGAAAGGTTCAGCT 3000
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8911 GGTTTAATCTTAAACCGTCCAACTCTTAGTAGACGATTCATGCCTGAGAAAGGTTCAGCT 8970
Query 3001 GAGTTCGAGGAGCTAGTGAAAAGTCCTCAAAAGGCTTACTTGAAGACAATTACGCCGAAG 3060
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 8971 GAGTTCGAGGAGCTAGTGAAAAGTCCTCAAAAGGCTTACTTGAAGACAATTACGCCGAAG 9030
Query 3061 TTTCAGACTCTTATTGATCTTTCTGTTATAGAAATATTGTCGAGGCATGCTTCCGATGAG 3120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 9031 TTTCAGACTCTTATTGATCTTTCTGTTATAGAAATATTGTCGAGGCATGCTTCCGATGAG 9090
Query 3121 TTGTACCTTGGGGAGAGAGACAATCCGAATTGGACATCGGATAAAAGGGCATTAGAGGCT 3180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 9091 TTGTACCTTGGGGAGAGAGACAATCCGAATTGGACATCGGATAAAAGGGCATTAGAGGCT 9150
Query 3181 TTTAAGAAGTTTGGAAACAAGTTGGCTGAAATTGAGAAGAAACTCACTCAGAGAAACAAT 3240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 9151 TTTAAGAAGTTTGGAAACAAGTTGGCTGAAATTGAGAAGAAACTCACTCAGAGAAACAAT 9210
Query 3241 GATGAGAAGCTAAGAAATCGTCATGGACCGGTTGAGATGCCTTATACTTTGCTCTATCCT 3300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 9211 GATGAGAAGCTAAGAAATCGTCATGGACCGGTTGAGATGCCTTATACTTTGCTCTATCCT 9270
Query 3301 TCTAGTAAAGAAGGACTAACTTTTAGAGGAATTCCTAATAGTATCTCCATCTGA 3354
||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 9271 TCTAGTAAAGAAGGACTAACTTTTAGAGGAATTCCTAATAGTATCTCCATCTGA 9324
Lipoxygenases are classified as either 9-LOX or 13-LOX lipoxygenases based on positional specificity of linoleic acid oxygenation (Chen et al (2016) Plants. Front. Genet. 7:176 (published 9/30/2016, hereafter Chen) page 2, left column, paragraph 2). The specificity of the LOX enzymes to generate 9- or 13- hydroperoxides affects subsequent metabolism into downstream products (Forster et al (1999) Plant Molecular Biology. 39:1209–1220: page 1209, right column, paragraph 1). The instant specification similarly teaches that 9-LOX and 13-LOX lipoxygenases lead to different biosynthetic pathways from linolenic acid (figure 1).
Because LOX genes in some species have been named in order of their discovery (eg CaLOX1 and CaLOX2, see Sarde et al (2018) Plant Molecular Biology 98:375–387, published 10/13/2018, hereafter Sarde, page 376, right column, paragraph 2), a LOX-3 protein may fall into either the 9-LOX or 13-LOX classification, depending on the species of plant the LOX-3 protein comes from (Sarde figure 1).
LOX-3 genes in different species comprise different numbers of exons (Chen figure 2). LOX-3 proteins may play a role in different biological functions. LOX3 in Arabidopsis is essential for flower growth and male fertility (Sarde page 376, left column, paragraph 2) while tobacco LOX3 is involved in jasmonic acid biosynthesis (Sarde page 376, left column, paragraph 2). Pepper LOX3 is part of a clade with Arabidopsis LOX5, which is involved in lateral root development and defense, although this gene was not induced over time in response to thrips feeding (Sarde page 380, left column, paragraph 2 & page 383, left column, paragraph 2).
The instant specification does not define the activity of a LOX-3 protein, as claimed, so as to differentiate it from the activity of another LOX protein. Thus, the specification fails to make up for the lack of knowledge on the art.
Hence, Applicant has not, in fact, described LOX-3 proteins over the full scope of the claims, and the specification fails to provide an adequate written description of the claimed invention. Therefore, given the lack of written description in the specification with regard to the structural and functional characteristics of the claimed compositions, Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
C. Claims 1, 3, 10, 16, 30, 36-37, 83-89 & 91-94 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a NEW MATTER rejection.
Amended claim 1 recites a mutated LOX-2 gene comprising one or more mutations in a coding region corresponding to upstream of exon 7 of the LOX-2 gene (lines 4-6). Original claim 15, and now canceled claim 92, recited a mutation located at least partially in a region that corresponds to a region upstream of exon 7 (lines 2-3). This is in line with the support in the specification for a mutation in a nucleotide region upstream of exon 7 found on pages
Applicant provides examples of mutations found in coding regions upstream of exon 7, in particular in exon 4 (original claims 44 & 47, page 5 lines 12-14; page 37 lines 3-20; page 92 lines 1-9). Nevertheless, the few examples provided by the Applicant do not describe the full scope of mutations found in coding regions upstream of exon 7. Thus, one of ordinary skill in the art would not reasonably conclude that Applicant was in possession of insertions, deletions, or substitutions found in a coding region upstream of exon 7 of a lox-2 gene over the full scope of the claimed mutations at the time of filing of the instant application.
Applicant urges that support for the amendments are found in original claims 15 and 33 and page 35 line 30-page 36 line 8 (remarks, page 10, paragraph 2).
This argument is unpersuasive because a nucleotide region upstream is distinct and not equivalent in scope to a coding region upstream. Original claim 33 and page 35 line 30-page 36 line 8 do not mention exon 7 or where the mutation may fall relative to it.
Scope of Enablement
A. Claim 84 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Based on Applicant’s amendments of the claims, this rejection is modified from the rejection set forth in the Office action mailed 2/11/2025, as applied to claim 84. Applicant' s arguments filed 7/23/2025 have been fully considered but they are not persuasive.
Claim 84 is drawn to a plant or plant part with reduced activity in a LOX-2 gene and reduced FAD activity, wherein the amount of polyunsaturated lipid is reduced by 50-90% compared to a control plant. The claim is broadly drawn to plants with reduced activity in a LOX-2 and FAD3 gene wherein the amount of any polyunsaturated lipid is reduced by 50-90%.
The instant specification describes linolenic acid and linoleic acid to be polyunsaturated acids (page 76, lines 26-30). The instant specification provides examples of plants with fad2b, fad3c, and fad3d mutations with reduced linoleic and linolenic percentage, but a reduction in linoleic and linolenic acid was not observed for a plant with a lox-2 mutation (table 9).
The instant specification does not provide any examples of a plant with reduced LOX-2 activity and FAD activity, that has a reduced amount of a polyunsaturated lipid. Furthermore, the instant specification does not provide any examples of reduced polyunsaturated lipid that is not linolenic acid and linoleic acid or in any plant that is not pea.
The impact of LOX proteins on polyunsaturated lipids is described in the art. Bhowmik et al (2023) Front. Plant Sci. Sec. Plant Biotechnology. 14. (published 9/20/2023 after the effective filing date of the instant application; hereafter Bhowmik) describes yellow pea lines with null alleles of PsLOX2 and reduced LOX activity that have higher content of linoleic and α-linolenic acids in flour (page 1, paragraph 3) and describes that CRISPR-editing of the LOX gene minimized the oxidation of these polyunsaturated fatty acids. Bhowmik describes that polyunsaturated fatty acids, especially linoleic and α-linolenic acids, significantly increased in LOX2-edited lines TGP-7, -8, and -9 (page 5, right column, paragraph 1). Bhowmik also describes lines of knockout PsLOX2 wherein polyunsaturated fatty acid (PUFA) levels decreased (lines TPG-3, -4, and -5 table 3), but even in the line that had the greatest decrease in total PUFA the reduction was only about 8% (49.07 vs 53.54%). Bhowmik describes that LOX activity is negatively correlated with total PUFA, linoleic acid and α-linolenic acids (page 09, right column, paragraph 3 and figure 6).
In contrast, FAD3 enzymes are known in the art to affect the fraction of linolenic acid as total of fatty acids (Held et al (2019) Agrosyst. Geosci. Environ. 2:190006. Published 7/1/2019, hereafter Held; abstract). In soybean, mutation in either FAD3B or FAD3C have a less significant impact on linolenic acid levels than mutations in FAD3A, and some functional redundancy among FAD3 genes in soybean is indicated (Held, page 2, left column, paragraph 1). Moreover, in some soybean plants comprising a mutation in FAD3C, reduction in linoleic acid was associated with a compensatory increase in linoleic acid, another polyunsaturated fatty acid (Bilyeu et al (2005) Crop Sci. 45:1830–1836 published 8/1/2005, hereafter Bilyeu; page 1834, right column, paragraph 3).
The instant specification does not provide guidance for how to decrease activity of a LOX2 protein and a FAD3 protein to achieve the recited reduction in polyunsaturated lipid, especially across plant species. No examples are found in the instant specification or the art for a reduction of 50-90% in PUFA in a plant with both decreased LOX2 and FAD3C activity when compared to a control plant. No examples are found in the specification for a species other than pea, despite evidence in the art that FAD3 genes in soybean have functional redundancy and mutations may increase linoleic acid. In addition, a person of ordinary skill in the art would not immediately know which polyunsaturated lipids other than linolenic, if any, would be decreased by a mutation in a LOX2 gene and a mutation in a FAD gene. Undue trial and error experimentation would be required to screen LOX2/FAD3C mutants across species to find one with the level of reduction of PUFA claimed, if such a reduction is possible.
Given the claim breadth and lack of guidance in the specification, the instant invention is not enabled for claim 84.
Applicant urges that amended claim 84 depends from claim 94 which requires decreased FAD activity and a mutated FAD3 gene, and because the specification discloses plants with mutations in the FAD3 gene with reduced linoleic acid and/or linolenic acid, one skilled in the art can practice the claimed invention without undue burden (Remarks, page 15, paragraph 2-3).
This argument is unpersuasive, because applicant has not disclosed plants with reduced polyunsaturated lipids across the full scope of the species encompassed nor the full genus of all polyunsaturated lipids. Furthermore, the specification does not teach any examples of plants with a mutated LOX2 and FAD3 gene with the recited reduction in polyunsaturated lipid.
B. Claims 1, 10, 16, 84, 86-87, 91, & 93-95 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a plant comprising a mutated FAD3C gene of SEQ ID NO: 46 encoding SEQ ID NO: 43 does not reasonably provide enablement for any insertion, substitution, or deletion in any FAD3C gene leading to increased oleic acid, reduced linolenic acid or linolenic acid plus linoleic acid, or reduced polyunsaturated lipid. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
This is a new rejection necessitated by Applicant’s amendments.
The claims require a plant or plant part comprising decreased fatty acid desaturase activity and comprising a mutation in a genus of proteins that are functional FAD3C proteins or retain FAD3C functional activity. However, the claims do not specify a biological activity of the FAD3C gene. Thus, the claims encompass FAD3 genes broadly. Claim 16 further recites one or more insertions, substitutions, or deletions in one more genes selected from FAD3 located at least partially in the nucleotide region corresponding to exon 2 of the FAD3C gene. Claim 91 further requires a protein encoded by SEQ ID NO: 46 or a functional FAD3C protein with at least 90% sequence identity to SEQ ID NO: 46. Claim 95 further requires a gene encoding for a protein comprising SEQ ID NO: 43 or a sequence having 90% sequence identity to SEQ ID NO: 43 and FAD3C activity.
The specification teaches two examples of pea FAD3 genes, FAD3C (SEQ ID NO: 46, encoding SEQ ID NO: 43) and FAD3D (SEQ ID NO: 56, encoding SEQ ID NO: 53). The instant specification teaches a method to mutate FAD3 by targeting a region in exon 2 of the FAD3C gene or exon 3 of the FAD3D gene (specification, page 129, lines 9-25) and teaches truncated FAD3C proteins of SEQ ID NOs: 44 or 45 that have reduced function (page 97, lines 7-22) and truncated pea FAD3D proteins of SEQ ID NO: 54 or 55 (page 97, line 23-page 98 line 10).
As presented above, no FAD3C-specific activity is defined in the instant specification and no structure is provided for the FAD3C activity. FAD3 genes in other species may follow different naming conventions (Blume table 4) or may have expressional differences based on cis-acting regulatory elements, leading to different functional effect from other FAD3 genes (Blume page 8, paragraphs 4-5).
The instant specification does not provide guidance for how to use a plant with decreased activity of a FAD3C protein that has a biological activity or expression pattern different from the FAD3C protein provided in the instant specification. Additionally, a person of ordinary skill in the art would not immediately know what insertions, substitutions, or deletions would be sufficient to reduce FAD3C activity in a plant such that oleic acid is increased (claim 10), linolenic acid is reduced by at least 50% or the amount of linolenic acid plus linoleic acid is reduced by at least 4% (claim 86), the amount of oleic acid is increased by at least 4% (claim 87), or the amount of polyunsaturated lipid is reduced by 50-90% (claim 84) in a FAD3C gene with a different activity and function. The exon where the mutation is located (claim 16) may not correspond to the same position in the resulting FAD3C protein. Undue trial and error experimentation would be required to screen insertions, substitutions, or deletions in FAD3C genes to find a use for a plant comprising such genes if such a use is possible.
Given the claim breadth and lack of guidance in the specification, the instant invention is not enabled through the full scope of claims 1, 10, 16, 84, 86-87, 91, & 93-95.
C. Claims 1, 10, 16, 84, 86-87, 91, & 93-95 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a plant comprising a mutated FAD3C gene of SEQ ID NO: 27 encoding SEQ ID NO: 25 does not reasonably provide enablement for any insertion, substitution, or deletion in any LOX-3 gene leading to increased oleic acid, reduced linolenic acid or linolenic acid plus linoleic acid, or reduced polyunsaturated lipid. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
This is a new rejection necessitated by Applicant’s amendments.
The claims are drawn to plants comprising a mutation in a genus of proteins that are LOX-3 proteins. However, the claims do not specify a biological activity of the LOX-3 gene. Thus, the claims encompass LOX-3 genes broadly.
The species of LOX-3 genes taught by the specification is the pea LOX-3 gene (instant SEQ ID NO: 27). The instant specification teaches a method to mutate LOX-3 by targeting a region in exon 4 of pea LOX-3 (page 129, lines 9-10).
As presented above, no LOX-3-specific activity is defined in the instant specification and no structure is provided for the LOX-3 activity. LOX-3 genes in other species may fall into a different LOX classification (Sarde figure 1) or participate in a different biological activity (Sarde page 376, left column, paragraph 2). In addition, LOX-3 genes in other species may have exon numbers other than the pea LOX-3 gene (Chen figure 2).
Additionally, claim 94 is drawn to the plant of claim 1, comprising decreased lipoxygenase activity and further comprising a mutated LOX-3 gene. However, lipoxygenase activity for lox-2 mutant plants is higher than a standard plant, presumably due to overexpression of lox-3 (Davies et al WO 00/43529 (published) page 3, line 26-page 4 line 8).
The instant specification does not provide guidance for how to use a plant with decreased activity of a LOX-3 protein that has a biological activity different from the LOX-3 protein provided in the instant specification. Additionally, a person of ordinary skill in the art would not immediately know what insertions, substitutions, or deletions would be sufficient to reduce LOX activity in a plant such that hexanal, hexanol, or linolenic acid is reduced in a LOX-3 gene with a different activity and function. The exon where the mutation is located (claim 16) may not correspond to the same position in the resulting LOX-3 protein. Undue trial and error experimentation would be required to screen insertions, substitutions, or deletions in LOX-3 genes to find a use for a plant comprising such genes if such a use is possible.
Given the claim breadth and lack of guidance in the specification, the instant invention is not enabled through the full scope of claims 1, 10, 16, 84, 86-87, 91, & 93-95.
D. Claims 1, 3, 10, 16, 30, 36-37, 83-89 & 91-95 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a plant comprising a mutated LOX-2 gene with 90% sequence identity to SEQ ID NO: 10 encoding an amino acid with 90% sequence identity to SEQ ID NO: 7 in pea does not reasonably provide enablement for a plant of any species comprising a mutated LOX-2 over the full scope of the claims. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make the invention commensurate in scope with these claims.
This is a new rejection necessitated by Applicant’s amendments.
Claims 1, 3, 10, 16, 30, 36-37, 83-89 & 91-95 require a plant comprising decreased LOX activity and a mutated LOX-2 gene with 90% sequence identity to SEQ ID NO: 10. Claim 36 further requires that the plant be selected from a list of species.
However, the most similar sequence to SEQ ID NO: 10 in a species other than garden pea has 91.9% similarity with only 83.9% match (GenBank OZ206515.1, from nucleotide 57,382,228 to 57,385,782; available 12/1/2024, after the filing of the instant application). See alignment below.
OZ206515s5
LOCUS OZ206515s5 12010020 bp DNA linear PLN 01-DEC-2024
COMMENT segment of length 12010020: from 48000001 to 60010020
DEFINITION Lathyrus linifolius genome assembly, chromosome: 1.
ACCESSION OZ206515
VERSION OZ206515.1
DBLINK BioProject: PRJEB82905
BioSample: SAMEA7522408
Sequence Read Archive: ERR13245272, ERR13245273, ERR13245274,
ERR13245275, ERR13245276, ERR13245277, ERR13245278, ERR13245279,
ERR13245280, ERR13248951
KEYWORDS .
SOURCE Lathyrus linifolius
ORGANISM Lathyrus linifolius
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50
kb inversion clade; NPAAA clade; Hologalegina; IRL clade; Fabeae;
Lathyrus.
REFERENCE 1
CONSRTM Wellcome Sanger Tree of Life Programme
TITLE Direct Submission
JOURNAL Submitted (27-NOV-2024) WELLCOME SANGER INSTITUTE, Tree of Life,
Wellcome Genome Campus, Hinxton CB10 1SA, United Kingdom
COMMENT The assembly drLatLini1.hap1.1 is based on 25x PacBio data and
Arima2 Hi-C data generated by the Darwin Tree of Life Project
(https://www.darwintreeoflife.org/). The assembly process included
the following sequence of steps: initial PacBio assembly generation
with Hifiasm in Hi-C integrated assembly mode, and Hi-C based
scaffolding with YaHS. The mitochondrial and chloroplast genomes
were assembled using OATK. Finally, each haplotype assembly was
analysed and manually improved using TreeVal. Chromosome-scale
scaffolds confirmed by the Hi-C data have been named in order of
size.
FEATURES Location/Qualifiers
source 1..1034507165
/organism="Lathyrus linifolius"
/mol_type="genomic DNA"
/db_xref="taxon:313096"
/chromosome="1"
/geo_loc_name="United Kingdom:Surrey | RBG Kew | rock
garden. Origin, UNITED KINGDOM | within Mardale Mountain
Meadow sheep exclosure below Harter Fell | S of RSPB
Haweswater | 400 m"
/collection_date="2020-09-03"
assembly_gap 2024811..2025010
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 9988247..9988446
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 10665447..10665646
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 13523647..13523846
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 16600821..16601020
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 23274443..23274642
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 37963169..37963368
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 44009573..44009772
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 44868407..44868606
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 52705073..52705272
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 52985381..52985580
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 56138735..56138934
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 70781293..70781492
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 73261349..73261548
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 79999658..79999857
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 80578164..80578363
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 82136172..82136371
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 83734854..83735053
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 100759416..100759615
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 113326226..113326425
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 117501645..117501844
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 119976334..119976533
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 125478369..125478568
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 127094526..127094725
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 127191360..127191559
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 130576090..130576289
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 140679596..140679795
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 143263879..143264078
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 150349287..150349486
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 153116487..153116686
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 156393048..156393247
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 158344959..158345158
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 165714287..165714486
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 167396384..167396583
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 167474242..167474441
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 168586209..168586408
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 173056769..173056968
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 176515928..176516127
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
assembly_gap 180249173..180249372
/estimated_length=200
/gap_type="unknown"
/linkage_evidence="unspecified"
Query Match 83.9%; Score 2969.6; Length 12010020;
Best Local Similarity 91.9%;
Matches 3321; Conservative 0; Mismatches 174; Indels 117; Gaps 13;
Qy 1 ATGTTTCCAAATGTGACAGGACTCCTAAACAAGGGCCACAAGATAAGAGGGACAGTGGTG 60
||||||||||||||||||||| |||||||||||||||||||||| |||||||||||||||
Db 9385781 ATGTTTCCAAATGTGACAGGATTCCTAAACAAGGGCCACAAGATTAGAGGGACAGTGGTG 9385722
Qy 61 TTGATGCGTAAGAATGTGTTGGACTTCAACACAATTGTGAGTATTGGTGGTGGAAACGTC 120
|||||||||||||||||||| |||||||||||||||||||||||||||||||||||| ||
Db 9385721 TTGATGCGTAAGAATGTGTTAGACTTCAACACAATTGTGAGTATTGGTGGTGGAAACATC 9385662
Qy 121 CATGGTGTCATCGACTCCGGCATCAATATCATTGGTTCAACTCTTGATGGCCTTACTGCC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 9385661 CATGGTGTCATCGACTCCGGCATCAATATCATTGGTTCAACTCTTGATGGCCTTACTGCC 9385602
Qy 181 TTCTTAGGCCGCAGTGTCTCCCTCCAGCTGATCAGTGCTACCAAGTCTGATGGTTAGTTC 240
|||||||||||||||||||||||||| || ||||||||||||||||||||||||||||||
Db 9385601 TTCTTAGGCCGCAGTGTCTCCCTCCAACTAATCAGTGCTACCAAGTCTGATGGTTAGTTC 9385542
Qy 241 ATTCATTTCTTCTTACTTTTATATATCTAGACATGTAGCACTTTTATATCTAGACATGTA 300
|||||||||||||||||||||||| | | | || | |
Db 9385541 ATTCATTTCTTCTTACTTTTATATCTAGACATATAT----------------------CA 9385504
Qy 301 TCATCAGAATCATCTTAAGTTTTTGGAACTCCTGAATAGGAGTTTTTGGAACTCCTGTAT 360
|| ||||| |||||| |||||||||| |||||| |
Db 9385503 TCTGCAGAACAATCTTA-----------------------AGTTTTTGGAGGTCCTGTGT 9385467
Qy 361 AGGTTAGTTGCAGTTTAACTTCGACAGAAT--ATAGAAGTTCTATTTAATCACGATTTAT 418
|| ||||||||||||||| ||| ||| ||||| ||||||||||| || ||||||
Db 9385466 AGATTAGTTGCAGTTTAATCATAACAAAATAGATAGAGATTCTATTTAATTACAATTTAT 9385407
Qy 419 TTGTGATAAATATTTTATGAGACCCTACTTAACT-----------GTGACAAATTTTGGA 467
|||||||||||| |||| |||||| ||||||||| ||||||||||||||
Db 9385406 TTGTGATAAATACTTTACGAGACCTTACTTAACTACGGTTTTAACGTGACAAATTTTGGG 9385347
Qy 468 CTT-----ATGCGGTAGCCTGCCTTGCACGGTCCTGATCAGGAGTATAGTCACTAAATGA 522
|| |||||||| |||||||| |||| ||| |||| ||||||| |||||||||||
Db 9385346 TTTGTGCGGTGCGGTAGTCTGCCTTGTACGGCCCTAATCATGAGTATACTCACTAAATGA 9385287
Qy 523 ATGAATTTAATGATATGTATGTAGCAAATGGAAAAGGAAAAGTTGGAAAGGATACATTTC 582
| || |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 9385286 ACGAGTTTAATGATATGTATGTAGCAAATGGAAAAGGAAAAGTTGGAAAGGATACATTTC 9385227
Qy 583 TTGAAGGTGTTCTTGCTTCATTACCAACCTTGGGAGCTGGTGAATCTGCATTCAATATTC 642
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 9385226 TTGAAGGTGTTCTTGCTTCATTACCAACCTTGGGAGCTGGTGAATCTGCATTCAATATTC 9385167
Qy 643 ATTTTGAATGGGATCATGAAATGGGAATTCCAGGTGCATTTTACATCAAAAACTATATGC 702
|||||||||||||| |||| ||||||||||||||||||||||||||||||||||||||||
Db 9385166 ATTTTGAATGGGATGATGAGATGGGAATTCCAGGTGCATTTTACATCAAAAACTATATGC 9385107
Qy 703 AAGTTGAGTTTTTTCTCAAGAGTTTAACTCTAGAAGATGTTCCAAATCATGGAACCATTC 762
||||||| ||||| ||||||||| ||||||||||||||||||||||||||||||||||||
Db 9385106 AAGTTGAATTTTTCCTCAAGAGTCTAACTCTAGAAGATGTTCCAAATCATGGAACCATTC 9385047
Qy 763 GCTTCGTATGCAACTCTTGGGTTTACAACTCAAAACTCTACAAAAGTCCTCGCATTTTCT 822
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 9385046 GATTCGTATGCAACTCTTGGGTTTACAACTCAAAACTCTACAAAAGTCCTCGCATTTTCT 9384987
Qy 823 TCGCCAACAAGGTAATTTATTTACATCTATATGTTAGTGCGTGGTT-------------- 868
|||||||||||||| ||||||||||||||||||||| |||
Db 9384986 TCGCCAACAAGGTACTTTATTTACATCTATATGTTAAGTGCATGTTTTGTATCACGGTAG 9384927
Qy 869 ---------TGTTAGAATCACGATGAATCATTATGA----------------------TT 897
||| |||||||||||||||| |||||| ||
Db 9384926 GTTTGTCAGTGTCAGAATCACGATGAATCGTTATGATTTTGCGAAGATTTAAACTAACTT 9384867
Qy 898 TTACTTGATTGTTATCATGCAGTCATATCTTCCGAGTGAAACACCGTCTCCACTTGTCAA 957
|||||||||| ||||||||||||| |||||||||||| ||||||||||||||||||||||
Db 9384866 TTACTTGATTTTTATCATGCAGTCGTATCTTCCGAGTCAAACACCGTCTCCACTTGTCAA 9384807
Qy 958 GTATAGAGAAGAAGAATTGCAAACTCTAAGAGGAGATGGAACAGGAGAGCGCAAGTTACA 1017
||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||
Db 9384806 GTATAGAGAAGAAGAATTGCAAATTCTAAGAGGAGATGGAACAGGAGAGCGCAAGTTACA 9384747
Qy 1018 TGAAAGAATCTACGATTATGATGTCTATAACGATTTAGGCAATCCAGATCACGGCGAACA 1077
|||| | |||||||| ||||||||||||||||||||||||||||||||||||||||||||
Db 9384746 TGAACGGATCTACGACTATGATGTCTATAACGATTTAGGCAATCCAGATCACGGCGAACA 9384687
Qy 1078 TCTTGCTCGACCTATTCTCGGAGGGTCTAGCACACATCCCTATCCTCGTAGGGGTAGGAC 1137
|||||||||||||||||| |||||||||||||| ||||||||||||||||||||||||||
Db 9384686 TCTTGCTCGACCTATTCTTGGAGGGTCTAGCACGCATCCCTATCCTCGTAGGGGTAGGAC 9384627
Qy 1138 CGGTCGATATCCAACGAGGAAAGGTTAGATACAAGAACATGGTACAAATAATGATA-AAA 1196
||||||||||||||||||||||||||||||||||| |||||||| ||||||||| ||
Db 9384626 CGGTCGATATCCAACGAGGAAAGGTTAGATACAAGGTTATGGTACAGATAATGATAGAAG 9384567
Qy 1197 ATGAGATAAACTAACCTTAAGCTATTGTGTTCTTTTGAACAGATCCGAATAGCGAGAAAC 1256
||| |||||||||||||||||||||||||| |||||||||||| |||||||||||||||
Db 9384566 ATGGTATAAACTAACCTTAAGCTATTGTGTTATTTTGAACAGATTCGAATAGCGAGAAAC 9384507
Qy 1257 CAGCTACAGAAACATATGTTCCAAGAGATGAAAATTTTGGTCACTTGAAGTCCTCTGACT 1316
|||| ||||||| ||||||||||||||||||||||||||||||||||||||| |||||||
Db 9384506 CAGCAACAGAAATATATGTTCCAAGAGATGAAAATTTTGGTCACTTGAAGTCTTCTGACT 9384447
Qy 1317 TTCTTGCATATGGAATAAAATCTGTATCTCAATGTGTAGTACCTGCATTTGAATCTGCAT 1376
||||||||||||||||||||||| ||||||||||||||||||| ||||||||||||||||
Db 9384446 TTCTTGCATATGGAATAAAATCTTTATCTCAATGTGTAGTACCCGCATTTGAATCTGCAT 9384387
Qy 1377 TTGATTTGAATTTTACGCCTAACGAGTTTGATAGTTTTCAAGATGTGCGCAACCTCTTCG 1436
||||||||||||||||||||||||||||||||||||||||||||||||| | |||||||
Db 9384386 TTGATTTGAATTTTACGCCTAACGAGTTTGATAGTTTTCAAGATGTGCGTGATCTCTTCG 9384327
Qy 1437 AAGGTGGAATTAAGCTTCCTCTAGATGTAATTAGCACAATTAGTCCTTTACCTGTGGTCA 1496
|||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||
Db 9384326 AAGGTGGAATTAAGCTTCCTCTAGATGTAATTAGCACAATTAGTCCTTTACCTGTGATCA 9384267
Qy 1497 AAGAAATCTTTCGTACCGATGGTGAACAAGTCCTCAAGTTTACACCACCACATGTCATTC 1556
|||||||||| ||||||||||||||||||||||||||||||| ||||||||||||||| |
Db 9384266 AAGAAATCTTCCGTACCGATGGTGAACAAGTCCTCAAGTTTATACCACCACATGTCATAC 9384207
Qy 1557 GAGGTCCGACAAAATACATATTATAACGTAAATTATACTACGCTTTGAGTAATTTCATTT 1616
|||||||||| ||| |||||||||||||||||||||||||||||| ||||||||||||||
Db 9384206 GAGGTCCGAC-AAACACATATTATAACGTAAATTATACTACGCTTCGAGTAATTTCATTT 9384148
Qy 1617 TATTATAAGTTTCT---TTGTTTTTCGCAGTGAGTAAGTCTGCGTGGATGACCGATGAAG 1673
||||| | ||||| ||||||||||||||||||||||||||||||||||| |||||||
Db 9384147 GATTATGATTTTCTTTCTTGTTTTTCGCAGTGAGTAAGTCTGCGTGGATGACTGATGAAG 9384088
Qy 1674 AATTTGCACGAGAAATGCTCGCTGGCGTAAATCCATGCATGATCCGCGGTCTTCAAGTAA 1733
||||||||||||||||||||||||| |||||||| |||||||||||||||||||||||||
Db 9384087 AATTTGCACGAGAAATGCTCGCTGGTGTAAATCCTTGCATGATCCGCGGTCTTCAAGTAA 9384028
Qy 1734 GTTCAAGAATTTATTTTAATATTTCGGAGAAATTTTTGCTATTCACATTAAATAATTGCC 1793
||||||||||| ||||||||||||||||||||||||||||||| |||||||||||||||
Db 9384027 GTTCAAGAATTCTTTTTAATATTTCGGAGAAATTTTTGCTATTCGCATTAAATAATTGCC 9383968
Qy 1794 TATCTAATTGTAGGAGTTTCCTCCGAAAAGCAATCTAGATCCCGCAGAATACGGTGATCA 1853
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 9383967 TATCTAATTGTAGGAGTTTCCTCCGAAAAGCAATCTAGATCCCGCAGAATACGGTGATCA 9383908
Qy 1854 CACTAGTAAGATATCTGTAGATGTCTTGAACCTTGATGGTTGCACCATAGATGAGGTAAA 1913
||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Db 9383907 CACTAGTAAGATATCTGCAGATGTCTTGAACCTTGATGGTTGCACCATAGATGAGGTAAA 9383848
Qy 1914 CACATAATAATCATAATTAAAAAAATATGATTTTGGACTTAATTTGGTGACATAAAGTGA 1973
|||||| ||||| |||||||||||||||||||||||||||||||||||||||||| ||||
Db 9383847 CACATATTAATCTTAATTAAAAAAATATGATTTTGGACTTAATTTGGTGACATAATGTGA 9383788
Qy 1974 TTAAGATTAA-TTTTACATGGAACAGGCACTTGCTAGTGGGAGATTATTTATACTAGATT 2032
|||||| ||| |||| |||||||||||||||||||||||||||||||||||||||| |||
Db 9383787 TTAAGACTAATTTTTTCATGGAACAGGCACTTGCTAGTGGGAGATTATTTATACTAAATT 9383728
Qy 2033 ATCATGACACATTTATTCCATTTCTGAGAAGGATCAATGAGACTTCTGCAAAAGCTTATG 2092
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 9383727 ACCATGACACATTTATTCCATTTCTGAGAAGGATCAATGAGACTTCTGCAAAAGCTTATG 9383668
Qy 2093 CTACTAGAACAATACTTTTTCTAAAAGAAAATGGAACTTTAAAGCCAGTGGCCATTGAAT 2152
||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||
Db 9383667 CTACTAGAACAATCCTTTTTCTAAAAGAAAATGGAACTTTAAAACCAGTGGCCATTGAAT 9383608
Qy 2153 TAAGTTTGCCACATCCTGATGGTGACAAATCAGGTTTTGTTAGTAAAGTTATCTTACCTG 2212
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 9383607 TAAGTTTGCCACATCCTGATGGTGACAAATCAGGTTTTGTTAGTAAAGTTATCTTACCTG 9383548
Qy 2213 CAGATGAAGGTGTTGAGAGTACTATTTGGCTTCTAGCAAAAGCTTATGTGGTGGTTAACG 2272
|||||||||||||||| |||||||||||| | |||||||||||||||||||||||||| |
Db 9383547 CAGATGAAGGTGTTGAAAGTACTATTTGGTTACTAGCAAAAGCTTATGTGGTGGTTAATG 9383488
Qy 2273 ATTCTTGCTATCATCAACTCATGAGCCATTGGTAAAATATAGTAATGTTTATATTTTCAC 2332
|||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Db 9383487 ATTCTTGCTATCATCAACTCATGAGCCATTGGTAAAATATCATAATGTTTATATTTTCAC 9383428
Qy 2333 GTATGTGCGCTCTAAAATATCAGGTAGGATTTGAACTCTGAATATATGTATTACTTATTG 2392
| |||||||||||||||||||||||||||||||||| ||||| | ||||||| ||||
Db 9383427 GCGTGTGCGCTCTAAAATATCAGGTAGGATTTGAACTTTGAATCTCGATATTACTGATTG 9383368
Qy 2393 ATGATTTTTATATA--TTTATTGGAATAGGTTGAATACTCATGCGGTAATTGAGCCGTTT 2450
||||||||| |||| |||||||| ||||||||||||||||||| |||||||||||||||
Db 9383367 ATGATTTTTTTATACGTTTATTGGTATAGGTTGAATACTCATGCAGTAATTGAGCCGTTT 9383308
Qy 2451 GTTATAGCAACAAATCGGCAGCTTAGTGTGGTTCATCCGATTAATAAACTTTTAGCTCCT 2510
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 9383307 GTTATAGCAACAAATCGGCAGCTTAGTGTGGTTCATCCGATTAATAAACTTTTAGCTCCT 9383248
Qy 2511 CATTATCGCGACACGATGAACATCAATGCACTTGCAAGAGATTCTCTAATTAATGCCAAT 2570
|| ||||| |||||||||||||| ||||||||||||||||||||||| |||||||| ||
Db 9383247 CACTATCGTGACACGATGAACATAAATGCACTTGCAAGAGATTCTCTGATTAATGCTGAT 9383188
Qy 2571 GGCATAATAGAGAGAAGTTTTTTGCCTTCGAAGTATGCTGTGGAAATGTCTTCAGCGGTT 2630
||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Db 9383187 GGCATAATAGAGAGAAGTTTTTTGCCTTCGAAGTATGCTGTGGAAATGTCTTCGGCGGTT 9383128
Qy 2631 TACAAGTATTGGGTTTTCACAGATCAAGCTCTGCCGAATGATCTTATCAAGAGGTAATAG 2690
|||||||||||||||||||||||||||||||||||||| ||||| |||||||||||||||
Db 9383127 TACAAGTATTGGGTTTTCACAGATCAAGCTCTGCCGAACGATCTCATCAAGAGGTAATAG 9383068
Qy 2691 AATGATCATAGGTTCGAAAAATGAACAATCTTTTTAAAGATGATTCTATATTTAAGGACT 2750
|||||||||| |||| ||||| | ||||| ||| |||||| ||||||||||||||||||
Db 9383067 AATGATCATACGTTCAAAAAACGGACAATTTTTGTAAAGAGGATTCTATATTTAAGGACG 9383008
Qy 2751 GAGATAG-TAACATGTATATGCATTTTGCTTGATTCAGAAACATGGCAGTTAAAGATTCG 2809
||||||| |||||||||||||| |||||||||||||||||| |||||||||| ||||||
Db 9383007 GAGATAGTTAACATGTATATGCGTTTTGCTTGATTCAGAAATGTGGCAGTTAAGGATTCG 9382948
Qy 2810 TCGTCTCCATATGGACTCCGTCTTCTGATAGAGGACTACCCGTACGCTGTTGACGGATTA 2869
||| ||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Db 9382947 TCGGCTCCATATGGACTCCGTCTTCTGATAGAGGACTACCCTTACGCTGTTGACGGATTA 9382888
Qy 2870 GAGATATGGACGGCTATTAAAACATGGGTCCAAGATTATGTCTCGCTGTATTATGCAACG 2929
||||||||||||||||||||| ||||||||||||||||||||||| ||||||| ||||||
Db 9382887 GAGATATGGACGGCTATTAAATCATGGGTCCAAGATTATGTCTCGTTGTATTACGCAACG 9382828
Qy 2930 GACAATGATATCAAAAATGATTCCGAGCTTCAACATTGGTGGAAAGAGGTTGTAGAGAAA 2989
|| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 9382827 GAAAATGATATCAAAAATGATTCCGAGCTTCAACATTGGTGGAAAGAGGTTGTAGAGAAA 9382768
Qy 2990 GGTCATGGTGACTTGAAAGATAAGCCATGGTGGCCTAAGTTGCAAACGTTTGACGAGCTC 3049
||||| || || ||||||||||||||||||||||||||||||||||| |||||||||||
Db 9382767 GGTCACGGCGATTTGAAAGATAAGCCATGGTGGCCTAAGTTGCAAACATTTGACGAGCTT 9382708
Qy 3050 GTTGAAGTTTGCACTATCATCATATGGACGGCTTCTGCTCTCCACGCAGCTGTTAATTTT 3109
||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Db 9382707 GTTGAAGTTTGCACTATCATCATATGGACGGCTTCTGCTCTCCACGCGGCTGTTAATTTT 9382648
Qy 3110 GGACAATATCCTTACGGCGGTTTAATTCTAAACCGTCCAACTCTGAGTAGAAGATTGCTT 3169
|||||||||||||| || ||||| ||||||||||||||||||||||||||||||||||||
Db 9382647 GGACAATATCCTTATGGAGGTTTTATTCTAAACCGTCCAACTCTGAGTAGAAGATTGCTT 9382588
Qy 3170 CCTGAGGAAGGAACTGCGGAATACGATGAAATGGTGAAGAGTTCTCAAAAGGCTTACTTG 3229
|||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Db 9382587 CCTGAGGAAGGAACTGCGGAATACGATGAAATGGTGAAGAGTCCTCAAAAGGCTTACTTG 9382528
Qy 3230 AGGACAATCACGCCGAAGTTTCAGACTCTTATTGATCTTTCAGTGATAGAAATATTGTCA 3289
||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Db 9382527 AGGACAATCACGCCGAAGTTTCAGACTCTTATTGATCTTTCGGTGATAGAAATATTGTCA 9382468
Qy 3290 AGACATGCTTCTGATGAAGTCTATCTCGGACAAAGGGAAAATCCACACTGGACATCTGAT 3349
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 9382467 AGACATGCTTCTGATGAAGTCTATCTCGGACAAAGGGAAAATCCACACTGGACATCTGAT 9382408
Qy 3350 TCTAAAGCTTTACAAGCATTTCAAAAGTTTGGAAATAAATTGGCGGAAATTGAGGCCAAA 3409
|||| |||||||||||||||||||||||||||||||||||||||||||| |||||||||
Db 9382407 GCTAAGGCTTTACAAGCATTTCAAAAGTTTGGAAATAAATTGGCGGAAATCGAGGCCAAA 9382348
Qy 3410 CTTACGAATAAGAACAATGATCCGAGCCTGTACCATCGGGTCGGGCCGGTTCAATTGCCA 3469
||||| |||||||||||||||||||||||||||||| |||||||||||||||||||||||
Db 9382347 CTTACAAATAAGAACAATGATCCGAGCCTGTACCATAGGGTCGGGCCGGTTCAATTGCCA 9382288
Qy 3470 TACACTTTGCTTCATCCCAGCAGCAAGGAAGGGTTAACCTTTAGAGGAATTCCTAATAGT 3529
||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Db 9382287 TACACTTTGCTTCATCCCAGCAGCAAGGAAGGGTTAACCTTTAGAGGAATTCCCAATAGT 9382228
Qy 3530 ATCTCTATTTAA 3541
|||||||| |||
Db 9382227 ATCTCTATCTAA 9382216
Because LOX-2 genes with a sequence with 90% sequence identity to instant SEQ ID NO: 10 are not known in the art in species other than pea, one of skill in the art would be required through trial and error experimentation to generate plants of other species comprising a mutated LOX-2 gene with 90% sequence identity to instant SEQ ID NO: 10 that have decreased LOX activity, if such plants are possible. Because such plants are not known in the art and the specification fails to teach species other than pea comprising a mutated LOX-2 gene over the scope of the claimed nucleic acid sequences, the invention is not enabled over the full scope of the claims.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 1, 3, 30, 36-37, 85, 88-89, 91 & 93-95 are rejected under 35 U.S.C. 103 as being unpatentable over Davies et al WO 0043529 A1 (published 7/27/2000, hereafter Davies) in view of Forster et al (1999) Plant Molecular Biology 39: 1209–1220, hereafter Forster, and Wang et al (2020) The Crop Journal. 8(3): 432-439 (available online 12/10/2019, hereafter Wang) taken with the evidence of GenBank accession X78580.1 (available 11/14/2006) and GenBank accession X78581.1 (available 11/14/2006).
This is a new rejection necessitated by Applicant’s amendments filed 7/11/2025. Applicant’s arguments filed 7/11/2025 have been addressed to the extent they are applicable to the new rejection.
Claims 1, 3, 30, 36-37, 85, 88-89, 91 & 93-95 are drawn to a plant comprising decreased LOX activity comprising a mutated LOX-2 gene comprising insertions or deletions in a coding region upstream of exon 7 of a LOX-2 gene with at least 90% sequence identity to instant SEQ ID NO: 10 and encoding a protein comprising a sequence having at least 90% sequence identity to instant SEQ ID NO: 7, and a plant product from such a plant. Claims 91 & 93-95 further require a mutated LOX-3 gene comprising one or more insertions, substitutions, or deletions.
Davies teaches a method to increase antioxidant content in peas by decreasing activity of lipoxygenase type 2 (LOX 2). In the method of Davies, lox2 mutant peas lacking the LOX-2 isoenzyme were grown in greenhouse conditions, peas were collected, and seeds were homogenized (page 14, line 30-page 15, line 17). Davies teaches peas obtained by this method, including frozen peas (Davies claims 7 or 8). The variety used by Davies method was the “Birte” pea variety (page 7, lines 9-2).
Davies teaches a motivation to reduce activity of LOX-2 because lipoxygenases lead to flavor and aroma formation (page 2, lines 8-14) and that mutants lacking lox2 in soybean have improved flavor (page 3, lines 1-3). Lox-2 mutant peas have higher total lipoxygenase activity compared to standard indicating overexpression of lox-3 in a lox-2 mutant background (page 3, lines 26-32). However, mutant lox-2 pea plants have decreased lox-2 activity (page 6, lines 16-20).
Davies teaches that there are alternative methods for developing pea plants with a lox2- trait, including a mutagenesis program to generate mutations affecting the LOX-2 gene including site-directed mutagenesis (page 7, line 21-page 8 line 9).
Davies teaches that plants with mutant lox-2 would be suitable to combine with additional modifications to increase pea ascorbate content (page 11, lines 23-29) and envisions combination of the genetic modification reducing the activity of LOX-2 with a further genetic modification at any locus capable of reducing activity of an enzyme involved in the sucrose to starch biosynthetic pathway (Davies claim 4).
Davies does not teach the sequence of the pea lox-2 or lox-3 genes and does not teach insertion, substitution, or deletion in a coding region corresponding to upstream of exon 7 of the lox-2 gene.
GenBank accession X78580.1 teaches a sequence for the pea LOX-2 gene from the Birte variety that has 99.3% sequence identity to instant SEQ ID NO: 10. See alignment below. GenBank accession X78580.1 teaches that exon 2 is located between nucleotides 1912 and 2198 and exon 4 begins at nucleotide 2604 of the sequence.
LOCUS X78580 5785 bp DNA linear PLN 14-NOV-2006
DEFINITION P.sativum (Birte) Lox1:Ps:2 gene.
ACCESSION X78580
VERSION X78580.1
KEYWORDS lipoxygenase; Lox1 gene.
SOURCE Pisum sativum (garden pea)
ORGANISM Pisum sativum
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50
kb inversion clade; NPAAA clade; Hologalegina; IRL clade; Fabeae;
Pisum.
REFERENCE 1 (bases 1 to 5785)
AUTHORS Forster,C., Knox,M., Domoney,C. and Casey,R.
TITLE lox1:Ps:2, a Pisum sativum seed lipoxygenase gene
JOURNAL Plant Physiol. 106 (3), 1227-1228 (1994)
PUBMED 7824652
REFERENCE 2 (bases 1 to 5785)
AUTHORS Casey,R.
TITLE Direct Submission
JOURNAL Submitted (01-APR-1994) R. Casey, John Innes Institute, Colney
Lane, Norwich, NR4 7UH, UK
FEATURES Location/Qualifiers
source 1..5785
/organism="Pisum sativum"
/mol_type="genomic DNA"
/cultivar="Birte"
/db_xref="taxon:3888"
/chromosome="linkage group 4"
/clone="2"
/clone_lib="lambda GEM-12 CF"
gene 1241..5091
/gene="Lox1:Ps:2"
regulatory 1241..1245
/regulatory_class="CAAT_signal"
/gene="Lox1:Ps:2"
regulatory 1256..1260
/regulatory_class="CAAT_signal"
/gene="Lox1:Ps:2"
regulatory 1278..1281
/regulatory_class="TATA_box"
/gene="Lox1:Ps:2"
regulatory 1296..1299
/regulatory_class="TATA_box"
/gene="Lox1:Ps:2"
mRNA join(1340..1597,1912..2198,2285..2525,2604..2924,
3009..3094,3172..3273,3363..3667,3783..4046,4151..5091)
/gene="Lox1:Ps:2"
/product="lipoxygenase"
exon 1340..1597
/gene="Lox1:Ps:2"
/number=1
CDS join(1366..1597,1912..2198,2285..2525,2604..2924,
3009..3094,3172..3273,3363..3667,3783..4046,4151..4904)
/gene="Lox1:Ps:2"
/codon_start=1
/product="lipoxygenase"
/protein_id="CAA55318.1"
/db_xref="GOA:P14856"
/db_xref="InterPro:IPR000907"
/db_xref="InterPro:IPR001024"
/db_xref="InterPro:IPR001246"
/db_xref="InterPro:IPR008976"
/db_xref="InterPro:IPR013819"
/db_xref="InterPro:IPR020833"
/db_xref="InterPro:IPR020834"
/db_xref="UniProtKB/Swiss-Prot:P14856"
/translation="MFPNVTGLLNKGHKIRGTVVLMRKNVLDFNTIVSIGGGNVHGVI
DSGINIIGSTLDGLTAFLGRSVSLQLISATKSDANGKGKVGKDTFLEGVLASLPTLGA
GESAFNIHFEWDHEMGIPGAFYIKNYMQVEFFLKSLTLEDVPNHGTIRFVCNSWVYNS
KLYKSPRIFFANKSYLPSETPSPLVKYREEELQTLRGDGTGERKLHERIYDYDVYNDL
GNPDHGEHLARPILGGSSTHPYPRRGRTGRYPTRKDPNSEKPATETYVPRDENFGHLK
SSDFLAYGIKSVSQCVVPAFESAFDLNFTPNEFDSFQDVRNLFEGGIKLPLDVISTIS
PLPVVKEIFRTDGEQVLKFTPPHVIRVSKSAWMTDEEFAREMLAGVNPCMIRGLQEFP
PKSNLDPAEYGDHTSKISVDVLNLDGCTIDEALASGRLFILDYHDTFIPFLRRINETS
AKAYATRTILFLKENGTLKPVAIELSLPHPDGDKSGFVSKVILPADEGVESTIWLLAK
AYVVVNDSCYHQLMSHWLNTHAVIEPFVIATNRQLSVVHPINKLLAPHYRDTMNINAL
ARDSLINANGIIERSFLPSKYAVEMSSAVYKYWVFTDQALPNDLIKRNMAVKDSSSPY
GLRLLIEDYPYAVDGLEIWTAIKTWVQDYVSLYYATDNDIKNDSELQHWWKEVVEKGH
GDLKDKPWWPKLQTFDELVEVCTIIIWTASALHAAVNFGQYPYGGLILNRPTLSRRLL
PEEGTAEYDEMVKSSQKAYLRTITPKFQTLIDLSVIEILSRHASDEVYLGQRENPHWT
SDSKALQAFQKFGNKLAEIEAKLTNKNNDPSLYHRVGPVQLPYTLLHPSSKEGLTFRG
IPNSISI"
intron 1598..1911
/gene="Lox1:Ps:2"
/number=1
exon 1912..2198
/gene="Lox1:Ps:2"
/number=2
intron 2199..2284
/gene="Lox1:Ps:2"
/number=2
exon 2285..2525
/gene="Lox1:Ps:2"
/number=3
intron 2526..2603
/gene="Lox1:Ps:2"
/number=3
exon 2604..2924
/gene="Lox1:Ps:2"
/number=4
intron 2925..3008
/gene="Lox1:Ps:2"
/number=4
exon 3009..3094
/gene="Lox1:Ps:2"
/number=5
intron 3095..3171
/gene="Lox1:Ps:2"
/number=5
exon 3172..3273
/gene="Lox1:Ps:2"
/number=6
intron 3274..3362
/gene="Lox1:Ps:2"
/number=6
exon 3363..3667
/gene="Lox1:Ps:2"
/number=7
intron 3668..3782
/gene="Lox1:Ps:2"
/number=7
exon 3783..4046
/gene="Lox1:Ps:2"
/number=8
intron 4047..4150
/gene="Lox1:Ps:2"
/number=8
exon 4151..5091
/gene="Lox1:Ps:2"
/number=
Query Match 99.3%; Score 3515.4; Length 5785;
Best Local Similarity 99.9%;
Matches 3538; Conservative 0; Mismatches 1; Indels 2; Gaps 2;
Qy 1 ATGTTTCCAAATGTGACAGGACTCCTAAACAAGGGCCACAAGATAAGAGGGACAGTGGTG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1366 ATGTTTCCAAATGTGACAGGACTCCTAAACAAGGGCCACAAGATAAGAGGGACAGTGGTG 1425
Qy 61 TTGATGCGTAAGAATGTGTTGGACTTCAACACAATTGTGAGTATTGGTGGTGGAAACGTC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1426 TTGATGCGTAAGAATGTGTTGGACTTCAACACAATTGTGAGTATTGGTGGTGGAAACGTC 1485
Qy 121 CATGGTGTCATCGACTCCGGCATCAATATCATTGGTTCAACTCTTGATGGCCTTACTGCC 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1486 CATGGTGTCATCGACTCCGGCATCAATATCATTGGTTCAACTCTTGATGGCCTTACTGCC 1545
Qy 181 TTCTTAGGCCGCAGTGTCTCCCTCCAGCTGATCAGTGCTACCAAGTCTGATGGTTAGTTC 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1546 TTCTTAGGCCGCAGTGTCTCCCTCCAGCTGATCAGTGCTACCAAGTCTGATGGTTAGTTC 1605
Qy 241 ATTCATTTCTTCTTACTTTTATATATCTAGACATGTAGCACTTTTATATCTAGACATGTA 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1606 ATTCATTTCTTCTTACTTTTATATATCTAGACATGTAGCACTTTTATATCTAGACATGTA 1665
Qy 301 TCATCAGAATCATCTTAAGTTTTTGGAACTCCTGAATAGGAGTTTTTGGAACTCCTGTAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1666 TCATCAGAATCATCTTAAGTTTTTGGAACTCCTGAATAGGAGTTTTTGGAACTCCTGTAT 1725
Qy 361 AGGTTAGTTGCAGTTTAACTTCGACAGAATATAGAAGTTCTATTTAATCACGATTTATTT 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1726 AGGTTAGTTGCAGTTTAACTTCGACAGAATATAGAAGTTCTATTTAATCACGATTTATTT 1785
Qy 421 GTGATAAATATTTTATGAGACCCTACTTAACTGTGACAAATTTTGGACTTATGCGGTAGC 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1786 GTGATAAATATTTTATGAGACCCTACTTAACTGTGACAAATTTTGGACTTATGCGGTAGC 1845
Qy 481 CTGCCTTGCACGGTCCTGATCAGGAGTATAGTCACTAAATGAATGAATTTAATGATATGT 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1846 CTGCCTTGCACGGTCCTGATCAGGAGTATAGTCACTAAATGAATGAATTTAATGATATGT 1905
Qy 541 ATGTAGCAAATGGAAAAGGAAAAGTTGGAAAGGATACATTTCTTGAAGGTGTTCTTGCTT 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1906 ATGTAGCAAATGGAAAAGGAAAAGTTGGAAAGGATACATTTCTTGAAGGTGTTCTTGCTT 1965
Qy 601 CATTACCAACCTTGGGAGCTGGTGAATCTGCATTCAATATTCATTTTGAATGGGATCATG 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1966 CATTACCAACCTTGGGAGCTGGTGAATCTGCATTCAATATTCATTTTGAATGGGATCATG 2025
Qy 661 AAATGGGAATTCCAGGTGCATTTTACATCAAAAACTATATGCAAGTTGAGTTTTTTCTCA 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2026 AAATGGGAATTCCAGGTGCATTTTACATCAAAAACTATATGCAAGTTGAGTTTTTTCTCA 2085
Qy 721 AGAGTTTAACTCTAGAAGATGTTCCAAATCATGGAACCATTCGCTTCGTATGCAACTCTT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2086 AGAGTTTAACTCTAGAAGATGTTCCAAATCATGGAACCATTCGCTTCGTATGCAACTCTT 2145
Qy 781 GGGTTTACAACTCAAAACTCTACAAAAGTCCTCGCATTTTCTTCGCCAACAAGGTAATTT 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2146 GGGTTTACAACTCAAAACTCTACAAAAGTCCTCGCATTTTCTTCGCCAACAAGGTAATTT 2205
Qy 841 ATTTACATCTATATGTTAGTGCGTGGTTTGTTAGAATCACGATGAATCATTATGATTTTA 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2206 ATTTACATCTATATGTTAGTGCGTGGTTTGTTAGAATCACGATGAATCATTATGATTTTA 2265
Qy 901 CTTGATTGTTATCATGCAGTCATATCTTCCGAGTGAAACACCGTCTCCACTTGTCAAGTA 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2266 CTTGATTGTTATCATGCAGTCATATCTTCCGAGTGAAACACCGTCTCCACTTGTCAAGTA 2325
Qy 961 TAGAGAAGAAGAATTGCAAACTCTAAGAGGAGATGGAACAGGAGAGCGCAAGTTACATGA 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2326 TAGAGAAGAAGAATTGCAAACTCTAAGAGGAGATGGAACAGGAGAGCGCAAGTTACATGA 2385
Qy 1021 AAGAATCTACGATTATGATGTCTATAACGATTTAGGCAATCCAGATCACGGCGAACATCT 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2386 AAGAATCTACGATTATGATGTCTATAACGATTTAGGCAATCCAGATCACGGCGAACATCT 2445
Qy 1081 TGCTCGACCTATTCTCGGAGGGTCTAGCACACATCCCTATCCTCGTAGGGGTAGGACCGG 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2446 TGCTCGACCTATTCTCGGAGGGTCTAGCACACATCCCTATCCTCGTAGGGGTAGGACCGG 2505
Qy 1141 TCGATATCCAACGAGGAAAGGTTAGATACAAGAACATGGTACAAATAATGATAAAAATGA 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2506 TCGATATCCAACGAGGAAAGGTTAGATACAAGAACATGGTACAAATAATGATAAAAATGA 2565
Qy 1201 GATAAACTAACCTTAAGCTATTGTGTTCTTTTGAACAGATCCGAATAGCGAGAAACCAGC 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2566 GATAAACTAACCTTAAGCTATTGTGTTCTTTTGAACAGATCCGAATAGCGAGAAACCAGC 2625
Qy 1261 TACAGAAACATATGTTCCAAGAGATGAAAATTTTGGTCACTTGAAGTCCTCTGACTTTCT 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2626 TACAGAAACATATGTTCCAAGAGATGAAAATTTTGGTCACTTGAAGTCCTCTGACTTTCT 2685
Qy 1321 TGCATATGGAATAAAATCTGTATCTCAATGTGTAGTACCTGCATTTGAATCTGCATTTGA 1380
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2686 TGCATATGGAATAAAATCTGTATCTCAATGTGTAGTACCTGCATTTGAATCTGCATTTGA 2745
Qy 1381 TTTGAATTTTACGCCTAACGAGTTTGATAGTTTTCAAGATGTGCGCAACCTCTTCGAAGG 1440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2746 TTTGAATTTTACGCCTAACGAGTTTGATAGTTTTCAAGATGTGCGCAACCTCTTCGAAGG 2805
Qy 1441 TGGAATTAAGCTTCCTCTAGATGTAATTAGCACAATTAGTCCTTTACCTGTGGTCAAAGA 1500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2806 TGGAATTAAGCTTCCTCTAGATGTAATTAGCACAATTAGTCCTTTACCTGTGGTCAAAGA 2865
Qy 1501 AATCTTTCGTACCGATGGTGAACAAGTCCTCAAGTTTACACCACCACATGTCATTCGAGG 1560
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2866 AATCTTTCGTACCGATGGTGAACAAGTCCTCAAGTTTACACCACCACATGTCATTCGAGG 2925
Qy 1561 TCCGACAAAATACATATTATAACGTAAATTATACTACGCTTTGAGTAATTTCATTTTATT 1620
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2926 TCCGACAAAATACATATTATAACGTAAATTATACTACGCTTTGAGTAATTTCATTTTATT 2985
Qy 1621 ATAAGTTTCTTTGTTTTTCGCAGTGAGTAAGTCTGCGTGGATGACCGATGAAGAATTTGC 1680
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 2986 ATAAGTTTCTTTGTTTTTCGCAGTGAGTAAGTCTGCGTGGATGACCGATGAAGAATTTGC 3045
Qy 1681 ACGAGAAATGCTCGCTGGCGTAAATCCATGCATGATCCGCGGTCTTCAAGTAAGTTCAAG 1740
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3046 ACGAGAAATGCTCGCTGGCGTAAATCCATGCATGATCCGCGGTCTTCAAGTAAGTTCAAG 3105
Qy 1741 AATTTATTTTAATATTTCGGAGAAATTTTTGCTATTCACATTAAATAATTGCCTATCTAA 1800
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3106 AATTTATTTTAATATTTCGGAGAAATTTTTGCTATTCACATTAAATAATTGCCTATCTAA 3165
Qy 1801 TTGTAGGAGTTTCCTCCGAAAAGCAATCTAGATCCCGCAGAATACGGTGATCACACTAGT 1860
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3166 TTGTAGGAGTTTCCTCCGAAAAGCAATCTAGATCCCGCAGAATACGGTGATCACACTAGT 3225
Qy 1861 AAGATATCTGTAGATGTCTTGAACCTTGATGGTTGCACCATAGATGAGGTAAACACATAA 1920
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3226 AAGATATCTGTAGATGTCTTGAACCTTGATGGTTGCACCATAGATGAGGTAAACACATAA 3285
Qy 1921 TAATCATAATTAAAAAAATATGATTTTGGACTTAATTTGGTGACATAAAGTGATTAAGAT 1980
||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||
Db 3286 TAATCATAATT-AAAAAATATGATTTTGGACTTAATTTGGTGACATAAAGTGATTAAGAT 3344
Qy 1981 TAATTTTACATGGAACAGGCACTTGCTAGTGGGAGATTATTTATACTAGATTATCATGAC 2040
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3345 TAATTTTACATGGAACAGGCACTTGCTAGTGGGAGATTATTTATACTAGATTATCATGAC 3404
Qy 2041 ACATTTATTCCATTTCTGAGAAGGATCAATGAGACTTCTGCAAAAGCTTATGCTACTAGA 2100
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3405 ACATTTATTCCATTTCTGAGAAGGATCAATGAGACTTCTGCAAAAGCTTATGCTACTAGA 3464
Qy 2101 ACAATACTTTTTCTAAAAGAAAATGGAACTTTAAAGCCAGTGGCCATTGAATTAAGTTTG 2160
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3465 ACAATACTTTTTCTAAAAGAAAATGGAACTTTAAAGCCAGTGGCCATTGAATTAAGTTTG 3524
Qy 2161 CCACATCCTGATGGTGACAAATCAGGTTTTGTTAGTAAAGTTATCTTACCTGCAGATGAA 2220
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3525 CCACATCCTGATGGTGACAAATCAGGTTTTGTTAGTAAAGTTATCTTACCTGCAGATGAA 3584
Qy 2221 GGTGTTGAGAGTACTATTTGGCTTCTAGCAAAAGCTTATGTGGTGGTTAACGATTCTTGC 2280
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3585 GGTGTTGAGAGTACTATTTGGCTTCTAGCAAAAGCTTATGTGGTGGTTAACGATTCTTGC 3644
Qy 2281 TATCATCAACTCATGAGCCATTGGTAAAATATAGTAATGTTTATATTTTCACGTATGTGC 2340
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |
Db 3645 TATCATCAACTCATGAGCCATTGGTAAAATATAGTAATGTTTATATTTTCACGTATGT-C 3703
Qy 2341 GCTCTAAAATATCAGGTAGGATTTGAACTCTGAATATATGTATTACTTATTGATGATTTT 2400
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3704 GCTCTAAAATATCAGGTAGGATTTGAACTCTGAATATATGTATTACTTATTGATGATTTT 3763
Qy 2401 TATATATTTATTGGAATAGGTTGAATACTCATGCGGTAATTGAGCCGTTTGTTATAGCAA 2460
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3764 TATATATTTATTGGAATAGGTTGAATACTCATGCGGTAATTGAGCCGTTTGTTATAGCAA 3823
Qy 2461 CAAATCGGCAGCTTAGTGTGGTTCATCCGATTAATAAACTTTTAGCTCCTCATTATCGCG 2520
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3824 CAAATCGGCAGCTTAGTGTGGTTCATCCGATTAATAAACTTTTAGCTCCTCATTATCGCG 3883
Qy 2521 ACACGATGAACATCAATGCACTTGCAAGAGATTCTCTAATTAATGCCAATGGCATAATAG 2580
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3884 ACACGATGAACATCAATGCACTTGCAAGAGATTCTCTAATTAATGCCAATGGCATAATAG 3943
Qy 2581 AGAGAAGTTTTTTGCCTTCGAAGTATGCTGTGGAAATGTCTTCAGCGGTTTACAAGTATT 2640
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 3944 AGAGAAGTTTTTTGCCTTCGAAGTATGCTGTGGAAATGTCTTCAGCGGTTTACAAGTATT 4003
Qy 2641 GGGTTTTCACAGATCAAGCTCTGCCGAATGATCTTATCAAGAGGTAATAGAATGATCATA 2700
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4004 GGGTTTTCACAGATCAAGCTCTGCCGAATGATCTTATCAAGAGGTAATAGAATGATCATA 4063
Qy 2701 GGTTCGAAAAATGAACAATCTTTTTAAAGATGATTCTATATTTAAGGACTGAGATAGTAA 2760
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4064 GGTTCGAAAAATGAACAATCTTTTTAAAGATGATTCTATATTTAAGGACTGAGATAGTAA 4123
Qy 2761 CATGTATATGCATTTTGCTTGATTCAGAAACATGGCAGTTAAAGATTCGTCGTCTCCATA 2820
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4124 CATGTATATGCATTTTGCTTGATTCAGAAACATGGCAGTTAAAGATTCGTCGTCTCCATA 4183
Qy 2821 TGGACTCCGTCTTCTGATAGAGGACTACCCGTACGCTGTTGACGGATTAGAGATATGGAC 2880
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4184 TGGACTCCGTCTTCTGATAGAGGACTACCCGTACGCTGTTGACGGATTAGAGATATGGAC 4243
Qy 2881 GGCTATTAAAACATGGGTCCAAGATTATGTCTCGCTGTATTATGCAACGGACAATGATAT 2940
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4244 GGCTATTAAAACATGGGTCCAAGATTATGTCTCGCTGTATTATGCAACGGACAATGATAT 4303
Qy 2941 CAAAAATGATTCCGAGCTTCAACATTGGTGGAAAGAGGTTGTAGAGAAAGGTCATGGTGA 3000
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4304 CAAAAATGATTCCGAGCTTCAACATTGGTGGAAAGAGGTTGTAGAGAAAGGTCATGGTGA 4363
Qy 3001 CTTGAAAGATAAGCCATGGTGGCCTAAGTTGCAAACGTTTGACGAGCTCGTTGAAGTTTG 3060
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4364 CTTGAAAGATAAGCCATGGTGGCCTAAGTTGCAAACGTTTGACGAGCTCGTTGAAGTTTG 4423
Qy 3061 CACTATCATCATATGGACGGCTTCTGCTCTCCACGCAGCTGTTAATTTTGGACAATATCC 3120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4424 CACTATCATCATATGGACGGCTTCTGCTCTCCACGCAGCTGTTAATTTTGGACAATATCC 4483
Qy 3121 TTACGGCGGTTTAATTCTAAACCGTCCAACTCTGAGTAGAAGATTGCTTCCTGAGGAAGG 3180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4484 TTACGGCGGTTTAATTCTAAACCGTCCAACTCTGAGTAGAAGATTGCTTCCTGAGGAAGG 4543
Qy 3181 AACTGCGGAATACGATGAAATGGTGAAGAGTTCTCAAAAGGCTTACTTGAGGACAATCAC 3240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4544 AACTGCGGAATACGATGAAATGGTGAAGAGTTCTCAAAAGGCTTACTTGAGGACAATCAC 4603
Qy 3241 GCCGAAGTTTCAGACTCTTATTGATCTTTCAGTGATAGAAATATTGTCAAGACATGCTTC 3300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4604 GCCGAAGTTTCAGACTCTTATTGATCTTTCAGTGATAGAAATATTGTCAAGACATGCTTC 4663
Qy 3301 TGATGAAGTCTATCTCGGACAAAGGGAAAATCCACACTGGACATCTGATTCTAAAGCTTT 3360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4664 TGATGAAGTCTATCTCGGACAAAGGGAAAATCCACACTGGACATCTGATTCTAAAGCTTT 4723
Qy 3361 ACAAGCATTTCAAAAGTTTGGAAATAAATTGGCGGAAATTGAGGCCAAACTTACGAATAA 3420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4724 ACAAGCATTTCAAAAGTTTGGAAATAAATTGGCGGAAATTGAGGCCAAACTTACGAATAA 4783
Qy 3421 GAACAATGATCCGAGCCTGTACCATCGGGTCGGGCCGGTTCAATTGCCATACACTTTGCT 3480
||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||
Db 4784 GAACAATGATCCGAGCCTGTACCATAGGGTCGGGCCGGTTCAATTGCCATACACTTTGCT 4843
Qy 3481 TCATCCCAGCAGCAAGGAAGGGTTAACCTTTAGAGGAATTCCTAATAGTATCTCTATTTA 3540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 4844 TCATCCCAGCAGCAAGGAAGGGTTAACCTTTAGAGGAATTCCTAATAGTATCTCTATTTA 4903
Qy 3541 A 3541
|
Db 4904 A 4904
The translated sequence of this gene, provided in the block immediately above, has 100% sequence similarity to instant SEQ ID NO: 7. See alignment below.
Score
Expect
Method
Identities
Positives
Gaps
1784 bits(4620)
0.0
Compositional matrix adjust.
863/863(100%)
863/863(100%)
0/863(0%)
Query 1 MFPNVTGLLNKGHKIRGTVVLMRKNVLDFNTIVSIGGGNVHGVIDSGINIIGSTLDGLTA 60
MFPNVTGLLNKGHKIRGTVVLMRKNVLDFNTIVSIGGGNVHGVIDSGINIIGSTLDGLTA
Sbjct 1 MFPNVTGLLNKGHKIRGTVVLMRKNVLDFNTIVSIGGGNVHGVIDSGINIIGSTLDGLTA 60
Query 61 FLGRSVSLQLISATKSDANGKGKVGKDTFLEGVLASLPTLGAGESAFNIHFEWDHEMGIP 120
FLGRSVSLQLISATKSDANGKGKVGKDTFLEGVLASLPTLGAGESAFNIHFEWDHEMGIP
Sbjct 61 FLGRSVSLQLISATKSDANGKGKVGKDTFLEGVLASLPTLGAGESAFNIHFEWDHEMGIP 120
Query 121 GAFYIKNYMQVEFFLKSLTLEDVPNHGTIRFVCNSWVYNSKLYKSPRIFFANKSYLPSET 180
GAFYIKNYMQVEFFLKSLTLEDVPNHGTIRFVCNSWVYNSKLYKSPRIFFANKSYLPSET
Sbjct 121 GAFYIKNYMQVEFFLKSLTLEDVPNHGTIRFVCNSWVYNSKLYKSPRIFFANKSYLPSET 180
Query 181 PSPLVKYREEELQTLRGDGTGERKLHERIYDYDVYNDLGNPDHGEHLARPILGGSSTHPY 240
PSPLVKYREEELQTLRGDGTGERKLHERIYDYDVYNDLGNPDHGEHLARPILGGSSTHPY
Sbjct 181 PSPLVKYREEELQTLRGDGTGERKLHERIYDYDVYNDLGNPDHGEHLARPILGGSSTHPY 240
Query 241 PRRGRTGRYPTRKDPNSEKPATETYVPRDENFGHLKSSDFLAYGIKSVSQCVVPAFESAF 300
PRRGRTGRYPTRKDPNSEKPATETYVPRDENFGHLKSSDFLAYGIKSVSQCVVPAFESAF
Sbjct 241 PRRGRTGRYPTRKDPNSEKPATETYVPRDENFGHLKSSDFLAYGIKSVSQCVVPAFESAF 300
Query 301 DLNFTPNEFDSFQDVRNLFEGGIKLPLDVISTISPLPVVKEIFRTDGEQVLKFTPPHVIR 360
DLNFTPNEFDSFQDVRNLFEGGIKLPLDVISTISPLPVVKEIFRTDGEQVLKFTPPHVIR
Sbjct 301 DLNFTPNEFDSFQDVRNLFEGGIKLPLDVISTISPLPVVKEIFRTDGEQVLKFTPPHVIR 360
Query 361 VSKSAWMTDEEFAREMLAGVNPCMIRGLQEFPPKSNLDPAEYGDHTSKISVDVLNLDGCT 420
VSKSAWMTDEEFAREMLAGVNPCMIRGLQEFPPKSNLDPAEYGDHTSKISVDVLNLDGCT
Sbjct 361 VSKSAWMTDEEFAREMLAGVNPCMIRGLQEFPPKSNLDPAEYGDHTSKISVDVLNLDGCT 420
Query 421 IDEALASGRLFILDYHDTFIPFLRRINETSAKAYATRTILFLKENGTLKPVAIELSLPHP 480
IDEALASGRLFILDYHDTFIPFLRRINETSAKAYATRTILFLKENGTLKPVAIELSLPHP
Sbjct 421 IDEALASGRLFILDYHDTFIPFLRRINETSAKAYATRTILFLKENGTLKPVAIELSLPHP 480
Query 481 DGDKSGFVSKVILPADEGVESTIWLLAKAYVVVNDSCYHQLMSHWLNTHAVIEPFVIATN 540
DGDKSGFVSKVILPADEGVESTIWLLAKAYVVVNDSCYHQLMSHWLNTHAVIEPFVIATN
Sbjct 481 DGDKSGFVSKVILPADEGVESTIWLLAKAYVVVNDSCYHQLMSHWLNTHAVIEPFVIATN 540
Query 541 RQLSVVHPINKLLAPHYRDTMNINALARDSLINANGIIERSFLPSKYAVEMSSAVYKYWV 600
RQLSVVHPINKLLAPHYRDTMNINALARDSLINANGIIERSFLPSKYAVEMSSAVYKYWV
Sbjct 541 RQLSVVHPINKLLAPHYRDTMNINALARDSLINANGIIERSFLPSKYAVEMSSAVYKYWV 600
Query 601 FTDQALPNDLIKRNMAVKDSSSPYGLRLLIEDYPYAVDGLEIWTAIKTWVQDYVSLYYAT 660
FTDQALPNDLIKRNMAVKDSSSPYGLRLLIEDYPYAVDGLEIWTAIKTWVQDYVSLYYAT
Sbjct 601 FTDQALPNDLIKRNMAVKDSSSPYGLRLLIEDYPYAVDGLEIWTAIKTWVQDYVSLYYAT 660
Query 661 DNDIKNDSELQHWWKEVVEKGHGDLKDKPWWPKLQTFDELVEVCTIIIWTASALHAAVNF 720
DNDIKNDSELQHWWKEVVEKGHGDLKDKPWWPKLQTFDELVEVCTIIIWTASALHAAVNF
Sbjct 661 DNDIKNDSELQHWWKEVVEKGHGDLKDKPWWPKLQTFDELVEVCTIIIWTASALHAAVNF 720
Query 721 GQYPYGGLILNRPTLSRRLLPEEGTAEYDEMVKSSQKAYLRTITPKFQTLIDLSVIEILS 780
GQYPYGGLILNRPTLSRRLLPEEGTAEYDEMVKSSQKAYLRTITPKFQTLIDLSVIEILS
Sbjct 721 GQYPYGGLILNRPTLSRRLLPEEGTAEYDEMVKSSQKAYLRTITPKFQTLIDLSVIEILS 780
Query 781 RHASDEVYLGQRENPHWTSDSKALQAFQKFGNKLAEIEAKLTNKNNDPSLYHRVGPVQLP 840
RHASDEVYLGQRENPHWTSDSKALQAFQKFGNKLAEIEAKLTNKNNDPSLYHRVGPVQLP
Sbjct 781 RHASDEVYLGQRENPHWTSDSKALQAFQKFGNKLAEIEAKLTNKNNDPSLYHRVGPVQLP 840
Query 841 YTLLHPSSKEGLTFRGIPNSISI 863
YTLLHPSSKEGLTFRGIPNSISI
Sbjct 841 YTLLHPSSKEGLTFRGIPNSISI 863
Forster teaches a pea LOX-2 null mutant (title; page 1210, left column, paragraph 3). Forster teaches that the null LOX-2 pea mutant produces less 13- than 9- hydroperoxides compared to a control plant (page 1215, right column, paragraph 4; figure 6). Forster teaches that LOX-2 removal in pea lines reduces hexanal production (page 1219, left column, paragraph 1). Forster teaches that seed LOX has no agronomic significance and that removal does not impair yield (page 1218, right column, paragraph 3). Finally, Forster teaches pea seed meal (page 1210, right column, paragraph 4) and proposes the introduction of the LOX-2 null mutation into freezer peas which would reduce n-hexanal production and reduction of off-flavor (page 1219, left column, paragraph 1).
Wang teaches a method of generating lipoxygenase-free soybean by generating knockouts of GmLox1, GmLox2, and GmLox3 via CRISPR-Cas9 targeting (page 433, right column, paragraph 2). The gene editing targeted sites in the second exon and third exon of the LOX2 and LOX3 genes respectively (figure 1, GGAAAGGATACGTTCTTGGAAGG for LOX-2 and CCTTTGGTTATCCTCGTAGGGGG for LOX-3) and caused deletion, insertion, and/or substitution mutations at these sites (figure 2). The target sequence for the soy LOX-2 gene aligns most closely with the pea LOX-2 sequence of GenBank accession X78580.1 at nucleotides 1932-1954. See MUSCLE alignment below. Triple mutants with mutations in all three lipoxygenase genes were recovered (page 437, left column, paragraph 1). The triple mutants lacked activity of both LOX2 and LOX3 (page 437, right column, paragraph 1).
PNG
media_image1.png
154
1224
media_image1.png
Greyscale
Wang teaches a motivation to use the CRISPR-Cas9 method to knockout lox loci, because the knockouts can be done in elite cultivars with existing agriculture traits to rapidly and cost-effectively create LOX-free varieties (page 437, right column, paragraph 3). Wang teaches a motivation to mutate both LOX2 and LOX3 because all three lipoxygenase isozymes are involved in the formation of beany flavor (page 433, left column, paragraph 2).
GenBank accession X78581.1 provides evidence of a Birte pea lipoxygenase gene lox1:Ps:3 with 99% sequence identity to instant SEQ ID NO: 27 (see alignment above) encoding a protein with 99.88% sequence identity to SEQ ID NO: 25. See alignment below.
Score
Expect
Method
Identities
Positives
Gaps
1782 bits(4616)
0.0
Compositional matrix adjust.
860/861(99%)
861/861(100%)
0/861(0%)
Query 1 MFSGVTGILNRGHKIKGTVVLMRKNVLDINSLTTVGGVIGQGFDILGSTVDNLTAFLGRS 60
MFSGVTGILNRGHKIKGTVVLMRKNVLDINSLTTVGGVIGQGFDILGSTVDNLTAFLGRS
Sbjct 1 MFSGVTGILNRGHKIKGTVVLMRKNVLDINSLTTVGGVIGQGFDILGSTVDNLTAFLGRS 60
Query 61 VSLQLISATKPDATGKGKLGKATFLEGIISSLPTLGAGQSAFKIHFEWDDDMGIPGAFYI 120
VSLQLISATKPDATGKGKLGKATFLEGIISSLPTLGAGQSAFKIHFEWDDDMGIPGAFYI
Sbjct 61 VSLQLISATKPDATGKGKLGKATFLEGIISSLPTLGAGQSAFKIHFEWDDDMGIPGAFYI 120
Query 121 KNFMQTEFFLVSLTLDDIPNHGSIYFVCNSWIYNAKHHKIDRIFFANQTYLPSETPAPLV 180
KNFMQTEFFLVSLTLDDIPNHGSIYFVCNSWIYNAKHHKIDRIFFANQTYLPSETPAPLV
Sbjct 121 KNFMQTEFFLVSLTLDDIPNHGSIYFVCNSWIYNAKHHKIDRIFFANQTYLPSETPAPLV 180
Query 181 HYREEELNNLRGDGTGERKEWERIYDYDVYNDLGNPDSGENHARPVLGGSETYPYPRRGR 240
HYREEELNNLRGDGTGERKEWERIYDYDVYNDLGNPDSGENHARPVLGGSETYPYPRRGR
Sbjct 181 HYREEELNNLRGDGTGERKEWERIYDYDVYNDLGNPDSGENHARPVLGGSETYPYPRRGR 240
Query 241 TGRKPTRKDPNSESRSDYVYLPRDEAFGHLKSSDFLTYGLKAVSQNVVPALESVFFDLNF 300
TGRKPTRKDPNSESRSDYVYLPRDEAFGHLKSSDFLTYGLKAVSQNVVPALESVFFDLNF
Sbjct 241 TGRKPTRKDPNSESRSDYVYLPRDEAFGHLKSSDFLTYGLKAVSQNVVPALESVFFDLNF 300
Query 301 TPNEFDSFDEVHGLYEGGIKLPTNILSQISPLPVLKEIFRTDGENTLKYPPPKVIQVSRS 360
TPNEFDSFDEVHGLYEGGIKLPTNILSQISPLPVLKEIFRTDGENTLKYPPPKVIQVSRS
Sbjct 301 TPNEFDSFDEVHGLYEGGIKLPTNILSQISPLPVLKEIFRTDGENTLKYPPPKVIQVSRS 360
Query 361 GWMTDEEFAREMLAGVNPNVICCLQEFPPRSKLDSQIYGDHTSKISKEHLEPNLEGLTVE 420
GWMTDEEFAREMLAGVNPNVICCLQEFPPRSKLDSQIYGDHTSKISKEHLEPNLEGLTVE
Sbjct 361 GWMTDEEFAREMLAGVNPNVICCLQEFPPRSKLDSQIYGDHTSKISKEHLEPNLEGLTVE 420
Query 421 EAIQNKKLFLLDHHDSIMPYLRRINSTSTKAYATRTILFLNNNQNLKPLAIELSLPHPQG 480
EAIQNKKLFLLDHHDSIMPYLRRINSTSTKAYATRTILFLNNNQNLKPLAIELSLPHPQG
Sbjct 421 EAIQNKKLFLLDHHDSIMPYLRRINSTSTKAYATRTILFLNNNQNLKPLAIELSLPHPQG 480
Query 481 DEHGAVSYVYQPALEGVESNIWLLAKAYVIVNDSCYHQLVSHWLNTHAVVEPFVIATNRH 540
DEHGAVSYVYQPALEGVES+IWLLAKAYVIVNDSCYHQLVSHWLNTHAVVEPFVIATNRH
Sbjct 481 DEHGAVSYVYQPALEGVESSIWLLAKAYVIVNDSCYHQLVSHWLNTHAVVEPFVIATNRH 540
Query 541 LSCLHPIYKLLYPHYRDTMNINSLARLSLVNDGGIIEKTFLWGRYSMEMSSKVYKNWVFT 600
LSCLHPIYKLLYPHYRDTMNINSLARLSLVNDGGIIEKTFLWGRYSMEMSSKVYKNWVFT
Sbjct 541 LSCLHPIYKLLYPHYRDTMNINSLARLSLVNDGGIIEKTFLWGRYSMEMSSKVYKNWVFT 600
Query 601 EQALPADLIKRGMAIEDPSSPCGVKLVVEDYPYAVDGLEIWAIIKTWVQDYVSLYYTSDE 660
EQALPADLIKRGMAIEDPSSPCGVKLVVEDYPYAVDGLEIWAIIKTWVQDYVSLYYTSDE
Sbjct 601 EQALPADLIKRGMAIEDPSSPCGVKLVVEDYPYAVDGLEIWAIIKTWVQDYVSLYYTSDE 660
Query 661 KLRQDSELQAWWKELVEVGHGDKKNEPWWPKMQTREDLIEVCSIVIWTASALHAAVNFGQ 720
KLRQDSELQAWWKELVEVGHGDKKNEPWWPKMQTREDLIEVCSIVIWTASALHAAVNFGQ
Sbjct 661 KLRQDSELQAWWKELVEVGHGDKKNEPWWPKMQTREDLIEVCSIVIWTASALHAAVNFGQ 720
Query 721 YSYGGLILNRPTLSRRFMPEKGSAEFEELVKSPQKAYLKTITPKFQTLIDLSVIEILSRH 780
YSYGGLILNRPTLSRRFMPEKGSAEFEELVKSPQKAYLKTITPKFQTLIDLSVIEILSRH
Sbjct 721 YSYGGLILNRPTLSRRFMPEKGSAEFEELVKSPQKAYLKTITPKFQTLIDLSVIEILSRH 780
Query 781 ASDELYLGERDNPNWTSDKRALEAFKKFGNKLAEIEKKLTQRNNDEKLRNRHGPVEMPYT 840
ASDELYLGERDNPNWTSDKRALEAFKKFGNKLAEIEKKLTQRNNDEKLRNRHGPVEMPYT
Sbjct 781 ASDELYLGERDNPNWTSDKRALEAFKKFGNKLAEIEKKLTQRNNDEKLRNRHGPVEMPYT 840
Query 841 LLYPSSKEGLTFRGIPNSISI 861
LLYPSSKEGLTFRGIPNSISI
Sbjct 841 LLYPSSKEGLTFRGIPNSISI 861
Before the time of filing of the instant application, one of ordinary skill in the art would have been motivated to modify the method of Davies to generate a LOX-2 mutant pea plant with reduced LOX-2 lipoxygenase activity by breeding to incorporate site-directed mutagenesis as taught by Wang. One of ordinary skill in the art would have been motivated to use Wang’s CRISPR-Cas editing to rapidly and cost-effectively create LOX-free varieties in elite backgrounds of pea. One of ordinary skill would have had reasonable expectation of success because site-directed mutagenesis had been suggested by Davies as a reasonable alternative for generating a LOX-2 mutant in pea.
It would have been obvious to expect that the sequence of the mutagenized LOX-2 pea gene would have had at least 90% sequence identity to the sequence of instant SEQ ID NO: 10, because Davies used the Birte variety of pea and Birte LOX-2 has 99% sequence identity to SEQ ID NO: 10. See alignment above. It would have also been obvious to one of ordinary skill in the art to create an insertion, substitution, or deletion in a coding region upstream of exon 7 of the LOX-2 gene, because the mutations taught by Wang were located in a coding region of exon 2 of the soybean homolog, which corresponded to a coding region of exon 2 in the pea gene. Thus, the pea plant of instant claims 1, 30 & 36 would have been obvious.
Before the time of filing of the instant application, one of ordinary skill in the art would have been motivated to modify the method of Davies to mutate both a LOX-2 and LOX-3 gene in pea. One of ordinary skill in the art would have been motivated to mutate both genes, because Wang teaches that LOX-2 and LOX-3 may both play a role in producing beany off flavors and Davies teaches that pea lox-2 null mutants have over expression of lox-3. One of ordinary skill in the art would have had reasonable expectation of success because site-directed mutagenesis had been suggested by Davies as a reasonable alternative for generating a LOX mutant in pea. The lox1:Ps:2 and lox1:Ps:3 genes, which read on lox-2 and lox-3 in pea, share 99% identity with instant SEQ ID NO: 10 and SEQ ID NO: 27 respectively. Thus, the plant of instant claims 91 & 94-95 would have been obvious.
The knockout LOX-2 plant would have improved flavor characteristics (instant claim 88), as suggested by Davies due to reduction of beany flavors in soybean or Forster due to reduction in hexanal. LOX-2 null alleles inherently confer a decreased hexanal phenotype (Forster page 1219, left column, paragraph 1; instant specification, page 131, lines 16-30, table 7). Thus, Forster’s LOX-2 null mutants make obvious a plant wherein the amount of hexanal is reduced relative to a control plant including by at least 70% (instant claims 3 & 85).
Forster’s teachings make it obvious that a lox-2 mutant would have similar yield to wildtype and therefore at least 80% as compared to a control plant or plant part. Frozen peas read on a plant produce and would comprise DNA comprising at least a fragment identical to a fragment of the mutated LOX-2 gene of the LOX-2 null plant. Thus, the pea plants, peas or frozen peas of Davies and Forster in view of Wang make obvious instant (claims 3, 37, 89, and 93).
Applicant urges that Forster’s mutant pea line has a mutation in the LOX-2 promoter and does not disclose a mutation in the coding region upstream of exon 7 (Remarks, page 18, paragraph 3).
This argument is unpersuasive, because mutations in a region corresponding to the coding region of the pea protein upstream of the equivalent of exon 7 had been shown to be effective at producing a null allele in soybean prior to the filing of the instant application. So, a mutation in the coding region upstream of exon 7 in the pea gene for LOX-2 would have been obvious to one of skill in the art.
Applicant urges that LOX-2 null plants may not necessarily have reduced hexanal levels, including reduced by at least 70%, because plants have other enzymes that produce hexanal. Applicant urges that even though Forster 1999 discloses reduced hexanal, Forster does not provide evidence of reduced hexanal by 75% or more in plants having reduced LOX-2 activity, so Applicant urges claim 1 is novel (Remarks, page 18, paragraph 3).
This argument is unpersuasive, because Forster’s silence regarding whether the null mutant LOX-2 pea plants have reduced hexanal by 70% is not the same as the art teaching null mutant LOX-2 pea plants without the phenotype.
Claim(s) 10, 83, 84, 86 & 87 are rejected under 35 U.S.C. 103 as being unpatentable over Davies, Forster, and Wang as applied to claims 1, 3, 30, 36-37, 85, 88-89, 91 & 93-95 above, and further in view of Bilyeu et al (2005) Crop Sci. 45:1830–1836 (published 8/1/2005, hereafter Bilyeu) and Glaser et al (2021) J. Agric. Food Chem. 69, 8768−8776 (published 7/29/2021, hereafter Glaser).
Claims 10, 83, 84, 86 & 87 are drawn to a plant comprising reduced LOX-2 activity and decreased FAD activity and a mutated FAD3 gene comprising one or more insertions, substitutions, or deletions.
The teachings of Davies, Forster, and Wang are presented above. They do not teach a mutated FAD3C gene.
Glaser teaches that linolenic acid is a key inducer to bitterness in pea protein extract (abstract), and bitterness is a significant limiting factor for the use of pea-protein isolates for the food processing industry (page 8767, left column, paragraph 1).
Bilyeu teaches that mutations at both FAD3A and FAD3C in soybean lead to a reduction in linolenic acid, and both mutations together result in 2/3 reduction in linolenic acid (page 1833, right column, paragraph 2; figure 3; table 1). Bilyeu teaches a FAD3C mutant allele in soybean with a single nucleotide polymorphism, which reads on a substitution, at base 383 of the coding sequence (page 1832, right column, paragraph 1; figure 2).
Before the time of filing of the instant application, one of ordinary skill in the art would have been motivated to modify the method of Davies, Forster, and Wang above to additionally mutate a FAD3 gene in pea. One of ordinary skill in the art would have been motivated to mutate a FAD3 gene to reduce bitterness flavor in pea. One of ordinary skill would have had reasonable expectation of success, because mutations to FAD3 genes in soybean had accomplished the desired effect.
A plant comprising reduced FAD3 activity and reduced LOX-2 and LOX-3 activity as taught by Bilyeu would have reduced polyunsaturated lipid (claim 83) including reduced by 50-90% (claim 84), and the amount of linolenic acid would be reduced by at least 50% (claim 86). When knocked out in pea, the amount of oleic acid would inherently increase, including by at least by 4% (claims 10, 87).
Thus, claims 1, 3, 10, 30, 36-37, 83-89, 91 & 93-95 are obvious over Davies, Wang, Forster, Glaser, and Bilyeu.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claim 37 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 36 of copending Application No. 18/853,521 (reference application) in view of Xia et al (2021) Food Control. 123 107859 (available 12/31/2020, hereafter Xia).
This is a new rejection necessitated by Applicant’s amendments filed 7/11/2025. Applicant’s arguments filed 7/11/2025 have been considered as they apply to this rejection, but they are not found persuasive.
Although the claims at issue are not identical, they are not patentably distinct from each other because oil produced by a population of soybean plants comprising low linolenic acid relative to oil produced from a control population, as claimed in ‘521 (claim 36, lines 8, 10, 11, or 12), reads on a plant product produced from a plant with decreased LOX activity that has decreased amount of linolenic acid, as claimed in the instant application (instant claim 37).
Xia teaches that soybean oil comprises DNA (table 3), although fragmented and degraded (page 7, left column, paragraph 3).
Although ‘521 claim 36 is not drawn to a plant comprising reduced LOX activity specifically, instant claim 37 is drawn to a plant product so includes seed with reduced LOX activity. Because the oil of ‘521 claim 36 would comprise fragments of DNA, and because the length of fragments and unique features to a fragment of a mutated LOX-2 gene are not defined by claim 37, the oil of ‘521 claim 36, makes obvious the plant product of instant claim 37
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Applicant urges that amended claim 37 requires that the plant product comprises the mutated LOX-2 gene of the plant of claim 1, while ‘521 is directed to oil without the feature of the mutated LOX-2 gene making instant claim 37 and 36 patentably distinct (Remarks, page 18, paragraph 6-page 19, paragraph 1).
This argument is unpersuasive, because soybean oil as a plant product would comprise DNA fragments. Amended claim 37 merely requires a fragment of the mutated gene, which does not require the mutation itself. The oil of ‘521 would comprise DNA and thus would comprise fragments found within the gene sequence of a mutated LOX-2.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/VICTORIA L DELEO/Examiner, Art Unit 1662
/Anne Kubelik/Primary Examiner, Art Unit 1663