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TGFam-Finder: a novel solution for target-gene family annotation in plants.

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Τίτλος: TGFam-Finder: a novel solution for target-gene family annotation in plants.
Συγγραφείς: Kim S; Department of Plant Science, Plant Immunity Research Center, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.; Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea., Cheong K; Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea., Park J; Department of Plant Science, Plant Immunity Research Center, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea., Kim MS; Department of Plant Science, Plant Immunity Research Center, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.; Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea., Kim J; Department of Plant Science, Plant Immunity Research Center, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea., Seo MK; Department of Plant Science, Plant Immunity Research Center, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea., Chae GY; Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea., Jang MJ; Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Korea., Mang H; Department of Plant Science, Plant Immunity Research Center, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea., Kwon SH; Department of Pharmacology, Seoul National University College of Medicine, Seoul, 03080, Korea., Kim YM; Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea., Koo N; Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Korea., Min CW; Department of Plant Bioscience, Life and Energy Convergence Research Institute, Pusan National University, Miryang, 627-706, Korea., Kim KS; Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 13488, Korea., Oh N; Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 13488, Korea., Kim KT; Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea., Jeon J; Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea., Kim H; Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea., Lee YY; Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Korea., Sohn KH; Department of Life Sciences, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Korea.; School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, 37673, Korea., McCann HC; New Zealand Institute for Advanced Study, Massey University Auckland, Auckland, 0632, New Zealand., Ye SK; Department of Pharmacology, Seoul National University College of Medicine, Seoul, 03080, Korea., Kim ST; Department of Plant Bioscience, Life and Energy Convergence Research Institute, Pusan National University, Miryang, 627-706, Korea., Park KS; Department of Biomedical Science, College of Life Science, CHA University, Seongnam, 13488, Korea., Lee YH; Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea.; Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea., Choi D; Department of Plant Science, Plant Immunity Research Center, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.; Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826, Korea.
Πηγή: The New phytologist [New Phytol] 2020 Sep; Vol. 227 (5), pp. 1568-1581. Date of Electronic Publication: 2020 Jun 05.
Τύπος έκδοσης: Journal Article; Research Support, Non-U.S. Gov't
Γλώσσα: English
Στοιχεία περιοδικού: Publisher: Wiley on behalf of New Phytologist Trust Country of Publication: England NLM ID: 9882884 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1469-8137 (Electronic) Linking ISSN: 0028646X NLM ISO Abbreviation: New Phytol Subsets: MEDLINE
Imprint Name(s): Publication: Oxford : Wiley on behalf of New Phytologist Trust
Original Publication: London, New York [etc.] Academic Press.
Ιατρικοί όροι (MeSH): Genome, Plant*/genetics , Plants*/genetics, Molecular Sequence Annotation
Περίληψη: Whole-genome annotation error that omits essential protein-coding genes hinders further research. We developed Target Gene Family Finder (TGFam-Finder), an alternative tool for the structural annotation of protein-coding genes containing target domain(s) of interest in plant genomes. TGFam-Finder took considerably reduced annotation run-time and improved accuracy compared to conventional annotation tools. Large-scale re-annotation of 50 plant genomes identified an average of 150, 166 and 86 additional far-red-impaired response 1, nucleotide-binding and leucine-rich-repeat, and cytochrome P450 genes, respectively, that were missed in previous annotations. We detected significantly higher number of translated genes in the new annotations using mass spectrometry data from seven plant species compared to previous annotations. TGFam-Finder along with the new gene models can provide an optimized platform for comprehensive functional, comparative, and evolutionary studies in plants.
(©2020 The Authors. New Phytologist ©2020 New Phytologist Trust.)
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Contributed Indexing: Keywords: CYP450; FAR1; NLR; plant defense; plant genomics; structural gene annotation
Entry Date(s): Date Created: 20200512 Date Completed: 20210514 Latest Revision: 20210514
Update Code: 20260130
PubMed Central ID: PMC7496378
DOI: 10.1111/nph.16645
PMID: 32392385
Βάση Δεδομένων: MEDLINE
Περιγραφή
ISSN:1469-8137
DOI:10.1111/nph.16645