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

Seungill Kim; Kyeongchae Cheong; Jieun Park; Myung Shin Kim; Jihyun Kim; Min Ki Seo; Geun Young Chae; Min Jeong Jang; Hyunggon Mang; Sun Ho Kwon; Yong Min Kim; Namjin Koo; Cheol Woo Min; Kwang Soo Kim; Nuri Oh; Ki Tae Kim; Jongbum Jeon; Hyunbin Kim; Yoon Young Lee; Kee Hoon Sohn; Honour C. McCann; Sang Kyu Ye; Sun Tae Kim; Kyung Soon Park; Yong Hwan Lee; Doil Choi

doi:10.1111/nph.16645

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

Seungill Kim, Kyeongchae Cheong, Jieun Park, Myung Shin Kim, Jihyun Kim, Min Ki Seo, Geun Young Chae, Min Jeong Jang, Hyunggon Mang, Sun Ho Kwon, Yong Min Kim, Namjin Koo, Cheol Woo Min, Kwang Soo Kim, Nuri Oh, Ki Tae Kim, Jongbum Jeon, Hyunbin Kim, Yoon Young Lee, Kee Hoon SohnHonour C. McCann, Sang Kyu Ye, Sun Tae Kim, Kyung Soon Park, Yong Hwan Lee, Doil Choi

Department of Environmental Horticulture

Research output: Contribution to journal › Article › peer-review

17 Scopus citations

Abstract

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.

Original language	English
Pages (from-to)	1568-1581
Number of pages	14
Journal	New Phytologist
Volume	227
Issue number	5
DOIs	https://doi.org/10.1111/nph.16645
State	Published - 1 Sep 2020

Keywords

CYP450
FAR1
NLR
plant defense
plant genomics
structural gene annotation

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Kim, S., Cheong, K., Park, J., Kim, M. S., Kim, J., Seo, M. K., Chae, G. Y., Jang, M. J., Mang, H., Kwon, S. H., Kim, Y. M., Koo, N., Min, C. W., Kim, K. S., Oh, N., Kim, K. T., Jeon, J., Kim, H., Lee, Y. Y., ... Choi, D. (2020). TGFam-Finder: a novel solution for target-gene family annotation in plants. New Phytologist, 227(5), 1568-1581. https://doi.org/10.1111/nph.16645

@article{1f9b168e0c4d4cf1b4b7ab86b7e3510c,

title = "TGFam-Finder: a novel solution for target-gene family annotation in plants",

abstract = "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.",

keywords = "CYP450, FAR1, NLR, plant defense, plant genomics, structural gene annotation",

author = "Seungill Kim and Kyeongchae Cheong and Jieun Park and Kim, {Myung Shin} and Jihyun Kim and Seo, {Min Ki} and Chae, {Geun Young} and Jang, {Min Jeong} and Hyunggon Mang and Kwon, {Sun Ho} and Kim, {Yong Min} and Namjin Koo and Min, {Cheol Woo} and Kim, {Kwang Soo} and Nuri Oh and Kim, {Ki Tae} and Jongbum Jeon and Hyunbin Kim and Lee, {Yoon Young} and Sohn, {Kee Hoon} and McCann, {Honour C.} and Ye, {Sang Kyu} and Kim, {Sun Tae} and Park, {Kyung Soon} and Lee, {Yong Hwan} and Doil Choi",

note = "Publisher Copyright: {\textcopyright}2020 The Authors. New Phytologist {\textcopyright}2020 New Phytologist Trust",

year = "2020",

month = sep,

day = "1",

doi = "10.1111/nph.16645",

language = "English",

volume = "227",

pages = "1568--1581",

journal = "New Phytologist",

issn = "0028-646X",

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Kim, S, Cheong, K, Park, J, Kim, MS, Kim, J, Seo, MK, Chae, GY, Jang, MJ, Mang, H, Kwon, SH, Kim, YM, Koo, N, Min, CW, Kim, KS, Oh, N, Kim, KT, Jeon, J, Kim, H, Lee, YY, Sohn, KH, McCann, HC, Ye, SK, Kim, ST, Park, KS, Lee, YH & Choi, D 2020, 'TGFam-Finder: a novel solution for target-gene family annotation in plants', New Phytologist, vol. 227, no. 5, pp. 1568-1581. https://doi.org/10.1111/nph.16645

TY - JOUR

T1 - TGFam-Finder

T2 - a novel solution for target-gene family annotation in plants

AU - Kim, Seungill

AU - Cheong, Kyeongchae

AU - Park, Jieun

AU - Kim, Myung Shin

AU - Kim, Jihyun

AU - Seo, Min Ki

AU - Chae, Geun Young

AU - Jang, Min Jeong

AU - Mang, Hyunggon

AU - Kwon, Sun Ho

AU - Kim, Yong Min

AU - Koo, Namjin

AU - Min, Cheol Woo

AU - Kim, Kwang Soo

AU - Oh, Nuri

AU - Kim, Ki Tae

AU - Jeon, Jongbum

AU - Kim, Hyunbin

AU - Lee, Yoon Young

AU - Sohn, Kee Hoon

AU - McCann, Honour C.

AU - Ye, Sang Kyu

AU - Kim, Sun Tae

AU - Park, Kyung Soon

AU - Lee, Yong Hwan

AU - Choi, Doil

PY - 2020/9/1

Y1 - 2020/9/1

N2 - 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.

AB - 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.

KW - CYP450

KW - FAR1

KW - NLR

KW - plant defense

KW - plant genomics

KW - structural gene annotation

UR - http://www.scopus.com/inward/record.url?scp=85085930801&partnerID=8YFLogxK

U2 - 10.1111/nph.16645

DO - 10.1111/nph.16645

M3 - Article

C2 - 32392385

AN - SCOPUS:85085930801

SN - 0028-646X

VL - 227

SP - 1568

EP - 1581

JO - New Phytologist

JF - New Phytologist

IS - 5

ER -

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

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Keywords

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