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

Research output: Contribution to journalArticlepeer-review

16 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 languageEnglish
Pages (from-to)1568-1581
Number of pages14
JournalNew Phytologist
Volume227
Issue number5
DOIs
StatePublished - 1 Sep 2020

Keywords

  • CYP450
  • FAR1
  • NLR
  • plant defense
  • plant genomics
  • structural gene annotation

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