TGFam-Finder: An optimal solution for target-gene family annotation in eukaryotic genomes

Seungill Kim; Kyeongchae Cheong; Jieun Park; Myung‐Shin Kim; Jihyun Kim; Min‐Ki Seo; Sun-Ho Kwon; Yong‐Min Kim; Namjin Koo; Kwangsoo Kim; Nuri Oh; Ki‐Tae Kim; Jongbum Jeon; Hyunbin Kim; Yoonyoung Lee; Kee Hoon Sohn; Honour C. McCann; Sang‐Kyu Ye; Kyung‐Soon Park; Yong‐Hwan Lee; Doil Choi

doi:10.1101/372433

BioinformaticsbioRxivJul 19, 2018

Preprint

TGFam-Finder: An optimal solution for target-gene family annotation in eukaryotic genomes

Seungill Kim iD, Kyeongchae Cheong iD, Jieun Park iD, Myung‐Shin Kim iD, Jihyun Kim iD, Min‐Ki Seo iD, Sun-Ho Kwon, Yong‐Min Kim iD, Namjin Koo, Kwangsoo Kim iD, Nuri Oh iD, Ki‐Tae Kim iD, Jongbum Jeon iD, Hyunbin Kim iD, Yoonyoung Lee iD, Kee Hoon Sohn iD, Honour C. McCann iD, Sang‐Kyu Ye iD, Kyung‐Soon Park iD, Yong‐Hwan Lee iD, Doil Choi iD

Abstract

Whole genome annotation errors that omit essential protein-coding genes hinder further research. We developed Target Gene Family Finder (TGFam-Finder), an optimal tool for structural annotation of protein-coding genes containing target domain(s) of interest in eukaryotic genomes. Large-scale re-annotation of 100 publicly available eukaryotic genomes led to the discovery of essential genes that were missed in previous annotations. An average of 117 (346%) and 148 (45%) additional FAR1 and NLR genes were newly identified in 50 plant genomes. Furthermore, 117 (47%) additional C2H2 zinc finger genes were detected in 50 animal genomes including human and mouse. Accuracy of the newly annotated genes was validated by RT-PCR and cDNA sequencing in human, mouse and rice. In the human genome, 26 newly annotated genes were identical with known functional genes. TGFam-Finder along with the new gene models provide an optimized platform for unbiased functional and comparative genomics and comprehensive evolutionary study in eukaryotes.

PDF DOI