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 (US) |
|---|---|
| Pages (from-to) | 1568-1581 |
| Number of pages | 14 |
| Journal | New Phytologist |
| Volume | 227 |
| Issue number | 5 |
| DOIs | |
| State | Published - Sep 1 2020 |
Funding
The authors appreciate the assistance from the KOBIC Research Support Program. The authors also acknowledge the following researchers who performed iterative beta testing of TGFam‐Finder : Ho‐Sub Shin, Myung‐Shin Kim, and Jun‐Ki Lee at Seoul National University; Namjin Koo at the Korea Research Institute of Bioscience and Biotechnology; and Eunyoung Seo at the University of California, Berkeley. This study was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF‐2017R1A6A3A04004014) to SK, by a grant from the Agricultural Genome Center of the Next Generation Biogreen 21 Program of RDA (Project no. PJ013153) to DC, and by a NRF grant funded by the Korean Government (no. 2018R1A5A1023599, SRC: Plant Immunity Research Center) to DC. The authors declare that there is no conflict of interest. The authors appreciate the assistance from the KOBIC Research Support Program. The authors also acknowledge the following researchers who performed iterative beta testing of TGFam-Finder: Ho-Sub Shin, Myung-Shin Kim, and Jun-Ki Lee at Seoul National University; Namjin Koo at the Korea Research Institute of Bioscience and Biotechnology; and Eunyoung Seo at the University of California, Berkeley. This study was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (NRF-2017R1A6A3A04004014) to SK, by a grant from the Agricultural Genome Center of the Next Generation Biogreen 21 Program of RDA (Project no. PJ013153) to DC, and by a NRF grant funded by the Korean Government (no. 2018R1A5A1023599, SRC: Plant Immunity Research Center) to DC. The authors declare that there is no conflict of interest.
Keywords
- CYP450
- FAR1
- NLR
- plant defense
- plant genomics
- structural gene annotation
ASJC Scopus subject areas
- Physiology
- Plant Science