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.
New Phytol. 2020 Sep;227(5):1568-1581. doi: 10.1111/nph.16645. Epub 2020 Jun 5.
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.
全基因组注释错误会导致重要的蛋白质编码基因缺失，从而阻碍进一步的研究。我们开发了 Target Gene Family Finder（TGFam-Finder），这是一种用于植物基因组中含有目标结构域的蛋白质编码基因结构注释的替代工具。与传统的注释工具相比，TGFam-Finder 的注释运行时间大大缩短，准确性也得到了提高。对 50 个植物基因组进行的大规模重新注释平均分别鉴定出 150、166 和 86 个额外的远红受损反应 1、核苷酸结合和亮氨酸丰富重复以及细胞色素 P450 基因，这些基因在前一次注释中被遗漏。与之前的注释相比，我们使用来自七个植物物种的质谱数据在新注释中检测到数量显著增加的翻译基因。TGFam-Finder 以及新的基因模型可以为植物的全面功能、比较和进化研究提供一个优化的平台。
