Articles

Genome information and its industrial applications for plants

Article number
1404_2
Pages
5 – 18
Language
English
Abstract
With current advances in sequencing technologies, genome sequences of various kinds of plant species have been determined at the chromosome scale.
Accordingly, genome information, such as genome and gene sequences as well as gene functions, has accumulated.
Currently, we have determined the genome sequences of more than 30 plant species by using next generation sequencing technologies.
Besides, we have joined to the database project in 2nd period (2018-2022) of the Cross-Ministerial Strategic Innovation Promotion Program (SIP) aimed to apply the genome information to industrial fields.
In the project, we have generated a data set Gene Curation DS to curate crucial information related to the following gene functions of plant species. 1) Functionally important genes described in the literature were curated according to their correspondence between the gene names appearing in the literature and gene IDs defined in genome sequences (112 species); 2) resistance gene analogs (RGAs), which are considered potential resistance genes (R-genes) against pathogens by producing R proteins, were searched for in genome sequences (134 species); 3) genes included in patent applications registered in the DNA Data Bank of Japan (DDBJ) were searched for in genome sequences (152 species); 4) gene functions were predicted by similarity searches against UniProtKB (the UniProt knowledgebase, which provides a comprehensive, high-quality, and freely accessible resource for protein sequences and functional information), Araport (a complete annotation of Arabidopsis thaliana), and EggNOG (a hierarchical, functionally and phylogenetically annotated orthology resource) (188 species); 5) orthologous groups of genes among 136 plant species were explored.
Gene Curation DS has been released at http://fgi.kazusa.or.jp/gcds. We expect this data set to provide useful information for both fundamental research and industrial applications such as molecular breeding, including genome editing.

Publication
Authors
H. Hirakawa, M. Hasegawa, N. Yokotani, S. Isobe
Keywords
curation, gene function, R-gene, patent, non-coding RNA, orthologous groups
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