(preprint) Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice

Authors

Zhichao Yu (于志超), Yongming Chen (陈永明), Yong Zhou (周勇), Yulu Zhang (张雨露), Mengyuan Li (李梦圆), Yidan Ouyang (欧阳亦聃), Dmytro Chebotarov, Ramil Mauleon, Hu Zhao (赵虎), Weibo Xie (谢为博), Kenneth L. McNally, Rod A. Wing, Weilong Guo (郭伟龙), Jianwei Zhang (张建伟)

This article is a preprint and has not been certified by peer review [what does this mean?].

Preprinted:  15 February 2023

Abstract

To integrate the genomic information of the rice pan-genome, we performed comparative analyses and established a user-friendly Rice Gene Index (RGI, https://riceome.hzau.edu.cn) platform with 16 platinum standard reference genomes and supplementary transcriptome data. To logically organize and scientifically the index of 744,233 genes among rice accessions, we detected 112,658 Ortholog Gene Indices, and provide ‘GeneCard’ pages to query genomic, transcriptomic, and homology information for each gene. The RGI allows users to search for relationships and comprehensive information of genes in keyword-based, sequence-based, and relationship-based ways. Furthermore, users can visualize these relationships at local and global scales corresponding to ‘Microcollinearity’ and ‘Macrocollinearity’ modules.

 

2023.02.14.528456v1.full_.pdf

2023.02.14.528456v1.full_.pdf

Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice

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Additional Information

DOI
Date of publication:
2023