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Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice
来源: 时间:2023-03-30

Zhichao Yu, Yongming Chen, Yong Zhou, Yulu Zhang, Mengyuan Li, Yidan Ouyang, Dmytro Chebotarov, Ramil Mauleon, Hu Zhao, Weibo Xie, Kenneth L. McNally, Rod A. Wing, Weilong Guo, Jianwei Zhang

Molecular Plant, Published: March 25, 2023   DOI:https://doi.org/10.1016/j.molp.2023.03.012


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.