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

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

doi:10.1016/j.molp.2023.03.012

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

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

Research output: Contribution to journal › Article › peer-review

25 Scopus citations

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.

Original language	English (US)
Journal	Molecular Plant
DOIs	https://doi.org/10.1016/j.molp.2023.03.012
State	Published - Mar 24 2023

Bibliographical note

KAUST Repository Item: Exported on 2023-03-28
Acknowledgements: This research was supported by Fundamental Research Funds for the Central Universities (2662020SKPY010) and the Major Project of Hubei Hongshan Laboratory (2022HSZD031) to J.Z. We thank access to the annotation for the Magic 16 gene structure annotation from the Gramene project, specifically K. Chougule, Z. Lu, and D. Ware supported by USDA 8062-21000-041-00D. We sincerely thank the computing platform of the National Key Laboratory of Crop Genetic Improvement in HZAU and the ibex & Shaheen Cray XC40 platform at KAUST Supercomputing Laboratory for providing the computational resources.

ASJC Scopus subject areas

Plant Science
Molecular Biology

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10.1016/j.molp.2023.03.012

https://repository.kaust.edu.sa/bitstream/10754/690153/5/1-s2.0-S167420522300076X-main_removed.pdf

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@article{022ef4f60b65482b9d2e4c3fefa2aef5,

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

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 {\textquoteleft}GeneCard{\textquoteright} 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 {\textquoteleft}Microcollinearity{\textquoteright} and {\textquoteleft}Macrocollinearity{\textquoteright} modules.",

author = "Zhichao Yu and Yongming Chen and Yong Zhou and Yulu Zhang and Mengyuan Li and Yidan Ouyang and Dmytro Chebotarov and Ramil Mauleon and Hu Zhao and Weibo Xie and McNally, {Kenneth L} and Wing, {Rod Anthony} and Weilong Guo and Jianwei Zhang",

note = "KAUST Repository Item: Exported on 2023-03-28 Acknowledgements: This research was supported by Fundamental Research Funds for the Central Universities (2662020SKPY010) and the Major Project of Hubei Hongshan Laboratory (2022HSZD031) to J.Z. We thank access to the annotation for the Magic 16 gene structure annotation from the Gramene project, specifically K. Chougule, Z. Lu, and D. Ware supported by USDA 8062-21000-041-00D. We sincerely thank the computing platform of the National Key Laboratory of Crop Genetic Improvement in HZAU and the ibex & Shaheen Cray XC40 platform at KAUST Supercomputing Laboratory for providing the computational resources.",

year = "2023",

month = mar,

day = "24",

doi = "10.1016/j.molp.2023.03.012",

language = "English (US)",

journal = "Molecular Plant",

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T1 - Rice Gene Index (RGI): a comprehensive pan-genome database for comparative and functional genomics of Asian rice.

AU - Yu, Zhichao

AU - Chen, Yongming

AU - Zhou, Yong

AU - Zhang, Yulu

AU - Li, Mengyuan

AU - Ouyang, Yidan

AU - Chebotarov, Dmytro

AU - Mauleon, Ramil

AU - Zhao, Hu

AU - Xie, Weibo

AU - McNally, Kenneth L

AU - Wing, Rod Anthony

AU - Guo, Weilong

AU - Zhang, Jianwei

N1 - KAUST Repository Item: Exported on 2023-03-28 Acknowledgements: This research was supported by Fundamental Research Funds for the Central Universities (2662020SKPY010) and the Major Project of Hubei Hongshan Laboratory (2022HSZD031) to J.Z. We thank access to the annotation for the Magic 16 gene structure annotation from the Gramene project, specifically K. Chougule, Z. Lu, and D. Ware supported by USDA 8062-21000-041-00D. We sincerely thank the computing platform of the National Key Laboratory of Crop Genetic Improvement in HZAU and the ibex & Shaheen Cray XC40 platform at KAUST Supercomputing Laboratory for providing the computational resources.

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AB - 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.

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JF - Molecular Plant

ER -

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

Abstract

Bibliographical note

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