Rice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian rice

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dc.creatorYu, Zhichao
dc.creatorChen, Yongming
dc.creatorZhou, Yong
dc.creatorZhang, Yulu
dc.creatorLi, Mengyuan
dc.creatorOuyang, Yidan
dc.creatorChebotarov, Dmytro
dc.creatorMauleon, Ramil
dc.creatorZhao, Hu
dc.creatorXie, Weibo
dc.creatorMcNally, Kenneth L.
dc.creatorWing, Rod A.
dc.creatorGuo, Weilong
dc.creatorZhang, Jianwei
dc.date2023-05-01
dc.date2023-11-06T01:28:03Z
dc.date2023-11-06T01:28:03Z
dc.date.accessioned2026-06-27T04:08:52Z
dc.descriptionAsian rice (Oryza sativa) is the staple food for half the world and is a model crop that has been extensively studied. It contributes ∼20% of calories to the human diet (Stein et al., 2018). With the increase in global population and rapid changes in climate, rice breeders need to develop new and sustainable cultivars with higher yields, healthier grains, and reduced environmental footprints (Wing et al., 2018). Since the first gold-standard reference genome of rice variety Nipponbare was published (International Rice Genome Sequencing Project, 2005), an increasing number of rice accessions have been sequenced, assembled, and annotated with global efforts. Nowadays, a single reference genome is obviously insufficient to perform the genetic difference analysis for rice accessions. Therefore, the pan-genome has been proposed as a solution, which allows the discovery of more presence-absence variants compared with single-reference genome-based studies (Zhao et al., 2018). Over the past years, several databases, such as RAP-db (https://rapdb.dna.affrc.go.jp), RGAP (http://rice.uga.edu), and Gramene (https://www.gramene.org), have long-term served rice genomic research by providing information based on one or a series of individual reference genomes. To integrate and utilize the genomic information of multiple accessions, we performed comparative analyses and established the user-friendly Rice Gene Index (RGI; https://riceome.hzau.edu.cn) platform. RGI is the first gene-based pan-genome database for rice
dc.formatapplication/pdf
dc.identifierhttps://hdl.handle.net/10568/132729
dc.identifier.urihttp://hdl.handle.net/123456789/23084
dc.languageen
dc.publisherElsevier
dc.rightsOpen Access
dc.sourceYu, Zhichao, Yongming Chen, Yong Zhou, Yulu Zhang, Mengyuan Li, Yidan Ouyang, Dmytro Chebotarov et al. "Rice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian rice." Molecular plant 16, no. 5 (2023): 798-801.
dc.subjectoryza sativa
dc.subjectstaple food
dc.subjectcalories
dc.subjectdiet
dc.subjectyield increases
dc.subjectgenomes
dc.subjectgenomics
dc.subjectdatabases
dc.titleRice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian rice
dc.typeOpinion Piece

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Instituto Internacional de Investigación del Arroz (IRRI)