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

Simple item page
cg.identifier.doihttps://doi.org/10.1016/j.molp.2023.03.012
cg.issn1674-2052
cg.issue5
cg.journalMolecular Plant
cg.volume16
dc.contributor.authorYu, Zhichao
dc.contributor.authorChen, Yongming
dc.contributor.authorZhou, Yong
dc.contributor.authorZhang, Yulu
dc.contributor.authorLi, Mengyuan
dc.contributor.authorOuyang, Yidan
dc.contributor.authorChebotarov, Dmytro
dc.contributor.authorMauleon, Ramil
dc.contributor.authorZhao, Hu
dc.contributor.authorXie, Weibo
dc.contributor.authorMcNally, Kenneth L.
dc.contributor.authorWing, Rod A.
dc.contributor.authorGuo, Weilong
dc.contributor.authorZhang, Jianwei
dc.date.accessioned2024-12-19T12:53:13Zen
dc.date.available2024-12-19T12:53:13Zen
dc.identifier.urihttps://hdl.handle.net/10568/163955
dc.titleRice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian riceen
dcterms.abstractAsian 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 riceen
dcterms.accessRightsOpen Access
dcterms.bibliographicCitationYu, Zhichao; Chen, Yongming; Zhou, Yong; Zhang, Yulu; Li, Mengyuan; Ouyang, Yidan; Chebotarov, Dmytro; Mauleon, Ramil; Zhao, Hu; Xie, Weibo; McNally, Kenneth L.; Wing, Rod A.; Guo, Weilong and Zhang, Jianwei. 2023. Rice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian rice. Molecular Plant, Volume 16 no. 5 p. 798-801en
dcterms.extentpp. 798-801
dcterms.issued2023-05
dcterms.languageen
dcterms.licenseCC-BY-NC-ND-4.0
dcterms.publisherElsevier
dcterms.subjectyields caloriesen
dcterms.subjectclimate changeen
dcterms.subjectcultivarsen
dcterms.subjectdatabasesen
dcterms.subjectgenesen
dcterms.subjectgenomesen
dcterms.subjectoryza sativaen
dcterms.subjectplant breedersen
dcterms.subjectstaple foodsen
dcterms.typeJournal Article

Files

Collections

IRRI Journal Articles