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

作者：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 · 发表于：Molecular Plant · 年份：2023 · DOI：10.1016/j.molp.2023.03.012 · 被引用次数：77 · 研究领域：Genetic Mapping and Diversity in Plants and Animals、Genomics and Phylogenetic Studies、Rice Cultivation and Yield Improvement

Asian 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., 2018Stein J.C. Yu Y. Copetti D. Zwickl D.J. Zhang L. Zhang C. Chougule K. Gao D. Iwata A. Goicoechea J.L. et al.Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.Nat. Genet. 2018; 50: 285-296https://doi.org/10.1038/s41588-018-0040-0Crossref PubMed Scopus (278) Google Scholar). 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., 2018Wing R.A. Purugganan M.D. Zhang Q. The rice genome revolution: from an ancient grain to Green Super Rice.Nat. Rev. Genet. 2018; 19: 505-517https://doi.org/10.1038/s41576-018-0024-zCrossref PubMed Scopus (182) Google Scholar). Since the first gold-standard reference genome of rice variety Nipponbare was published (International Rice Genome Sequencing Project, 2005International Rice Genome Sequencing ProjectThe map-based sequence of the rice genome.Nature. 2005; 436: 793-800https://doi.org/10.1038/nature03895Crossref PubMed Scopus (3009) Google Scholar), an increasing number of rice accessions have been sequenced, assembled, and annotated with global efforts. Nowadays, a single reference genome is obviously insufficient to perfo...