The cultivated rice (Oryza sativa) is one of the most important crops in the world. Rice relatives, phylogenetically related species of rice or species with a similar ecological niche as rice, have many useful traits and could provide valuable genetic resources for rice research. RiceRelativesGD provides gene and genomic resources of 16 rice relatives from Poaceae, including the serious paddy weeds such as weedy rice and barnyardgrass (Echinochloa crus-galli), an ancient crop 'Gu' (Zizania latifolia), Leersia perrieri, nine wild rice species and the African cultivated rice. Specifically, the database provides specific genes to indica and japonica rice, respectively, in each rice relative species and their annotations. It also includes online services such as genome browser, search tools and phylogenetic tree building tools, which can help researchers to better utilize the genomic data in the database.
Rice relatives in the current release: Oryza sativa f. spontanea (indica and japonica type)(weedy rice) Oryza nivara Oryza rufipogonOryza glaberrimaOryza barthiiOryza glumaepatulaOryza meridionalisOryza punctacaOryza brachyanthaOryza granulataLeersia perrieriZizania latifoliaEchinochloa crus-galliEchinochloa colonaEchinochloa oryzicola
The genomic data used by the current release: 1. Chen, J. et al. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nat. Commun. 4, (2013). 2. Du, H. et al. Sequencing and de novo assembly of a near complete indica rice genome. Nat. Commun. 8, 1–12 (2017). 3. Guo, L. et al. A host plant genome (Zizania latifolia) after a century-long endophyte infection. Plant J. 83, 600–609 (2015). 4. Guo, L. et al. Echinochloa crus-galli genome analysis provides insight into its adaptation and invasiveness as a weed. Nat. Commun. 8, 1031 (2017). 5. Kawahara, Y. et al. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6, 1–10 (2013). 6. Mao, L. et al. Genomic evidence for convergent evolution of gene clusters for momilactone biosynthesis in land plants. PNAS 117, 12472-12480 (2020). 7. Qiu, J. et al. Diverse genetic mechanisms underlie worldwide convergent rice feralization. Genome Biol. 21, 70 (2020). 8. Stein, J. C. et al. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat. Genet. 50, 285–296 (2018). 9. Sun, J. et al. Population genomic analysis and de novo assembly reveal the origin of weedy rice as an evolutionary game. Mol. Plant 12, 632–647 (2019). 10. Wang, M. et al. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat. Genet. 46, 982–988 (2014). 11. Wu, Z. et al. De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution. Commun. Biol. 1, 1–10 (2018). 12. Ye, C. et al. The genomes of the allohexaploid Echinochloa crus-galli and its progenitors provide insights into polyploidization-driven adaptation. Mol. Plant (2020). 13. Wu, D. et al. Genomic insights into the evolution of Echinochloa species as weed and orphan crop. Nat. Commun. 13, 1–16 (2022).
Lingfeng Mao, Meihong Chen, Qinjie Chu, Lei Jia, Most Humaira Sultana, Dongya Wu,
Xiangdong Kong, Jie Qiu, Chy-Yu Ye, Qian-Hao Zhu, Xi Chen, Longjiang Fan.
RiceRelativesGD: a genomic database of rice relatives for rice research. Database, 2019.
2022-06-26: RiceRelativesGD Release 4.0 online!
2021-06-16: RiceRelativesGD Release 3.0 online!
2020-04-30: RiceRelativesGD Release 2.0 online!
2019-09-27: RiceRelativesGD 1.0 published in Database!
2019-05-20: Gene family clustering method was updated to OrthoFinder.
2018-08-28: RiceRelativesGD Release 1.0 online!
2018-06-28: RiceRelativesGD beta version online!
Institute of Crop Sciences
Institute of Bioinformatics
Zhejiang University, Hangzhou, China