The cultivated rice (Oryza sativa) is one of the most important crops in the world. Rice relatives, phylogenetically related species of rice or paddy field weeds 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 11 rice relatives from Poaceae, including the serious paddy weed barnyardgrass (Echinochloa crus-galli), an ancient crop 'Gu' (Zizania latifolia), Leersia perrieri, seven 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 data in RiceRelativesGD.
Rice relatives in the current release: Oryza nivara Oryza rufipogonOryza glaberrimaOryza barthiiOryza glumaepatulaOryza meridionalisOryza punctacaOryza brachyanthaLeersia perrieriZizania latifoliaEchinochloa crus-galli
The current database mainly based on the genomic data by following studies: 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. unpublished data (2020). 7.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. Ye, C. et al. Genomes of Echinochloa species. unpublished data (2020).
Mao, L., Chen, M., Chu, Q., Jia, L., Sultana, M. H., Wu, D., ... & Chen, X. (2019).
RiceRelativesGD: a genomic database of rice relatives for rice research. Database, 2019.
2019-09-27: RiceRelativesGD published in Database
2019-06-10: Type errors were corrected
2019-05-20: Gene family clustering method was updated to OrthoFinder
2019-02-20: Bugs were fixed
2018-08-28: RiceRelativesGD Release 1.0 online
2018-06-28: RiceRelativesGD beta version online
2017-08-01: Initiated the database