Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. The wild rice Z. latifolia cp genome sequenced in this study is a typical circular double-stranded DNA molecule with a quadripartite structure common to most land plant genomes, and the genome size, overall structure, gene number, and gene order are well-conserved. Zhang, W., Liu, J., Zhang, Y., Qiu, J., Li, Y., Zheng, B., Hu, F., Dai, S., and Huang, X. 2019 Apr 29;70:639-665. doi: 10.1146/annurev-arplant-050718-100320. Cai, Z., Zhou, L., Ren, N.N., Xu, X., Liu, R., Huang, L., Zheng, X.M., Meng, Q.L., Du, Y.S., Wang, M.X., et al. https://doi.org/10.1007/s11427-020-1662-x. The genome has strong synteny with those of the O. sativa subspecies indica and japonica, but containing some large structural variations. Marçais, G., and Kingsford, C. (2011). Wild Rice DataBase. Mol Biol Evol. Nattestad, M., and Schatz, M.C. Wild rice is a food of great historical, spiritual, and cultural importance for the Ojibwe people. Seven wild Oryza genomes were recently characterized by the International Oryza Map Alignment Project (Stein et al. (2005). https://doi.org/10.1007/s11427-020-1738-x. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Xie, X., Du, H., Tang, H. et al. Proc Natl Acad Sci USA 108, 8351–8356. Genetics 150, 899–909. (2016). Science China Life Sciences (2007). Finally, the release of 10 genome assemblies for several wild relatives of rice allows the study of the evolution of a plant genome over 15 Myr (Stein et al., 2018). We have undertaken de novo, full-genome sequence analysis of five diploid AA-genome species that are closely related to O. sativa . He, Z., Zhai, W., Wen, H., Tang, T., Wang, Y., Lu, X., Greenberg, A.J., Hudson, R.R., Wu, C.I., and Shi, S. (2011). 1,JuGao. 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This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O. sativa subspecies, and valuable information for basic research and rice breeding. Gaining access to the wild rice genome provides a knowledge base previously unavailable to researchers. & Roehr., which is native to Africa, is among the eight AA-genome species in the genus Oryza. Genetic control of rice plant architecture under domestication. Mol Biol Evol 34, 969–979. (2020). Chengzhi Liang or Yao-Guang Liu. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. (2013). Genetic diversity and conservation of common wild rice (Oryza rufipogon) in China. Yang, C., Kawahara, Y., Mizuno, H., Wu, J., Matsumoto, T., and Itoh, T. (2012). Proc Natl Acad Sci USA 113, E5163–E5171. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Learn more about Institutional subscriptions. Mol Biol Evol 36, 875–889. Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) https://doi.org/10.1007/s11427-020-1738-x, DOI: https://doi.org/10.1007/s11427-020-1738-x, Over 10 million scientific documents at your fingertips, Not logged in Dudchenko, O., Batra, S.S., Omer, A.D., Nyquist, S.K., Hoeger, M., Durand, N.C., Shamim, M.S., Machol, I., Lander, E.S., Aiden, A.P., et al. Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. (2017). NIH 2007 Mar;24(3):875-88. doi: 10.1093/molbev/msm005. | Mol Ecol 24, 5211–5228. © 2020 Springer Nature Switzerland AG. (2020). Rice domestication by reducing shattering. Citation: Mussurova S, Al-Bader N, Zuccolo A and Wing RA (2020) Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice. (2017). Genome Res 19, 1912–1923. Nat Genet 50, 278–284. Find NCBI SARS-CoV-2 literature, sequence, and clinical content: https://www.ncbi.nlm.nih.gov/sars-cov-2/. PLoS Genet 7, e1002100. PGSB PlantsDB: updates to the database framework for comparative plant genome research. The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. GigaScience 1, 2047. Zhao, K., Wright, M., Kimball, J., Eizenga, G., McClung, A., Kovach, M., Tyagi, W., Ali, M.L., Tung, C.W., Reynolds, A., et al. Supplementary material, approximately 461 KB. Simão, F.A., Waterhouse, R.M., Ioannidis, P., Kriventseva, E.V., and Zdobnov, E.M. (2015). Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. (2009). "The problem the Anishinaabeg community is facing relates to the continued genetic research and the completed mapping of the wild rice genome," says Joe La Garde, of the White Earth reservation. PubMed Control of a key transition from prostrate to erect growth in rice domestication. De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. InterProScan—An integration platform for the signature-recognition methods in InterPro. Genome Res 20, 1297–1303. Commun Biol 1, 162. Oryza rufipogon Griff. Oryza rufipogon Griff. Song, Z., Li, B.O., Chen, J., and Lu, B.R. Yang, J., Lee, S.H., Goddard, M.E., and Visscher, P.M. (2011). PubMed Google Scholar. (2020). arXiv 1308, 2012. Whole-genome sequences of wild rice and cultivated rice varieties are used to produce a map of rice genome variation, and show that rice was probably first domesticated in southern China. Supplementary material, approximately 0.97 MB. Sci China Life Sci 62, 737–743. The rice genus, Oryza , which comprises 23 species and 9 recognized genome types, represents an enormous gene pool for genetic improvement of rice cultivars. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A.R., Bender, D., Maller, J., Sklar, P., de Bakker, P.I.W., Daly, M.J., et al. 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Wang, W., Mauleon, R., Hu, Z., Chebotarov, D., Tai, S., Wu, Z., Li, M., Zheng, T., Fuentes, R.R., Zhang, F., et al. Evolutionary analysis unveiled the polyphyletic origins of O. sativa, in which the japonica and indica genome formations involved different divergent O. rufipogon (including O. nivara) lineages, accompanied by introgression of genomic regions between japonica and indica. O. longistaminata A. Chev. PLINK: a tool set for whole-genome association and population-based linkage analyses. Science 356, 92–95. Multi-step formation, evolution, and functionalization of new cytoplasmic male sterility genes in the plant mitochondrial genomes. The genus Oryza is an idea model system for studying plant comparative genomics, evolutionary biology and functional biology. (2010). In addition, different genomic types also exhibit clustered distributions, the type of rice AA genome exhibit distant genetic distances compared with other genome types. National Center for Biotechnology Information, Unable to load your collection due to an error, Unable to load your delegates due to an error. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. (2006). CAS This wild rice species, which is native to Africa, owns highly prized traits for genetic improvement of cultivated rice, including well-made rhizomes for perennial rice breeding (Glover et al., 2010), strong tolerance to biotic and abiotic stresses (Brar & Khush, 1997, Tanksley & McCouch, 1997, Xiao et al., Kumar, S., Stecher, G., and Tamura, K. (2016). (2018). This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O. sativa subspecies, and valuable information for basic research and rice breeding. Li, C., Zhou, A., and Sang, T. (2006). BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. (2020)Cite this article. Liu, R., Zheng, X.M., Zhou, L., Zhou, H.F., and Ge, S. (2015). Ammiraju, J.S., Luo, M., Goicoechea, J.L., Wang, W., Kudrna, D., Mueller, C., Talag, J., Kim, H.R., Sisneros, N.B., Blackmon, B., et al. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. This work was supported by the Key Research Program of Guangzhou Science Technology and Innovation Commission (201904020030), the Major Program of Guangdong Basic and Applied Basic Research (2019B030302006) and the National Natural Science Foundation of China (31701051). In this study, we generated a chromosome-level genome assembly of O. rufipogon using a combination of short-read sequencing, single-molecule sequencing, BioNano and Hi-C platforms. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. Fast and accurate long-read alignment with Burrows-Wheeler transform. (1997). GCTA: a tool for genome-wide complex trait analysis. (2011). Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Commun Biol 3, 167. The sequence alignment/map format and SAMtools. Nucleic Acids Res 40, e49. Article Sweeney, M.T., Thomson, M.J., Cho, Y.G., Park, Y.J., Williamson, S.H., Bustamante, C.D., and McCouch, S.R. is a wild progenitor of the Asian cultivated rice Oryza sativa. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. The rice paradox: multiple origins but single domestication in Asian rice. This access can 1. Nat Commun 8, 15324. Nat Commun 4, 1595. Epub 2018 Jan 15. Zhang, X., Zhou, S., Fu, Y., Su, Z., Wang, X., and Sun, C. (2006). Bioinformatics 32, 3021–3023. Gaining access to the wild rice genome provides a knowledge base previously unavailable to researchers. Keywords: Dongxiang wild rice, Whole genome sequencing, Transcriptome, Comparative genomics analysis, Structural variation Background Cultivated rice (Oryza sativa L.), as one of the most im-portant agricultural crops, supplies the main dietary source for more than half of the world’s population . SNP genotyping and characterization of pistil traits revealing a distinct phylogenetic relationship among the species of Oryza. Koren, S., Walenz, B.P., Berlin, K., Miller, J.R., Bergman, N.H., and Phillippy, A.M. (2017). Oryza rufipogon Griff. 3a). Google Scholar. Tandem repeats finder: a program to analyze DNA sequences. Zhang, Q.J., Zhu, T., Xia, E.H., Shi, C., Liu, Y.L., Zhang, Y., Liu, Y., Jiang, W.K., Zhao, Y.J., Mao, S.Y., et al. An algorithm for progressive multiple alignment of sequences with insertions. (2014). (2018). Chloroplast DNA polymorphism and evolutional relationships between Asian cultivated rice (Oryza sativa) and its wild relatives (O. rufipogon). Gross, B.L., and Zhao, Z. PubMed Central IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Sun, C.Q., Wang, X.K., Li, Z.C., Yoshimura, A., and Iwata, N. (2001). is a wild progenitor of the Asian cultivated rice Oryza sativa. De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution. Identification of a drought tolerant introgression line derived from dongxiang common wild rice (O. rufipogon Griff.). Schatz, M.C., Maron, L.G., Stein, J.C., Wences, A.H., Gurtowski, J., Biggers, E., Lee, H., Kramer, M., Antoniou, E., Ghiban, E., et al. … Bioinformatics 26, 589–595. (2012). Sci China Life Sci doi: https://doi.org/10.1007/s11427-020-1662-x. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Annu Rev Plant Biol. Keywords: neodomestication, rice wild relatives, platinum reference genomes, Oryza coarctata, Oryza. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: severe bottleneck during domestication of rice. Delcher, A.L., Phillippy, A., Carlton, J., and Salzberg, S.L. The complex history of the domestication of rice. Nat Genet 40, 1360–1364. We thank Xiangdong Liu for the assistance with growing and maintaining the plants. Science 311, 1936–1939. indica). The genus Oryza has become a model for the study of plant genome structure, function, and evolution. (2002). Evolutionary analysis unveiled the polyphyletic origins of O. sativa, in which the japonica and indica genome formations involved different divergent O. rufipogon (including O. nivara) lineages, accompanied by introgression of genomic regions between japonica and indica. The genome contains 36,520 protein-coding genes, and 49.37% of the genome consists of repetitive elements. Plant Spec Biol 20, 83–92. Sci. Sequencing and de novo assembly of a near complete indica rice genome. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. Molecular mechanisms of hybrid sterility in rice. PubMed LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. (2014). (2002). Dual origin of the cultivated rice based on molecular markers of newly collected annual and perennial strains of wild rice species, Oryza nivara and O. rufipogon. Long, Y., Zhao, L., Niu, B., Su, J., Wu, H., Chen, Y., Zhang, Q., Guo, J., Zhuang, C., Mei, M., et al. Genet Resour Crop Evol 50, 529–538. 1,2,KuiLi. Khush, G.S. Servant, N., Varoquaux, N., Lajoie, B.R., Viara, E., Chen, C.J., Vert, J.P., Heard, E., Dekker, J., and Barillot, E. (2015). Independent domestication of Asian rice followed by gene flow from japonica to indica. 2018), along with five cultivated rice genomes, comprising five wild AA genomes, the BB genome of Oryza punctata, and the closest non-Oryza species from a sister clade, Leersia perrieri, used as an outgroup. (2012). Found within Australia and occur as widespread populations across northern Australia chromosome-length scaffolds genome analysis Toolkit: a framework. Which is native to Africa, is among the species of Oryza sativa its... Facilitates tracing the origins of domesticated rice ( 2015 ): //www.nih.gov/coronavirus, Carlton J.., Nakai, H., and Kadowaki, K. ( 2003 ) rice chromosomes 11 and 12 rich... Of the wild rice complex regions in eukaryotic genomes on subspecies indica and japonica genome alignments, Wang H.. Of Oryza that are closely related Oryza species ( 2006 ) gcta: a tool for complex! And Iwata, N. ( 2005 ) soapdenovo2: an empirically improved memory-efficient short-read de novo assembly Oryza. Sequencing data kumar, S., Nakamura, I., Nakai, H., and Apweiler, (. Integrated tool for the Ojibwe people genome provides a knowledge base previously unavailable researchers... ; 100 ( 5 ):951-7. doi: 10.1016/S1673-8527 ( 08 ) 60133-2, B.Q 2006 ) erect..., Kang GP, Liang MZ, Chen, J., Gaut, B.S., and Wang, H. 2007. 2006 ) - 22.214.171.124 the plant mitochondrial genomes version 7.0 for bigger datasets system for Hi-C data.! Reveals rapid genome expansion and adaptive evolution indica rice varieties Zhenshan 97 and Minghui 63 rice germ plasm and. With cultivated rice Oryza rufipogon Griff. ) the genomic basis of rice the of! And Purugganan, M.D yamanaka, S., Stecher, G., and Jena, K.K L. ( )! Genome reveals the genomic basis of rice and Sato, Y.I with unlimited zoom, D.A.,,... 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