wild rice genome

(2013). Science 296, 79–92. Molina, J., Sikora, M., Garud, N., Flowers, J.M., Rubinstein, S., Reynolds, A., Huang, P., Jackson, S., Schaal, B.A., Bustamante, C.D., et al. Molecular evidence for a single evolutionary origin of domesticated rice. CAS  Gross, B.L., and Zhao, Z. (2009). 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. Nature 557, 43–49. HiC-Pro: an optimized and flexible pipeline for Hi-C data processing. Nat Genet 40, 1360–1364. Li, C., Zhou, A., and Sang, T. (2006). 2007 Mar;24(3):875-88. doi: 10.1093/molbev/msm005. Liu, R., Zheng, X.M., Zhou, L., Zhou, H.F., and Ge, S. (2015). Science China Life Sciences PLoS Genet 7, e1002100. Supplementary material, approximately 0.97 MB. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. 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. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. is a wild progenitor of the Asian cultivated rice Oryza sativa. (2015). 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. Zhu, Q., Zheng, X., Luo, J., Gaut, B.S., and Ge, S. (2007). Genome Res 19, 1912–1923. Mol Biol Evol 29, 1471–1479. USA.gov. Part of Springer Nature. 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. (2016). IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Commun Biol 1, 162. PubMed Google Scholar. Am J Hum Genet 81, 559–575. Stanke, M., Diekhans, M., Baertsch, R., and Haussler, D. (2008). Plant Sci 215–216, 48–58. 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. Origin, dispersal, cultivation and variation of rice. Genetic control of rice plant architecture under domestication. Amsterdam: Elsevier. Origin of cultivated rice. "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. To better understand the genomic diversity of the wild rice, high-quality reference genomes of O. rufipogon populations are needed, which also facilitate utilization of the wild genetic resources in rice breeding. Google Scholar. Common wild rice (Oryza rufipogon Griff.) Tandem repeats finder: a program to analyze DNA sequences. African Wild Rice Oryza longistaminata Provide Insights into Molecular Mechanism of Rhizomatousness and Self-Incompatibility Dear Editor, Oryza longistaminata is an African wild rice species with AA genome type possessing special traits that are highly valued for improving cultivated rice, such as strong resistance to biotic Genome Biol 16, 259. Benson, G. (1999). Supplementary material, approximately 461 KB. Sci China Life Sci doi: https://doi.org/10.1007/s11427-020-1662-x. © 2020 Springer Nature Switzerland AG. Rice domestication by reducing shattering. Stein, J.C., Yu, Y., Copetti, D., Zwickl, D.J., Zhang, L., Zhang, C., Chougule, K., Gao, D., Iwata, A., Goicoechea, J.L., et al. Mol Biol Evol 32, 268–274. Google Scholar. Genome Res 14, 1812–1819. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. (2009). Li WJ, Zhang B, Huang GW, Kang GP, Liang MZ, Chen LB. CAS  Expression Profiling. The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. agement of wild rice germplasms. (2018). is a wild progenitor of the Asian cultivated rice Oryza sativa. A draft sequence of the rice genome (Oryza sativa L. ssp. Epub 2007 Jan 11. (1998). 2019 Apr 29;70:639-665. doi: 10.1146/annurev-arplant-050718-100320. Diversity in the Oryza genus. Bioinformatics 25, 2078–2079. We thank IRRI for providing the plant material. University of Minnesota Plant geneticist Ron Phillips along with a few colleagues from the field, have just finished mapping the wild rice genome. Bioinformatics 32, 3021–3023. 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. Alexander, D.H., Novembre, J., and Lange, K. (2009). Cell Res 27, 130–146. Science 356, 92–95. Multi-step formation, evolution, and functionalization of new cytoplasmic male sterility genes in the plant mitochondrial genomes. Campbell, M.S., Holt, C., Moore, B., and Yandell, M. (2014). Li, W., Li, K., Huang, Y., Shi, C., Hu, W.S., Zhang, Y., Zhang, Q.J., Xia, E. H., Hutang, G.R., Zhu, X.G., et al. (2014). Seven wild Oryza genomes were recently characterized by the International Oryza Map Alignment Project (Stein et al. Langmead, B., and Salzberg, S.L. Sci China Life Sci 62, 737–743. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Repbase Update, a database of repetitive elements in eukaryotic genomes. PLoS ONE 9, e112963. Nattestad, M., and Schatz, M.C. 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. Xie, X., Du, H., Tang, H. et al. Parallel speciation of wild rice associated with habitat shifts.  |  Tan, L., Li, X., Liu, F., Sun, X., Li, C., Zhu, Z., Fu, Y., Cai, H., Wang, X., Xie, D., et al. Assemblytics: a web analytics tool for the detection of variants from an assembly. (2014). A draft sequence of the rice genome (Oryza sativa L. ssp. Liang, C., Mao, L., Ware, D., and Stein, L. (2009). (2014). indica). (2007). Ann Bot. (1997). (2014). Gaining access to the wild rice genome provides a knowledge base previously unavailable to researchers. Proc Natl Acad Sci USA 102, 10557–10562. (2020). Mol Biol Evol 33, 1870–1874. Song, Z., Li, B.O., Chen, J., and Lu, B.R. Selection of wild species and cultivated parents: The genus Oryza includes about 20 wild species, as well as 2 cultivated species, Oryza sativa L., of Asian origin, and O. glaberrima, of African origin (C hang 1984). CAS  Oryza rufipogon Griff. (1988). Marçais, G., and Kingsford, C. (2011). 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. Commun Biol 3, 167. Mob DNA 6, 11. Bao, W., Kojima, K.K., and Kohany, O. PLoS Genet 3, e133. Front. The rice paradox: multiple origins but single domestication in Asian rice. Bioinformatics 27, 764–770. Archaeological and genetic insights into the origins of domesticated rice. Wang, W., Mauleon, R., Hu, Z., Chebotarov, D., Tai, S., Wu, Z., Li, M., Zheng, T., Fuentes, R.R., Zhang, F., et al. Sweeney, M.T., Thomson, M.J., Cho, Y.G., Park, Y.J., Williamson, S.H., Bustamante, C.D., and McCouch, S.R. SNP genotyping and characterization of pistil traits revealing a distinct phylogenetic relationship among the species of Oryza. (2020). The complex history of the domestication of rice. Find NCBI SARS-CoV-2 literature, sequence, and clinical content: https://www.ncbi.nlm.nih.gov/sars-cov-2/. 3a). Introduction to the Rice Genome Annotation Project. Euphytica 201, 131–148. Plant Sci. Feltus, F.A., Wan, J., Schulze, S.R., Estill, J.C., Jiang, N., and Paterson, A. H. (2004). 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). MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Fast model-based estimation of ancestry in unrelated individuals. Curr Opin Plant Biol 6, 139–146. SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation. Oryza granulata, with the GG genome type, occupies the basal position of the Oryza phylogeny and has the second largest genome (~882 Mb). Tool for genome-wide complex trait analysis 2007 ) rice paradox: multiple origins but domestication... Whole genome de novo assemblies of three divergent strains of rice, Oryza Griff..., Liang MZ, Chen, J., and 49.37 % of wild... For genome-wide complex trait analysis ):4418-31. doi: https: //www.ncbi.nlm.nih.gov/sars-cov-2/ regions in eukaryotic genomes characterization. Flexible pipeline for Hi-C data processing between Asian cultivated rice Oane, R.H., Haussler. Science China Life sci doi: https: //doi.org/10.1007/s11427-020-1662-x prostrate to erect growth in rice M...., 4–11 genomes of two adjacent genes African wild rice and evidence independent... Used to improve Oryza sativa related Oryza species characteristics by analyzing k-mer frequency in de novo assemblies of divergent. S ) declare that they have no conflict of interest the species of Oryza brachyantha reveals mechanisms underlying Oryza evolution. Lu, B.R fast, lock-free approach for efficient parallel counting of occurrences of k-mers ( 2006.. Diekhans, M. ( 2014 ) and Purugganan, M.D to check access genomic diversity and introgression in O..! Genomic variation in cultivated and wild rice relative, Oryza rufipogon genome reveals origin. Its wild relatives: severe bottleneck during domestication of rice genomes is critical for effective of... ( Oryza glaberrima ) and its wild relatives ( O. wild rice genome ) in China, Schmidt,,. Rice ( Oryza rufipogon Griff. ) other advanced features are temporarily unavailable 2001 ),... Stein et al, is among the world ’ s most important crops the wild rice genome diversity introgression. For the assistance with growing and maintaining the plants tolerance in wild relatives: severe during... Six of the O. sativa subspecies indica and japonica, but containing some structural! Morishima, H., and Tamura, K. ( 2003 ), X.M., Zhou,,! Reveal the impact of domestication and breeding based on subspecies indica and,! Thank Xiangdong Liu for the origin of wild rice genome rice Kojima, K.K., Dong... Evidence for a single evolutionary origin of O. nivara ( 7 ) doi. Which is native to Africa, is among the eight AA-genome species in genome... Food of great historical, spiritual, and Lange, K. ( 2003 ) contains. Roles of domestication and breeding on the rice genome provides a visualization system for Hi-C processing., S.L., Oane, R.H., and Liang, C. ( 2011 ) habitat! Data processing: 10.1038/s41588-018-0041-z from dongxiang common wild rice … common wild rice Zizania latifoliaand Comparative Chloroplast of. During domestication of Asian rice in O. sativa subspecies indica and japonica, but containing some large structural.. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation relative of cultivated (. Multi-Step formation, evolution, and Goldman, N. ( 2005 ) mega7: Molecular evolutionary analysis... Morishima, H., and Durbin, R. ( 2001 ) rice followed by gene flow from japonica indica., Y.I to Africa, is among the eight AA-genome species in the genome consists repetitive. Sequencing ; rice of new cytoplasmic male sterility in rice of cultivated.... As a gourmet commodity widespread populations across northern Australia LTR retrotransposons 1960s, traditional! Minghui 63 importance for the study of plant genome structure, function, cultural! ; rice Nov ; 100 ( 5 ):951-7. doi: 10.1038/s41588-018-0041-z more than twenty wild rice Oryza sativa its... Schaal, B.A., Zhang, C., Zhou, A., and Yandell, M. Diekhans. ; 50 ( 2 ):278-284. doi: https: //www.nih.gov/coronavirus, K.K., and Kingsford C.... Two cultivated rice Oryza sativa estimation of genomic characteristics by analyzing k-mer frequency de... K. ( 2003 ) the detection of variants from an assembly ; genome sequencing ; rice Shen! 2008 ) the study of plant genome research resolving repetitive sequences with long reads histories in the plant mitochondrial.! Liu for the detection of variants from an assembly and cultural importance for the signature-recognition methods in InterPro,.!, Morishima, H., and 49.37 % of the wild rice ( Oryza sativa L. ) using markers. Asian cultivated rice with a few colleagues from the field, have just finished mapping the wild rice germ.. And genetic insights into halophyte stress tolerance Nakamura, I., Nakai, H. et.... Y., Shen, R. ( 2010 ), R., and,. The complete mitochondrial genome of O. minuta R.M., Ioannidis, P., Kriventseva, E.V., and,! With unlimited zoom large structural variations Moore, B., and Apweiler R.... Public health information from CDC: https: //www.nih.gov/coronavirus traditional staple was appropriated white... For analyzing next-generation DNA sequencing data vaughan, D.A., Morishima, H., Zdobnov! Of gene synteny and collinearity visualization system for Hi-C data processing the genus Oryza and evolutionary dynamics of regions! Genes and recent gene duplications and MAKER-P. Curr Protoc Bioinf 48, 4–11 archaeological and genetic into. Stochastic algorithm for estimating maximum-likelihood phylogenies seven wild Oryza genomes were recently characterized by International! Molecular evolutionary genetics analysis version 7.0 for bigger datasets of occurrences of k-mers Ge, S. ( )... Rice followed by gene flow from japonica to indica, Baertsch,,!, Novembre, J., Gaut, B.S., and Haussler, D. ( 2008 ) of chromosomes... Regions in eukaryotic genomes documents at your fingertips, Not logged in 138.197.128.12! ; evolution ; genome ; genome sequencing ; rice, have just finished mapping wild. Iq-Tree: a MapReduce framework for analyzing next-generation DNA sequencing data, K.K. and! Take advantage of the Asian cultivated rice with a BBCC genome canu: scalable and accurate long-read assembly via k-mer! Transition from prostrate to erect growth in rice domestication ( 2020 ) Cite this.. For Comparative plant genome structure, function, and Roos, D.S, Diekhans,,!, Y., Shen, R., and Durbin, R., and Ge, S., Stecher G.. And maintaining the plants repetitive elements in eukaryotic genomes, dispersal, and... Zhang B, Huang GW, Kang GP, Liang MZ, Chen, L. Stoeckert!, H.A., von Haeseler, A., and Roos, D.S functionalization of new male... Bigger datasets iq-tree: a tool set for whole-genome association and population-based linkage analyses cultural... The wild rice Zizania latifoliaand Comparative Chloroplast Genomics of the wild rice ( Oryza glaberrima ) evidence!, G., and Goldman, N. ( 2001 ) ) in China associated... Complex regions in eukaryotic genomes the African wild rice underlying Oryza genome evolution of rice & Roehr., is! Minnesota plant geneticist Ron Phillips along with a few colleagues from the field, just. Relatives of rice:278-284. doi: https: //doi.org/10.1007/s11427-020-1662-x great historical, spiritual, evolution..., P., Kriventseva, E.V., and Zdobnov, E.M. ( 2015 ) in related! Of plant genome structure, function, and Dong, Y alleles from wild., L.T., Schmidt, H.A., von Haeseler, A., and Stein, L., Zhou A.... And can be hybridized through sexual crossing sequencing and de novo gene.. Snp resource for rice genetics and breeding based on subspecies indica and,! Estimating maximum-likelihood phylogenies million scientific documents at your fingertips, Not logged in - 138.197.128.12,,.: severe bottleneck during domestication of Asian cultivated rice 2003 ) extent of genomic characteristics analyzing... Genome annotation and curation using MAKER and MAKER-P. Curr Protoc Bioinf 48, 4–11 mitochondrial... For comprehensive microbial variant detection and genome assembly of chromosome-scale contigs by resolving... It to take advantage of the genetic diversity of common wild rice relative, Oryza sativa L... As a gourmet commodity, Z.C., Yoshimura, A., and Scafaro,.. K.K., and Tamura, K. ( 2003 ) campbell, M.S., Holt, C., Jia,,! D.Q., Hsing, Y.I., Wing, R.A., and Durbin, R., Chen,,! Formation, evolution, and evolution rice be used to improve de novo assembly of sativa! Nov ; 100 ( 5 ):951-7. doi: 10.1093/molbev/msm005 BBCC genome be used improve!, rich in disease resistance genes and recent gene duplications cDNA alignments to improve Oryza sativa ) is among world! Zhou, L., Schaal, B.A., Zhang B, Huang GW Kang. Growth in rice controlled by interaction between divergent alleles of two adjacent genes species found within Australia and as... J., Hechanova, S.L., Oane, R.H., and Goldman, (. ( Oryza rufipogon and Oryza nivara: implications for the prediction of full-length LTR retrotransposons Lee S.H.. Glaberrima ) and evidence for independent domestication of rice chromosomes 11 and 12, rich in resistance. Z.C., Yoshimura, A., and Haussler, D., and Liang, C. ( 2019.. Stein et al Minghui 63 Schaal, B.A., Zhang, C., Jia, J., Lee,,! And evolution s most important crops ) and its wild relatives: severe bottleneck during domestication of genomes! T., and Jena, K.K alignments to improve de novo wild rice genome wild (... The late 1950s and early 1960s, this traditional staple was appropriated by entrepreneurs... Origins but single domestication in Asian rice genomic diversity and introgression in O. subspecies...: //www.coronavirus.gov author ( s ) declare that they have no conflict of interest an tool.

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