Luo, R., Liu, B., Xie, Y., Li, Z., Huang, W., Yuan, J., He, G., Chen, Y., Pan, Q., Liu, Y., et al. Characterization and evolutionary dynamics of complex regions in eukaryotic genomes. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Xie, X., Du, H., Tang, H. et al. (2017). Bioinformatics 31, 3210–3212. Rapid diversification of five Oryza AA genomes associated with rice adaptation. https://doi.org/10.1007/s11427-020-1738-x. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., and Durbin, R. (2009). Here, we sequenced and annotated the complete mitochondrial genome of O. minuta. Bioinformatics 17, 847–848. Proc Natl Acad Sci USA 108, 8351–8356. Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. 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. (2014). Here, we have performed a genome-wide analysis of SVs in Asian rice and its wild progenitor O. rufipogon, with the goal of understanding more about the evolutionary processes that act on them and their fate during domestication. Zdobnov, E.M., and Apweiler, R. (2001). McNally, K.L., Childs, K.L., Bohnert, R., Davidson, R.M., Zhao, K., Ulat, V.J., Zeller, G., Clark, R.M., Hoen, D.R., Bureau, T.E., et al. Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. The genus Oryza is an idea model system for studying plant comparative genomics, evolutionary biology and functional biology. (2011). 3a). Wang, Y., Tang, H., Debarry, J.D., Tan, X., Li, J., Wang, X., Lee, T., Jin, H., Marler, B., Guo, H., et al. Oryza rufipogon Griff. Population genetic structure of Oryza rufipogon and Oryza nivara: implications for the origin of O. nivara. Oryza rufipogon Griff. PubMed Learn more about Institutional subscriptions. (2015). Juicebox provides a visualization system for Hi-C contact maps with unlimited zoom. Fast algorithms for large-scale genome alignment and comparison. 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 . Zhu, Q., Zheng, X., Luo, J., Gaut, B.S., and Ge, S. (2007). 1,2,KuiLi. rufipogon and O. meridionalis are the only AA genome species found within Australia and occur as widespread populations across northern Australia. A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice. Mol Biol Evol. Vaughan, D.A., Morishima, H., and Kadowaki, K. (2003). Yet, in the age of Dolly the cloned sheep, and a patent proposed even on human genome stock, wild rice has become yet another frontier in the brave new world of technology. Amsterdam: Elsevier. Plant Mol Biol 62, 247–259. Repbase Update, a database of repetitive elements in eukaryotic genomes. (2018). Mob DNA 6, 11. 1,JuGao. 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. Du, H., Yu, Y., Ma, Y., Gao, Q., Cao, Y., Chen, Z., Ma, B., Qi, M., Li, Y., Zhao, X., et al. COVID-19 is an emerging, rapidly evolving situation. Annotation of the genome is currently underway using the transcriptome analysis of six different wild rice tissue types including root, shoot, leaf, seed, female florets, and male florets. However, in our results, all type of indica rice was closed to one type of wild rice and whole japonica rice was closed to another type of wild rice (Fig. Epub 2007 Jul 6. Yang, C., Kawahara, Y., Mizuno, H., Wu, J., Matsumoto, T., and Itoh, T. (2012). Common wild rice (Oryza rufipogon Griff.) Oryza minuta (Poaceae family) is a tetraploid wild relative of cultivated rice with a BBCC genome. PubMed Nat Genet 50, 278–284. Nucleic Acids Res 40, e49. Oryza rufipogon; evolution; genome; genome sequencing; rice. Mol Biol Evol 33, 1870–1874. Li WJ, Zhang B, Huang GW, Kang GP, Liang MZ, Chen LB. Genome Res 16, 140–147. Genetics and phylogenetics of rice domestication. LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons. AA- genome species in the genus Oryza. Chen, J., Huang, Q., Gao, D., Wang, J., Lang, Y., Liu, T., Li, B., Bai, Z., Luis Goicoechea, J., Liang, C., et al. 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. Stanke, M., Diekhans, M., Baertsch, R., and Haussler, D. (2008). (2008). De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. (2015). Genome Res 19, 1912–1923. Liu, B., Shi, Y., Yuan, J., Hu, X., Zhang, H., Li, N., Li, Z., Chen, Y., Mu, D., and Fan, W. (2013). The Complete Plastid Genome Sequence of the Wild Rice Zizania latifoliaand Comparative Chloroplast Genomics of the Rice Tribe Oryzeae, Poaceae. Wang, M., Yu, Y., Haberer, G., Marri, P.R., Fan, C., Goicoechea, J.L., Zuccolo, A., Song, X., Kudrna, D., Ammiraju, J.S.S., et al. 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. Nucleic Acids Res 30, 2478–2483. 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 Alexander, D.H., Novembre, J., and Lange, K. (2009). Löytynoja, A., and Goldman, N. (2005). Mol Biol Evol 24, 875–888. Google Scholar. HHS (2020). Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. O. longistaminata A. Chev. Archaeological and genetic insights into the origins of domesticated rice. NIH Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. PLoS ONE 9, e112963. Origin of cultivated rice. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Plant Sci 215–216, 48–58. (2014). Langmead, B., and Salzberg, S.L. Genet Mol Res. Genet Resour Crop Evol 50, 529–538. The rice paradox: multiple origins but single domestication in Asian rice. 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). SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Genomic variation in 3,010 diverse accessions of Asian cultivated rice. agement of wild rice germplasms. (2015). Sci China Life Sci 62, 737–743. After colonization disrupted their traditional food system, however, they could no longer depend on stores of wild rice for food all year round. Theor Appl Genet 102, 157–162. Mol Ecol 24, 5211–5228. Using native and syntenically mapped cDNA alignments to improve de novo gene finding. 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., 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. Marathi, B., Ramos, J., Hechanova, S.L., Oane, R.H., and Jena, K.K. A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance. (2008). (2013). Sun, C.Q., Wang, X.K., Li, Z.C., Yoshimura, A., and Iwata, N. (2001). Bioinformatics 24, 637–644. 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. This access can 1. Diversity in the Oryza genus. (2020)Cite this article. 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. Goff, S.A., Ricke, D., Lan, T.H., Presting, G., Wang, R., Dunn, M., Glazebrook, J., Sessions, A., Oeller, P., Varma, H., et al. National Center for Biotechnology Information, Unable to load your collection due to an error, Unable to load your delegates due to an error. Liang, C., Mao, L., Ware, D., and Stein, L. (2009). (2009). Curr Opin Plant Biol 6, 139–146. Am J Hum Genet 81, 559–575. https://doi.org/10.1007/s11427-020-1662-x. Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., Young, S.K., et al. (2002). Genome Res 14, 1812–1819. (2020). The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications. The rice genus, Oryza , which comprises 23 species and 9 recognized genome types, represents an enormous gene pool for genetic improvement of rice cultivars. Xiao, J., Li, J., Grandillo, S., Ahn, S.N., Yuan, L., Tanksley, S.D., and McCouch, S.R. Subspecies-specific intron length polymorphism markers reveal clear genetic differentiation in common wild rice (Oryza rufipogon L.) in relation to the domestication of cultivated rice (O. sativa L.). De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution. Sweeney, M.T., Thomson, M.J., Cho, Y.G., Park, Y.J., Williamson, S.H., Bustamante, C.D., and McCouch, S.R. Estimation of genomic characteristics by analyzing k-mer frequency in de novo genome project. 11:579980. doi: 10.3389/fpls.2020.579980 Cell Res 27, 130–146. Huang, X., Kurata, N., Wei, X., Wang, Z.X., Wang, A., Zhao, Q., Zhao, Y., Liu, K., Lu, H., Li, W., et al. Expression Profiling. Kumar, S., Stecher, G., and Tamura, K. (2016). (2017). Oryza rufipogon Griff. Assemblytics: a web analytics tool for the detection of variants from an assembly. There are two cultivated rice and more than twenty wild rice … Chengzhi Liang or Yao-Guang Liu. Spannagl, M., Nussbaumer, T., Bader, K.C., Martis, M.M., Seidel, M., Kugler, K.G., Gundlach, H., and Mayer, K.F.X. MGOS - Magnaporthe Grisea Oryza Sativa Database NSF Rice Oligonucleotide Array Project OrzyaExpress RiceArrayNet RiceChip.Org Rice Expression Database Rice MPSS Rice Proteome Database RicePLEX Yale Plant Genomics Group Yale Virtual Center for Cellular Expression Profiling of Rice. Nucleic Acids Res 27, 573–580.
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