Abstract
The species of Oryza rufipogon. dw was first discovered at Dongxiang, Jiangxi in 1978. It is recognized as abundant in genetic resources with the characteristics of cold and insect resistance. A total of 100.15 Gb raw data was obtained from seven pair-end libraries by Illumina Hiseq4000 platform. Subsequently, a draft assembly genome of O. rufipogon. dw was generated with a final size of 422.7 Mb with a contig N50 of 15 kb and a scaffold N50 of 296.2 bb. The assembly genome size was higher than the estimated genome size (413 Mb) based on k-mer analysis. The identified repeat sequences accounted for 40.09% of the entire genome, and 32,521 protein-coding genes with an average of 4.59 exons per gene was annotated in five databases. Phylogenetic analysis using 1460 single-copy gene, O. rufipogon. dw was close with O. rufipogon by Bayes method. The wild rice species of O. rufipogon. dw divergence was estimated at \({\sim }0.3\) million years ago (Mya) from O. rufipogon, and \({\sim }0.6\ \hbox {Mya}\) from the O. sativa. The draft genome of O. rufipogon. dw provided an essential resource for its origin and evolution study.
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References
Bennetzen J. L. 2007 Patterns in grass genome evolution. Curr. Opin. Plant Biol. 10, 176–181.
Griffiths-Jones S., Moxon S., Marshall M., Khanna A., Eddy S. R. and Bateman A. 2005 Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res. 33, 121–124.
Hu T. T., Pattyn P., Bakker E. G., Cao J., Cheng J. F, Clark R. M. et al. 2011 The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43, 476–481.
Huang X., Kurata N., Wei X., Wang Z. X., Wang A., Zhao Q. et al. 2012 A map of rice genome variation reveals the origin of cultivated rice. Nature 490, 497–501.
Kent W. J. 2002 BLAT–the BLAST-like alignment tool. Genome Res. 12, 656–664.
Kovach M. J., Sweeney M. T. and McCouch S. R. 2007 New insights into the history of rice domestication. Trends Genet. 23, 578–587.
Krishnan S. G., Waters D. L. and Henry R. J. 2014 Australian wild rice reveals pre-domestication origin of polymorphism deserts in rice genome. PLoS One 9, e98843.
Li R., Fan W., Tian G., Zhu H., He L., Cai J. et al. 2009 The sequence and de novo assembly of the giant panda genome. Nature 463, 311.
Lowe T. M. and Eddy S. R. 1997 tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964.
Marcais G. and Kingsford C. 2011 A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770.
Price A. L., Jones N. C. and Pevzner P. A. 2005 De novo identification of repeat families in large genomes. Bioinformatics 21, 351–358.
Sakai H., Kanamori H., Araikichise Y., Shibatahatta M., Ebana K., Oono Y. et al. 2014 Construction of pseudomolecule sequences of the aus rice cultivar kasalath for comparative genomics of asian cultivated rice. DNA Res. 21, 1131–1142.
Stanke M., Keller O., Gunduz I., Hayes A., Waack S. and Morgenstern B. B. 2006 AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic Acids Res. 34, 435–439.
Sun C. Q., Wang X. K., Li Z. C., Yoshimura A. and Iwata N. 2001 Comparison of the genetic diversity of common wild rice (Oryza rufipogon Griff.) and cultivated rice (O. sativa L.) using RFLP markers. Theor. Appl. Genet. 102, 157–162.
Tang H., Bowers J. E., Wang X., Ming R., Alam M. and Paterson A. H. 2008 Synteny and collinearity in plant genomes. Science 320, 486–488.
Tyagi A. K. and Mohanty A. 2000 Rice transformation for crop improvement and functional genomics. Plant Sci. 158,1–18.
Wang M., Yu Y., Haberer G., Marri P. R., Fan C., Goicoechea J. L. et al. 2014 The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat. Genet. 46, 982–988.
Yan L., Wang X., Liu H., Tian Y., Lian J., Yang R. et al. 2015 The Genome of Dendrobium officinale illuminates the biology of the important traditional chinese orchid herb. Mol. Plant. 8, 922–934.
Zhang F., Xu T., Mao L., Yan S., Chen X., Wu Z. et al. 2016 Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication. BMC Plant Biol. 16, 103.
Zhang X., Zhou S., Fu Y., Su Z., Wang X. and Sun C. 2006 Identification of a drought tolerant introgression line derived from Dongxiang common wild rice (O. rufipogon Griff.). Plant Mol. Biol. 62, 247–259.
Acknowledgements
The authors wish to thank three platforms, National Engineering Laboratory of Rice, National Improvement Center of rice (Nanchang), Ministry of Agriculture Wild Rice Scientific Observation and Experimental Station in Dongxiang, Jiangxi Province. This work was supported by Breeding Project of New Insect-resistant Rice Varieties in Rice Areas in the middle and lower reaches of the Yangtze river (2016zx08001001-001-005); Jiangxi Provincial Agricultural Science and Technology Innovation Project (JXTCX2015001); Jiangxi Province major science and technology special projects (20114BA03101); Jiangxi natural science funds (2010GQN0090); Area Funds of National natural science funds (3166041).
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Wang, J., Yan, S., Luo, S. et al. The evolution study on Oryza rufipogon. dw by whole-genome sequencing. J Genet 98, 90 (2019). https://doi.org/10.1007/s12041-019-1136-8
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DOI: https://doi.org/10.1007/s12041-019-1136-8