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Rice Sequencing Projects

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 Links to Dataset Paper Citation
Rathinasabapathi, P. et al (2015) Whole genome sequencing and analysis of Swarna, a widely cultivated indica rice variety with low glycemic index. Scientific Reports 5, Article number: 11303 . doi:10.1038/srep11303

Duitama J, Silva A, Sanabria Y, et al (2015) Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection. PLoS One 10:e0124617. doi: 10.1371/journal.pone.0124617
 Schatz, Michael C et al. “Whole Genome de Novo Assemblies of Three Divergent Strains of Rice, Oryza Sativa, Document Novel Gene Space of aus and indica.” Genome Biology 15.11 (2014): 506. PMC. Web. 17 Dec. 2015.

Zhang, Y., S. Zhang2, H. Liu, B. Fu, L. Li, M. Xie, Y. Song, X. Li, J. Cai, W. Wan, L. Kui, H. Huang, J. Lyu, Y. Dong, W. Wang, L. Huang, J. Zhang, Q. Yang, Q. Shan, Q. Li, W. Huang, D. Tao, M. Wang, M. Chen, Y. Yu, R.A. Wing*, W. Wang*, F. Hu* (*co-corresponding authors). 2015. Genome and comparative transcriptomics of African wild rice Oryza longistaminata provide insights into molecular mechanism of rhizomatousness and self-incompatibility. Molecular Plant 8:1683–1686.

The 3,000 rice genomes project (2014) The 3,000 rice genomes project. Gigascience 3:7. doi: 10.1186/2047-217X-3-7.
Sakai H, Kanamori H, Arai-Kichise Y, et al (2014) Construction of pseudomolecule sequences of the aus rice cultivar Kasalath for comparative genomics of Asian cultivated rice. DNA Res An Int J Rapid Publ Reports Genes Genomes 21:397–405. doi: 10.1093/dnares/dsu006.
Wang, M., Y. Yu, G. Haberer, P. Marri, C. Fan, J.L. Goicoechea, A. Zuccolo, X. Song, D. Kudrna, S.A. Jetty, R. Cossu , C. Maldonado, J. Chen , S. Lee, N. Sisneros, K. de Baynast , W. Golser, M. Wissotski, W. Kim , P. Sanchez, M.N. Ndjiondjop, K. Sanni , M. Long, J. Carney, O. Panaud, T. Wicker, C. Machado, M. Chen, K. Mayer, S. Rounsley, & R.A. Wing. 2014. The genome of African rice (Oryza glaberrima): Evidence for independent domestication. Nature Genetics 46:982-988.
Chen J, Q. Huang, D. Gao, J. Wang, Y. Lang, T. Liu, B. Li, Z. Bai, J.L. Goicoechea, C. Liang, C. Chen, W. Zhang, S. Sun, Y. Liao, X. Zhang, L. Yang, C. Song, M. Wang, J. Shi, G. Liu, J. Liu, H. Zhou, W. Zhou, Q. Yu, N. An, Y. Chen, Q. Cai, B. Wang, B. Liu, J. Min, Y. Huang, H. Wu, Z. Li, Y. Zhang, Y. Yin, W. Song, J. Jiang, S.A. Jackson, R.A. Wing, J. Wang, & M. Chen. 2013. Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution. Nature Commun 4: 1595.
Gao Z., et. al. (2013) Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences PNAS 2013 110 (35) 14492-14497.
Kawahara, Y., de la Bastide, M., Hamilton J. P., Kanamori, H., McCombie, W. R., Ouyang, S., Schwartz, D. C., Tanaka, T., Wu, J., Zhou, S., Childs, K. L., Davidson, R. M., Lin, H., Quesada-Ocampo, L., Vaillancourt, B., Sakai, H., Lee, S. S., Kim, J., Numa, H., Itoh, T., Buell, C. R., Matsumoto, T. 2013. Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.Rice 6:4.
Xu, X. et al. Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnol. 30, 105–111 (2012);;;
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. 10.1038/nature11532
Matsumoto, T, Wu JZ, Kanamori H, Katayose Y, Fujisawa M, Namiki N, Mizuno H, Yamamoto K, Antonio BA, Baba T et al.  2005.  The map-based sequence of the rice genome. Nature. 436:793-800.