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The International Rice Genome Sequencing Project (IRGSP)

Historically, PGIR was established as a high-throughput sequencing facility of medium capacity to participate in an international effort to sequence the rice genome. PGIR had been assigned the middle portion of chromosome 10 from 29.8 to 41.8 cM. We have completed the sequence of this region, the minimum-tiling path of which consists of 22 BAC clones that add up to approximately 2.9 Mb (3,131,203 bp including overlaps). A consortium of Clemson University, Cold Spring Harbor Laboratory, and Washington University has sequenced the upstream region of chromosome 10, whereas TIGR has undertaken sequencing of the downstream region. The entire chromosome has a length of 22.4 Mb and predicted to have 3,471 genes. PGIR has also participated in the sequencing of chromosome 11, which had been assigned to the US and India. We have sequenced a total of 22 BAC clones up to phase-2 level from this chromosome, which add up to a total of 2,919 kb (excluding overlaps). The University of Arizona (member of IRGSP) has finished these clones to phase-3 level with USDA support. The estimated length of chromosome 11 is 30MB.

Principal Investigators (PIs)

During the course of sequencing clones from chromosomes 10 and 11, we also sequenced one clone from chromosome 12 and two smaller clones from the indica variety Teqing that have also been deposited into GenBank.

The PI’s of the International Rice Genome Sequencing Project included Takuji Sasaki, Japan, Ben Burr, US, Bin Han, China, Francis Quetier, France, Akhilesh Tyagi, India, Dick McCombie, US, Robin Buell, US, Rod Wing, US, Joachim Messing, US, Jang Ho Hahn, South Korea, Yue-le Hsing, Taiwan, Antonio Costa de Oliveira, Brazil, and Mike Bevan, UK.

Publications

  • Messing, J. and Llaca, V. (1998). Importance of anchor genomes for any plant genome project.  Proc. Natl. Acad. Sci. 95, 2017-2020.

  • Bennetzen, J.L., Kellogg, E.A., Lee, M., and Messing, J. (1998). A plant genome initiative. The Plant Cell 10, 488-493.

  • Sasaki, T., Bevan, M., Burr, B., Eun, M.Y., Hong, G. and Messing, J. (1999) The international rice genome project.  Proceedings of the International Symposium on Rice Germplasm Evaluation and Enhancement. Rutger, J.N, Robinson, J.F. and Dilday, R.H. (Eds.) pp. 115-118.

  • Messing, Joachim. (2001) Do plants have more genes than humans? Trends in Plant Science, Vol. 6, No. 5., London, U.K., 195-196.

  • The Rice Chromosome 10 Sequencing Consortium (2003). In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300, 1566-1569.

  • Hamada, S., Ishiyama, K., Salkulsingharoj, C., Choi, S-B., Wu, Y., Wang, C., Singh, S., Kawai, N., Messing, J., and Okita, T.W. (2003). Multiple RNA Transport Pathways to the Cortical Region in Developing Rice Endosperm. Plant Cell 15, 2265-2272.

  • Singh, N.K., Raghuvanshi, S., Srivastava, S.K., Gaur, A., Pal, A.K., Dalal, V., Singh, A., Ghazi, I.A., Bhargav, A., Yadav, M., Dixit, A., Batra, K., Gaikwad, K., Sharma, T.R.. Mohapatra, T., Mohanty, A., Bharti, A.K., Kapur, A. Gupta, V., Kumar, D., Vij, S., Ravi, V., Khurana. Parul, Sharma, S., McCombie, D., Messing, J., Wing, R., Sasaki, T., Khurana, Paramjit, Khurana, J.P., and Tyagi, A.K. (2004). Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Funct. Integrat. Genomics 4, 102-117.

  • Washida, H., Sugino, A., Messing, J., Esen, A., and Okita, T. W. (2004). Asymmetric localization of seed storage protein RNAs to distinct subdomains of the endoplasmic reticulum in developing maize endosperm cells. Plant and Cell Phys. 45, 1830-1837.

  • The International Rice Genome Sequencing Project (2005). The map-based sequence of the rice genome. Nature 436, 793-800.

  • Rice-Chromosome-11-and-12-Sequencing-Consortia. (2005). The sequence of rice chromosome 11 and 12, rich in disease resistance genes and recent gene duplications. BMC Biology 3, e20.

  • Itoh, T., T. Tanaka, R.A. Barrero, C. Yamasaki, Y. Fujii, P.B. Hilton, B.A. Antonio, H. Aono, R. Apweiler, R. Bruskiewich, T. Bureau, F. Burr, A. Costa de Oliveira, G. Fuks, T. Habara, G. Haberer, B. Han, E. Harada, A.T. Hiraki, H. Hirochika, D. Hoen, H. Hokari, S. Hosokawa, Y. Hsing, H. Ikawa, K. Ikeo, T. Imanishi, Y. Ito, P. Jaiswal, M. Kanno, Y. Kawahara, T. Kawamura, H. Kawashima, J.P. Khurana, S. Kikuchi, S. Komatsu, K.O. Koyanagi, H. Kubooka, D. Lieberherr, Y.C. Lin, D. Lonsdale, T. Matsumoto, A. Matsuya, W.R. McCombie, J. Messing, A. Miyao, N. Mulder, Y. Nagamura, J. Nam, N. Namiki, H. Numa, S. Nurimoto, C. O'Donovan, H. Ohyanagi, T. Okido, S. Oota, N. Osato, L.E. Palmer, F. Quetier, S. Raghuvanshi, N. Saichi, H. Sakai, Y. Sakai, K. Sakata, T. Sakurai, F. Sato, Y. Sato, H. Schoof, M. Seki, M. Shibata, Y. Shimizu, K. Shinozaki, Y. Shinso, N.K. Singh, B. Smith-White, J. Takeda, M. Tanino, T. Tatusova, S. Thongjuea, F. Todokoro, M. Tsugane, A.K. Tyagi, A. Vanavichit, A. Wang, R.A. Wing, K. Yamaguchi, M. Yamamoto, N. Yamamoto, Y. Yu, H. Zhang, Q. Zhao, K. Higo, B. Burr, T. Gojobori, and T. Sasaki. 2007. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17, 175-183.

  • Itoh, T., T. Tanaka, R.A. Barrero, C. Yamasaki, Y. Fujii, P.B. Hilton, B.A. Antonio, H. Aono, R. Apweiler, R. Bruskiewich, T. Bureau, F. Burr, A. Costa de Oliveira, G. Fuks, T. Habara, G. Haberer, B. Han, E. Harada, A.T. Hiraki, H. Hirochika, D. Hoen, H. Hokari, S. Hosokawa, Y. Hsing, H. Ikawa, K. Ikeo, T. Imanishi, Y. Ito, P. Jaiswal, M. Kanno, Y. Kawahara, T. Kawamura, H. Kawashima, J.P. Khurana, S. Kikuchi, S. Komatsu, K.O. Koyanagi, H. Kubooka, D. Lieberherr, Y.C. Lin, D. Lonsdale, T. Matsumoto, A. Matsuya, W.R. McCombie, J. Messing, A. Miyao, N. Mulder, Y. Nagamura, J. Nam, N. Namiki, H. Numa, S. Nurimoto, C. O'Donovan, H. Ohyanagi, T. Okido, S. Oota, N. Osato, L.E. Palmer, F. Quetier, S. Raghuvanshi, N. Saichi, H. Sakai, Y. Sakai, K. Sakata, T. Sakurai, F. Sato, Y. Sato, H. Schoof, M. Seki, M. Shibata, Y. Shimizu, K. Shinozaki, Y. Shinso, N.K. Singh, B. Smith-White, J. Takeda, M. Tanino, T. Tatusova, S. Thongjuea, F. Todokoro, M. Tsugane, A.K. Tyagi, A. Vanavichit, A. Wang, R.A. Wing, K. Yamaguchi, M. Yamamoto, N. Yamamoto, Y. Yu, H. Zhang, Q. Zhao, K. Higo, B. Burr, T. Gojobori, and T. Sasaki. (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucl. Acid Res. 36, D1028-D1033.