IC4R001-Genome-2002-11935017

Project Title

• A Draft Sequence of the Rice Genome ( Oryza sativa L. ssp. indica )

The Background of This Project

• Rice is the most important crop for human consumption, providing staple food for more than half the world’s population. The euchromatic portion of the rice genome is estimated to be 430 Mb in size (1–3), which is the smallest of the cereal crops. It is 3.7 times larger than that of A. thaliana (4–6), and 6.7 times smaller than that of the human (7, 8). The well-established protocols for high-efficiency genetic transformation, widespread availability of high-density genetic and physical maps (9, 10), and high degrees of synteny among cereal gegenomes (11–15) combine to make rice a unique organism for studying the physiology, developmental biology, genetics, and evolution of plants.
• The International Rice Genome Sequencing Project (IRGSP) (16) has already delivered a substantial amount of sequence for the japonica (Nipponbare) subspecies, in bacterial artificial chromosome (BAC) and P1-derived artificial chromosome (PAC)–sized contigs. Working independently, Monsanto and Syngenta (17, 18) established proprietary working drafts for japonica, in April 2000 and February 2001, respectively. The Monsanto sequence has been used to assist in the efforts of the IRGSP.
• In this study We are releasing a draft genome sequence for rice from 93-11 (19), which is a cultivar of Oryza sativa L. ssp. indica, the major rice subspecies grown in China and many other Asia-Pacific regions.

Plant Culture & Treatment

• The researchers used a “whole-genome shotgun” approach, as successfully applied to Drosophila melanogaster (25) and Homo sapiens (8).The data are complementary to those of the IRGSP, which is sequencing Nipponbare, a cultivar of the subspecies japonica, with a

“clone-by-clone” approach. If assuming a euchromatic rice genome size of 430 Mb, and a Phred Q20 (26, 27) read length of 500 base pairs (bp), then 13 coverage would be equivalent to 0.86 million sequence reads, or 1 million reads after the typical success rate of 80 to 85% is factored in. Shotgun librarieswere constructed with a variety of methods for clone-insert preparation (28–30), to minimize the likelihood of systematic biases in genome representation. A total of 55 plasmid libraries were constructed for 93-11 and PA64s, with a 2-kb nominal clone-insert size.Overall, we prepared 2.75 million plasmid DNA samples (31, 32). Sequencing was performed on both ends of the inserts. By the 21 October 2001 freeze, there were 4.62 million successful reads, indicating an 84% success rate. The average Q20 read length was 546 bp.

Labs working on this Project

• Beijing Genomics Institute/Center of Genomics and Bioinformatics, Chinese Academy of Sciences, Beijing 101300, China.
• Hangzhou Genomics Institute–Institute of Bioinformatics of Zhejiang University–Key Laboratory of Bioinformatics of Zhejiang Province,Hangzhou 310007, China.
• Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, China.
• University of Washington Genome Center, Department of Medicine, Seattle, WA 98195, USA.
• College of Life Sciences, Peking University, Beijing 100871,China.
• Medical College, Xi’an Jiaotong University,Xi’an 710061, China.
• Fudan University, Shanghai 200433, China.
• National Hybrid Rice R&D Center,Changsha 410125, China.
• Laboratory of Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
• Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing 100080, China.
• Digital China Ltd., Beijing 100080,China.
• Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100080, China.

Corresponding Author

• Huanming Yang:hyang@genomics.org.cn.