A draft sequence of the rice (Oryza sativa ssp. indicd) genome |
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Authors: | YU Jun HU Songnian WANG Jun LI Songgang WONG Ka-Shu Gane LIU Bin DENG Yajun DAI Li YUAN Longping YANG Huanming |
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Institution: | (1) Beijing Genomics Institute/Center of Genomics & Bioinformatics, Chinese Academy of Sciences, 101300 Beijing, China;(2) Hangzhou Genomics Institute/Institute of Bioinformatics of Zhejiang University/Key Laboratory of Bioinformatics of Zhejiang Province, 310007 Hangzhou, China;(3) Institute of Genetics, Chinese Academy of Sciences, 100101 Beijing, China;(4) National Hybrid Rice R & D Center, 410125 Changsha, China;(5) Laboratory of Bioinformatics, Institute of Biophysics, Chinese Academy of Sciences, 100101 Beijing, China;(6) College of Life Sciences, Peking University, 100871 Beijing, China;(7) Institute of Theoretical Physics, Chinese Academy of Sciences, 100080 Beijing, China;(8) Digital China Ltd., 100080 Beijing, China;(9) Institute of Computing Technology, Chinese Academy of Sciences, 100080 Beijing, China;(10) Medical College, Xi’an Jiaotong University, 710061 Xi’an, China |
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Abstract: | The sequence of the rice genome holds fundamental information for its biology, including physiology, genetics, development,
and evolution, as well as information on many beneficial phenotypes of economic significance. Using a “whole genome shotgun”
approach, we have produced a draft rice genome sequence ofOryza sativa ssp.indica, the major crop rice subspecies in China and many other regions of Asia. The draft genome sequence is constructed from over
4.3 million successful sequencing traces with an accumulative total length of 2214.9 Mb. The initial assembly of the non-redundant
sequences reached 409.76 Mb in length, based on 3.30 million successful sequencing traces with a total length of 1797.4 Mb
from anindica variant cultivar93-11, giving an estimated coverage of 95.29% of the rice genome with an average base accuracy of higher than 99%. The coverage
of the draft sequence, the randomness of the sequence distribution, and the consistency of BIG-ASSEMBLER, a custom-designed
software package used for the initial assembly, were verified rigorously by comparisons against finished BAC clone sequences
from bothindica andjapanica strains, available from the public databases. Over all, 96.3% of full-length cDNAs, 96.4% of STS, STR, RFLP markers, 94.0%
of ESTs and 94.9% unigene clusters were identified from the draft sequence. Our preliminary analysis on the data set shows
that our rice draft sequence is consistent with the comman standard accepted by the genome sequencing community. The unconditional
release of the draft to the public also undoubtedly provides a fundamental resource to the international scientific communities
to facilitate genomic and genetic studies on rice biology.
These authors contributed equally to this work. |
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Keywords: | rice genome draft sequences |
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