Sequence and analysis of rice chromosome 4

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Abstract

Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research1. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely2. The finished sequence spans 34.6 Mb and represents 97.3% of the chromosome. In addition, we report the longest known sequence for a plant centromere, a completely sequenced contig of 1.16 Mb corresponding to the centromeric region of chromosome 4. We predict 4,658 protein coding genes and 70 transfer RNA genes. A total of 1,681 predicted genes match available unique rice expressed sequence tags. Transposable elements have a pronounced bias towards the euchromatic regions, indicating a close correlation of their distributions to genes along the chromosome. Comparative genome analysis between cultivated rice subspecies shows that there is an overall syntenic relationship between the chromosomes and divergence at the level of single-nucleotide polymorphisms and insertions and deletions. By contrast, there is little conservation in gene order between rice and Arabidopsis.

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Figure 1: Maps of rice chromosome 4.
Figure 2: Distribution of various repeats and features along chromosome 4.
Figure 3: Comparative sequence analyses between rice subspecies indica GLA4 and japonica Nipponbare.

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Acknowledgements

We thank T. Sasaki and the RGP for rice genetic and EST markers and a PAC genomic library of rice Nipponbare; R. Wing and the CUGI for providing BAC libraries of the Nipponbare variety; Monsanto for the rice working-draft sequence data; G. Barry and J. Liu for help; R. Buell and Q. Yuan for help with the annotation and analysis of chromosome 4 sequences; X. Huang and Z. Ning for help with using the AAT and the ssaha programs, respectively; members of the National Centre for Gene Research for assistance; Z. Xu, Z. Chen, G. Wang, Q. Ma and Q. Zhang for support; and X. Lin, X. Deng, Y. Li, L. Zhou, N. Zheng, X. Liu and members of the IRGSP for discussion. This work was supported by grants from the Ministry of Science and Technology of the People's Republic of China, Chinese Academy of Sciences, and the Shanghai Municipal Commission of Science and Technology.

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Correspondence to Bin Han.

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