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Published on December 29, 2005; 10.1104/pp.105.070060

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Received August 17, 2005
Returned for revision October 25, 2005
Accepted November 9, 2005

The Rice (Oryza sativa L.) Mitochondrial Genomes and Their Variations

Xiangjun Tian , Jing Zheng , Songnian Hu , and Jun Yu *

James D. Watson Institute of Genome Sciences, Zhejiang University; Hangzhou Genomics Institute, Zhejiang Provincial Key Laboratory of Genomic and Bioinformatics, Hangzhou, 310008, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China; College of Life Science, Zhejiang University, Hangzhou 310027, China
College of Life Science, Zhejiang University, Hangzhou 310027, China; Shanghai Information Center for Life Sciences, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200031, China
James D. Watson Institute of Genome Sciences, Zhejiang University; Hangzhou Genomics Institute, Zhejiang Provincial Key Laboratory of Genomic and Bioinformatics, Hangzhou, 310008, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China

* Corresponding author; email: junyu{at}genomics.org.cn.

Based on highly redundant and high-quality sequences, we assembled rice mitochondrial genomes for two cultivars, 93-11 (an indica variety) and PA64S (an indica-like variety with maternal origin of japonica), which are paternal and maternal strains of an elite super-hybrid rice LYP9, respectively. Following up with a previous analysis on rice chloroplast genomes, we define mitochondrial sequence variations into two basic categories, intravarietal and intersubspecific. Intravarietal polymorphisms account for variations within mitochondrial genomes of an individual variety. Intersubspecific polymorphisms refer to variations between subspecies among their major genotypes. In this study, we identified 96 single nucleotide polymorphisms (SNPs), 25 indels, and three segmental sequence variations as intersubspecific polymorphisms. A signature sequence fragment unique to indica varieties were confirmed experimentally and found in two wild rice samples, but absent in japonica varieties. The intersubspecific polymorphism rate for mitochondrial genomes are 0.02% for SNPs and 0.006% for indels, nearly 2.5 and 3 times lower than that of their chloroplast counterparts, 21 and 38 times lower than its corresponding rates of the rice nuclear genome, respectively. The intravarietal polymorphism rates among analyzed mitochondrial genomes, such as 93-11 and PA64S, are 1.26% and 1.38% for SNPs, 1.13% and 1.09% for indels, respectively. Based on the total number of SNPs between the two mitochondrial genomes, we estimate that the divergence of indica and japonica mitochondrial genomes occurred approximately 45,000 to 250,000 years ago.




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