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GENETICS, GENOMICS, AND MOLECULAR EVOLUTION

A Comparison of Rice Chloroplast Genomes^1,[w]

Institute of Genetics and Developmental Biology (J.T., H.X., X.Z., W.Z., J.Y, H.Y., L.Z.) and Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China (J.T., H.X., X.Z., S.H., W.T., J.W., J.W., J.Y., H.Y, L.Z.); National Hybrid Rice Research and Development Center, Changsha 410125, China (M.C.); and Hangzhou Genomics Institute, Hangzhou 310007, China (S.H., J.W.)

Using high quality sequence reads extracted from our whole genome shotgun repository, we assembled two chloroplast genome sequences from two rice (Oryza sativa) varieties, one from 93-11 (a typical indica variety) and the other from PA64S (an indica-like variety with maternal origin of japonica), which are both parental varieties of the super-hybrid rice, LYP9. Based on the patterns of high sequence coverage, we partitioned chloroplast sequence variations into two classes, intravarietal and intersubspecific polymorphisms. Intravarietal polymorphisms refer to variations within 93-11 or PA64S. Intersubspecific polymorphisms were identified by comparing the major genotypes of the two subspecies represented by 93-11 and PA64S, respectively. Some of the minor genotypes occurring as intravarietal polymorphisms in one variety existed as major genotypes in the other subspecific variety, thus giving rise to intersubspecific polymorphisms. In our study, we found that the intersubspecific variations of 93-11 (indica) and PA64S (japonica) chloroplast genomes consisted of 72 single nucleotide polymorphisms and 27 insertions or deletions. The intersubspecific polymorphism rates between 93-11 and PA64S were 0.05% for single nucleotide polymorphisms and 0.02% for insertions or deletions, nearly 8 and 10 times lower than their respective nuclear genomes. Based on the total number of nucleotide substitutions between the two chloroplast genomes, we dated the divergence of indica and japonica chloroplast genomes as occurring approximately 86,000 to 200,000 years ago.

² These authors contributed equally to the paper.

^[w] The online version of this article contains Web-only data.

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.103.031245.

^* Corresponding author; e-mail lhzhu{at}genetics.ac.cn; fax 86–10–64873428.

Received August 1, 2003; returned for revision January 28, 2004; accepted February 10, 2004.

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