DNA Research Advance Access published online on November 16, 2006
DNA Research, doi:10.1093/dnares/dsl012
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1 Laboratory of Crop evolution, Graduate School of Agriculture, Kyoto University, Nakajoh, Mozume, Mukoh 617-0001, Japan; Plant resource Laboratory, Graduate School and School of Life and Environmental, Osaka Prefectural University, 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
* To whom correspondence should be addressed. Microstructural changes such as insertions and deletions (=indels) are a major driving force in the evolution of non-coding DNA sequences. To better understand the mechanisms by which indel mutations arise, as well as the molecular evolution of non-coding regions, the number and pattern of indels and nucleotide substitutions were compared in the whole chloroplast genomes. Comparisons were made for a total of over 38 kb non-coding DNA sequences from 126 intergenic regions in two data sets representing species with different divergence times: sugarcane and maize and Oryza sativa var. indica and japonica. The main findings of this study are: (i) Approximately half of all indels are single nucleotide indels. This observation agrees with previous studies in various organisms. (ii) The distribution and number of indels was different between two data sets, and different patterns were observed for tandem repeat and non-repeat indels. (iii) Distribution pattern of tandem repeat indels showed statistically significant bias towards A/T-rich. (iv) The rate of indel mutation was estimated to be
Received August 3, 2006
Revised October 19, 2006
Full Papers
Pattern and Rate of Indel Evolution Inferred from Whole Chloroplast Intergenic Regions in Sugarcane, Maize and Rice
Kyoko Yamane 1 *, Kentaro Yano 2, and Taihachi Kawahara 3
2 Plant Breeding Laboratory, Graduate School of Agriculture, Kyoto University, Nakajoh, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan; Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
3 Laboratory of Crop evolution, Graduate School of Agriculture, Kyoto University, Nakajoh, Mozume, Mukoh 617-0001, Japan
Kyoko Yamane, E-mail: m52297{at}mbox.kudpc.kyoto-u.ac.jp
Abstract 
0.8 ± 0.04 x 10-9 per site per year, which was similar to previous estimates in other organisms. (v) The frequencies of nucleotide substitutions and indels were significantly lower in inverted repeat (IR).
Communicated by Masahiro Yano
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