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DNA Research Advance Access originally published online on November 16, 2006
DNA Research 2006 13(5):197-204; doi:10.1093/dnares/dsl012
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© The Author 2006. Kazusa DNA Research Institute.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Pattern and Rate of Indel Evolution Inferred from Whole Chloroplast Intergenic Regions in Sugarcane, Maize and Rice

Kyoko Yamane1,2,*, Kentaro Yano3,4 and Taihachi Kawahara1

1 Laboratory of Crop evolution, Graduate School of Agriculture, Kyoto University Nakajoh, Mozume, Mukoh 617-0001, Japan
2 Plant resource Laboratory, Graduate School and School of Life and Environmental, Osaka Prefectural University 1-1 Gakuen-cho, Nakaku, Sakai, Osaka 599-8531, Japan
3 Plant Breeding Laboratory, Graduate School of Agriculture, Kyoto University Nakajoh, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan
4 Kazusa DNA Research Institute 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan

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 {approx}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).

Key words: chloroplast genome; evolutionary rate; indels; non-coding DNA sequence; intergenic region

*To whom correspondence should be addressed. Tel. +81-75-921-0652, Fax. +81-75-932-8063, E-mail: m52297{at}mbox.kudpc.kyoto-u.ac.jp

Communicated by Masahiro Yano


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[Abstract] [Full Text] [PDF]


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