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Amounts and patterns of nucleotide variation within and between two Japanese conifers, sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) (Cupressaceae sensu lato)

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Abstract

Sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) are the most important timber species in Japan. To quantify and compare the level of nucleotide variation in these species, we investigated their variation at ten nuclear loci. Average values of nucleotide diversity at synonymous sites (π SYN) found in sugi and hinoki were 0.0038 and 0.0069, respectively. However, although the average value of nucleotide diversity was higher in hinoki than in sugi, their average values of haplotype diversity were similar. Deviations from the standard neutral model were detected at two loci in hinoki using Tajima’s D, Fay and Wu’s H, and Strobeck’s S statistics, which seem to be due to its historical population structure. Levels of divergence between the two species at synonymous sites of the ten genes ranged from 0.121 to 0.566 (0.28 on average). These values positively correlated with their guanine + cytosine contents at third-codon positions of synonymous sites (%GC3s).

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Acknowledgements

We thank Y. Taguchi for her technical support and both O. Savolainen and an anonymous reviewer for helpful comments. This study was supported by the Japan Society for the Promotion of Science, Grant-in-Aid for Scientific Research (B) no. 16380112.

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  1. Tomoyuki Kado

    Present address: Hayama Center for Advanced Studies, Graduate University for Advanced Studies, Hayama, Kanagawa, 240-0193, Japan

Authors and Affiliations

  1. Department of Forest Genetics, Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, 305-8687, Japan

    Tomoyuki Kado, Asako Matsumoto, Tokuko Ujino-Ihara & Yoshihiko Tsumura

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  1. Tomoyuki Kado
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Correspondence to Yoshihiko Tsumura.

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Communicated by O. Savolainen

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Kado, T., Matsumoto, A., Ujino-Ihara, T. et al. Amounts and patterns of nucleotide variation within and between two Japanese conifers, sugi (Cryptomeria japonica) and hinoki (Chamaecyparis obtusa) (Cupressaceae sensu lato). Tree Genetics & Genomes 4, 133–141 (2008). https://doi.org/10.1007/s11295-007-0094-0

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