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Development of polymorphic chloroplast DNA markers for the endangered tree Eusideroxylon zwageri through chloroplast isolation and next-generation sequencing

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Abstract

Borneo ironwood (Eusideroxylon zwageri) is a tall tropical tree that is threatened by illegal logging and exploitation due to its economic value. In the present study, approximately 10,618 bp of E. zwageri chloroplast DNA were sequenced genome-wide and 16 polymorphic markers of chloroplast DNA were developed, using next-generation sequencing technology. In total, 26 nucleotide substitutions, 3 indels, 1 sequence inversion, and 1 mononucleotide repeat variation were detected in samples of 10 trees collected from 5 populations in Kalimantan, Indonesia. These markers are a powerful tool that may be used to describe the phylogeographical genetic structure of E. zwageri and will be essential for the conservation and management of this endangered tree.

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Acknowledgments

This study was supported in part by a Grant-in-Aid for Scientific Research (B) from the JSPS to YI (No. 25304025).

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Author notes

    Authors and Affiliations

    1. Asian Natural Environmental Science Center, The University of Tokyo, 1-1-8 Midori-cho, Nishitokyo, Tokyo, 188-0002, Japan

      Hiroyuki Kurokochi

    2. Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo, 113-8657, Japan

      I. L. G. Nurtjahjaningsih, Engkong Tan, Shuichi Asakawa, Yoko Saito & Yuji Ide

    3. Faculty of Forestry, Mulawarman University, Campus Gunung Kelua, Jl. Ki Hajar Dewantara, Samarinda, East Kalimantan, 75119, Indonesia

      Sukartiningsih

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    1. Hiroyuki Kurokochi
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    2. I. L. G. Nurtjahjaningsih
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    3. Sukartiningsih
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    4. Engkong Tan
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    5. Shuichi Asakawa
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    6. Yoko Saito
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    7. Yuji Ide
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    Corresponding author

    Correspondence to Hiroyuki Kurokochi.

    Additional information

    Hiroyuki Kurokochi and I. L. G. Nurtjahjaningsih have contributed equally to this research.

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    Kurokochi, H., Nurtjahjaningsih, I.L.G., Sukartiningsih et al. Development of polymorphic chloroplast DNA markers for the endangered tree Eusideroxylon zwageri through chloroplast isolation and next-generation sequencing. Conservation Genet Resour 7, 845–850 (2015). https://doi.org/10.1007/s12686-015-0485-8

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    • DOI: https://doi.org/10.1007/s12686-015-0485-8

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