Development of polymorphic chloroplast DNA markers for the endangered tree Eusideroxylon zwageri through chloroplast iso
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METHODS AND RESOURCES ARTICLE
Development of polymorphic chloroplast DNA markers for the endangered tree Eusideroxylon zwageri through chloroplast isolation and next-generation sequencing Hiroyuki Kurokochi1 • I. L. G. Nurtjahjaningsih2 • Sukartiningsih3 Engkong Tan2 • Shuichi Asakawa2 • Yoko Saito2 • Yuji Ide2
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Received: 5 August 2015 / Accepted: 12 August 2015 Ó Springer Science+Business Media Dordrecht 2015
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.
Hiroyuki Kurokochi and I. L. G. Nurtjahjaningsih have contributed equally to this research.
Electronic supplementary material The online version of this article (doi:10.1007/s12686-015-0485-8) contains supplementary material, which is available to authorized users. & Hiroyuki Kurokochi [email protected]; [email protected] 1
Asian Natural Environmental Science Center, The University of Tokyo, 1-1-8 Midori-cho, Nishitokyo, Tokyo 188-0002, Japan
2
Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo, Tokyo 113-8657, Japan
3
Faculty of Forestry, Mulawarman University, Campus Gunung Kelua, Jl. Ki Hajar Dewantara, Samarinda, East Kalimantan 75119, Indonesia
Keywords Eusideroxylon zwageri Next-generation sequencing Chloroplast DNA Polymorphic markers Phylogeography
Introduction Borneo ironwood, Eusideroxylon zwageri (Lauraceae), is a tropical rainforest tree with a long lifespan that is distributed naturally in Brunei, Indonesia, Malaysia, and the Philippines. The wood has high specific gravity and is extremely hard, making it durable for decades or even a century (Whitten et al. 1987). The wood is economically valuable mainly for bridge construction and furniture manufacture. It uses insect-mediated pollination and gravity dispersal of seeds. Clearing of land for agriculture and overharvesting may threaten this species (Partomihardjo 1987). Thus, the conservation of E. zwageri is an urgent matter. In order to form an effective conservation strategy, it is essential to understand the underlying genetic structure of the species, because the spatial genetic structure of wild populations is often linked to specific local ecosystems. Evaluation of the intraspecific mutations of chloroplast DNA is a powerful tool for describing the phylogeographical genetic structure. Chloroplast DNA is ge
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