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Development of 13 polymorphic chloroplast DNA markers in Quercus gilva, a regionally endemic species in Japan

  • Microsatellite Letters
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Abstract

Quercus gilva is an evergreen oak species which is native to Japan, continental China and the islands of Taiwan. However, because of historical logging practices and habitat destruction in ancient times, Q. gilva is threatened with extinction in several regions of Japan. In this study, 13 polymorphic markers spanning the whole chloroplast DNA of Q. gilva were developed, using next-generation sequencing technology. These markers could distinguish between two individuals established in close proximity to one another as well as those from geographically-distinct regions. This indicates that the markers will be suitable for detecting the genetic structure and phylogeography of Q. gilva on both a large and a fine scale, potentially providing us with useful information for the conservation of this species.

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Acknowledgments

We thank Koishikawa Botanical Garden for providing us plant samples. Also, this study was supported in part by a Grant-in-Aid for Scientific Research (C) from the JSPS to YS (No. 25450206).

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Authors and Affiliations

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

    Nami Sugiura, Engkong Tan, Shuichi Asakawa, Yoko Saito & Yuji Ide

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

    Hiroyuki Kurokochi

  3. Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo, 153-8902, Japan

    Naoki Sato

Authors
  1. Nami Sugiura
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  2. Hiroyuki Kurokochi
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  3. Engkong Tan
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  4. Shuichi Asakawa
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  5. Naoki Sato
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  6. Yoko Saito
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  7. Yuji Ide
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Corresponding authors

Correspondence to Nami Sugiura or Hiroyuki Kurokochi.

Appendix

Appendix

We developed each marker within the following sequences.

Qg_01

  • GATATCAAAATCGATCGATCTATATTATCTAGCTGGATTCATCAGATTTTTTTAACTCATTTCATTCATTCAAAAAAAAAAAATAGAATTCGGATTTACATACATATAATTTAGATATTCGAATGGGTTGCCCGGGACTCGAACCCGGAACT

Qg_02

  • GACTGCTTTTTCTACACATTTACCCCCACACTCTAATGGAGAATAGCTACTAATAATTAGGATTTAAAAAAAAAAATCGATGATCCACTTATGGGAAAAGCATTTCCCGCATCAAGGACTAATCTATTTTTAA

Qg_03

  • GATTAAGATAAGGATATGGATTAAGTCAAAATTGATGTACTACCACGGATTTAGTTCGTATCTTATCCATTATTATCTTATCCGTTTTTTTTTTTTTCAATAAAATAAATAAAGGCTTCTCGTATCCCAGCAAATCCGACGAATCCGTCGTTTAAATAAAGTAAAATAAAAAAACCAAGT

Qg_04

  • GAATATAATGAACCTATCCTCTCTTCTCTATTCATATTTCATATTCAAAAAAAAACAAAACGGATCATTAATCCAAGACCAGAATATTCGGAGGACTCTTCTGAACAAACAAATAATTGTCAGCAACGTTGTTT

Qg_05

  • GCGAAATGCTATGGTTCTGAAATATGATTTCTTAATTTATTCAAAAGTAATTCGCGCGATCATGCACCCTTCCCTGTTATAACAAAAAAAAGTGCAGTTGGTTGGATCCAGCCTATTCTTGAAATAAACAACTCGCACACACTCCCTTT

Qg_06

  • GTTGTCTTATACTAATTAGAGTACATACATCTAGTTCGGCCCCCCCTAACCAATCCATTTTTTTTTATAAATTTGAAGTAGTTTTTTGTAAATCTTTATTTTTCTTTTTTTACTCGCCGACGCAGGTACAATCAATCTACATGGACAAATTCGTT

Qg_07

  • GTAAAAGAAAGGGAATGGTTAATTCCACAAAAGAAGTCTTTTTTTTTTTTTTCACGAGGTAGAACTAGAAATTCCTATTTATTTGTTACTGAAGAGCCCATAGACCAATTCCCCCTTTT

Qg_08

  • GGAAAGGGGATTATTAAATAAAAGAGGATTCCAGATACAAGTACAAAAACGAATACCCCCCCCGGAAAAAAAAGTGGAATATTTTCATATATTTTTTTGTACCGTTTTGGCGACATGGCCGAGCGGT

Qg_09

  • GTTCTTTTCGTGATTTGTTATATAGGGATCTAGCTCCTCTAATTTTTTATTTAGAATTTGAAGTTCCTACGACATAGTAGATCGGCGACTCTTGGAAAAAGGGGTACGAAGCTTTTTCAATATTCTTTGATTT

Qg_10

  • GTCAACATACATATTCATTACTAGTCTATATCATAATAGATACTTATCTATCTAGGTGTCTGAGAATATACCCTTTCCAGAATTATAGAATAGATGAGTAAAGAGTATGTCTATAAAATCTGTAAAA-TAAAAAAAAATTAGATTTTACTTCCTTTTCTTTTTTATTTGTTCATACGGTGCCTCTT

Qg_11

  • GTTTCGGCACGTGTCAACCTTCCGCTCACGATTCATCCACTCGAATCCCATTTCTAATATATATATATGACTTTTATACTATTTCTATTTATACTATAAAACTAAGAGTCTCGCGGTTTCACTTCACTTCGGATTTGAATTTT

Qg_12

  • GGTGCCCTTATCTCATTTCTTAGTTAATATTTCAGCCTATCGATTTATGCCTAGCCTATTTTTTTTTTTTACCTATACCCTTTAGTTTTAGAGTTTTAGTTTCATGCTTTGCTTTTTATGGACGAACTCCTCATATT

Qg_13

  • GAATCACAATATTCTTCAGAAAATTCTCTCAATTATTCCCGGACTATGCGTCGTTTTTTTTTTTTTCAAAAAATTGGATATTTTGATAGAAAGAGAGTTCTTTCGTTTCAAAATCTGAATAATATTTGTT

Qg_14

  • GTATCCTTAGGAACCGTACGCGCACCTTTTGATGCATACGGTTTACCAAAAATCGCGCAAAAAAAAAAGAATCAATGTGTAGATTGCAGCCCTCATTCTTTTTTATTTTCATAGGGGGCTCTTTCTAACTTCTAACAAAGGGCTT

Qg_15

  • GCATTCCTTTCGAGCAAAAGAAAAAGGACCCTTCCTAATTTGAATTTGAAATTACCATTTCTTTATCTTTAATATCTTTAATCAAAGGATTTACTTCTTTTTTTTTTTTATTTTATTTTAGGTGAATTTAAAATTGTTCGAATTGTATAATCGTCAATT

Qg_16

  • GAAAAGTTGACAAACTTGGTGGATACGTGAAGGATATCCTTTCTTTTCCATCACTTTTACATGTATGTATGAAAAAAGGATTGTGACATTTCATTTTTTACAGCATTTTGAAATCGGTCGTTTTTTAT

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Sugiura, N., Kurokochi, H., Tan, E. et al. Development of 13 polymorphic chloroplast DNA markers in Quercus gilva, a regionally endemic species in Japan. Conservation Genet Resour 6, 961–965 (2014). https://doi.org/10.1007/s12686-014-0256-y

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  • DOI: https://doi.org/10.1007/s12686-014-0256-y

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