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Front. Plant Sci. | doi: 10.3389/fpls.2018.00246

Development and application of genomic resources in an endangered palaeoendemic tree, Parrotia subaequalis (Hamamelidaceae) from eastern China

  • 1College of Life Sciences, Nanjing University, China
  • 2College of Life Sciences, Zhejiang University, China
  • 3College of Life Sciences, Tarim University, China
  • 4Asian Natural Environmental Science Center, The University of Tokyo, Japan

Parrotia subaequalis is an endangered palaeoendemic tree from disjunct montane sites in eastern China. Due to the lack of effective genomic resources, the genetic diversity and population structure of this endangered species are not clearly understood. In this study, we conducted paired-end shotgun sequencing (2x125 bp) of genomic DNA for two individuals of P. subaequalis on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of P. subaequalis, as well as identified the polymorphic chloroplast microsatellites (cpSSRs), nuclear microsatellites (nSSRs) and mutational hotspots of chloroplast. Ten polymorphic cpSSR loci and 12 polymorphic nSSR loci were used to genotype 96 individuals of P. subaequalis from six populations to estimate genetic diversity and population structure. Our results revealed that P. subaequalis exhibited abundant genetic diversity (e.g., cpSSRs: Hcp = 0.862; nSSRs: HT = 0.559) and high genetic differentiation (e.g., cpSSRs: RST = 0.652; nSSRs: RST = 0.331), and characterized by a low pollen-to-seed migration ratio (r ≈ 1.78). These genetic patterns are attributable to its long evolutionary histories and low levels of contemporary inter-population gene flow by pollen and seed. In addition, lack of isolation-by-distance pattern and strong population genetic structuring in both marker systems, suggests that long-term isolation and/or habitat fragmentation as well as genetic drift may have also contributed to the geographic differentiation of P. subaequalis. Therefore, long-term habitat protection is the most important methods to prevent further loss of genetic variation and a decrease in effective population size. Furthermore, both cpSSRs and nSSRs revealed that P. subaequalis populations consisted of three genetic clusters, which should be considered as separated conservation units.

Keywords: Parrotia subaequalis, palaeoendemic tree, Chloroplast genome, microsatellites, fragmentation, conservation genetics

Received: 16 Nov 2017; Accepted: 12 Feb 2018.

Edited by:

Renchao Zhou, Sun Yat-sen University, China

Reviewed by:

Andrea Coppi, Università degli Studi di Firenze, Italy
Zhonghu Li, Northwest University, China  

Copyright: © 2018 Zhang, Shi, Yang, Geng, Wang and Qiu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Prof. Zhongsheng Wang, Nanjing University, College of Life Sciences, 163 Xianlin Avenue, Qi Xia District, Nanjing, Jiangsu Province, China, Nanjing, 210023, Jiangsu Province, China,
Prof. Yingxiong Qiu, Zhejiang University, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, China, Hangzhou, 310058, Zhejiang Province, China,