AUTHOR=Zhang Yun-Yan , Shi En , Yang Zhao-Ping , Geng Qi-Fang , Qiu Ying-Xiong , Wang Zhong-Sheng 

TITLE=Development and Application of Genomic Resources in an Endangered Palaeoendemic Tree, Parrotia subaequalis (Hamamelidaceae) From Eastern China

JOURNAL=Frontiers in Plant Science

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2018.00246

DOI=10.3389/fpls.2018.00246

ISSN=1664-462X

ABSTRACT=<p><italic>Parrotia subaequalis</italic> 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 (2 × 125 bp) of genomic DNA for two individuals of <italic>P. subaequalis</italic> on the Illumina HiSeq platform. Based on the resulting sequences, we have successfully assembled the complete chloroplast genome of <italic>P. subaequalis</italic>, 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 <italic>P. subaequalis</italic> from six populations to estimate genetic diversity and population structure. Our results revealed that <italic>P. subaequalis</italic> exhibited abundant genetic diversity (e.g., cpSSRs: <italic>H</italic>cp = 0.862; nSSRs: <italic>H</italic><sub>T</sub> = 0.559) and high genetic differentiation (e.g., cpSSRs: <italic>R</italic><sub>ST</sub> = 0.652; nSSRs: <italic>R</italic><sub>ST</sub> = 0.331), and characterized by a low pollen-to-seed migration ratio (<italic>r</italic> ≈ 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 <italic>P. subaequalis</italic>. 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 <italic>P. subaequalis</italic> populations consisted of three genetic clusters, which should be considered as separated conservation units.</p>