A comparative plastomics approach reveals available molecular markers for the phylogeographic study of Dendrobium huoshanense, an endangered orchid with extremely small populations.

Zhitao Niu,Mengting Wang,Xiaoyu Ding,Benhou Zhang,Zhenyu Hou,Meirong Ye,Qingyun Xue,Wei Liu

doi:10.1002/ece3.6277

Abstract

Comparative plastomics approaches have been used to identify available molecular markers for different taxonomic level studies of orchid species. However, the adoption of such methods has been largely limited in phylogeographic studies. Therefore, in this study, Dendrobium huoshanense, an endangered species with extremely small populations, was used as a model system to test whether the comparative plastomic approaches could screen available molecular markers for the phylogeographic study. We sequenced two more plastomes of D. huoshanense and compared them with our previously published one. A total of 27 mutational hotspot regions and six polymorphic cpSSRs have been screened for the phylogeographic studies of D. huoshanense. The cpDNA haplotype data revealed that the existence of haplotype distribution center was located in Dabieshan Mts. (Huoshan). The genetic diversity and phylogenetic analyses showed that the populations of D. huoshanense have been isolated and evolved independently for long period. On the contrary, based on cpSSR data, the genetic structure analysis revealed a mixed structure among the populations in Anhui and Jiangxi province, which suggested that the hybridization or introgression events have occurred among the populations of D. huoshanense. These results indicated that human activities have played key roles in shaping the genetic diversity and distributional patterns of D. huoshanense. According to our results, both two markers showed a high resolution for the phylogeographic studies of D. huoshanense. Therefore, we put forth that comparative plastomic approaches could revealed available molecular markers for phylogeographic study, especially for the species with extremely small populations.

Highlights

The Orchidaceae, one of the largest families in the monocots, are well known for their tremendous diversity and innovative characters, including specialized pollination syndromes, epiphytic habits, and the presence of crassulacean acid metabolism (Chase, Cameron, Barrett, & Freudenstein, 2003; Silvera, Santiago, Cushman, & Winter, 2009)
The narrow geographical distribution and small population size of D. huoshanense have resulted in great challenges for its phylogeographic study
Negative correlations between GC content and the distribution of single nucleotide polymorphism (SNP) and InDel were detected (Spearman's, r = −.473, −.267, all p < .01). These results indicated that the plastomic mutational hotspots of D. huoshanense were accompanied by biased AT compositions

Summary

| INTRODUCTION

The Orchidaceae (orchids), one of the largest families in the monocots, are well known for their tremendous diversity and innovative characters, including specialized pollination syndromes, epiphytic habits, and the presence of crassulacean acid metabolism (Chase, Cameron, Barrett, & Freudenstein, 2003; Silvera, Santiago, Cushman, & Winter, 2009) Owing to these unique features, orchids are ideal examples for phylogeographic studies, which investigating the mechanisms and processes of geographical distribution in flowering plants (Avise, 2000). The noncoding sequences in chloroplast genomes (i.e., plastomes) are the most important genetic tools for plant studies at low taxonomic levels, especially for phylogeographic analysis (Beheregaray, 2008; Prince, 2015). Based on the comparative plastomic approaches, a total of 27 mutational hotspot regions and six polymorphic cpSSRs have been selected to assess the genetic diversity and distributional patterns of D. huoshanense

| MATERIALS AND METHODS

Findings

| DISCUSSION