Interspecific delimitation and relationships among four Ostrya species based on plastomes

Yanyou Jiang,Zhiqiang Lu,Guangpeng Ren,Yongzhi Yang,Dongshi Wan

doi:10.1186/s12863-019-0733-0

Abstract

BackgroundThe genus Ostrya (Betulaceae) contains eight species and four of them are distributed in China. However, studies based on limited informative sites of several chloroplast markers failed to resolve interspecific delimitation and relationships among the four Chinese species. In this study, we aimed to use the whole chloroplast genomes to address these two issues.ResultsWe assembled and annotated 33 complete chloroplast genomes (plastomes) of the four Chinese species, representing 17 populations across most of their geographical distributions. Each species contained samples of several individuals that cover most of geographic distributions of the species. All plastomes are highly conserved in genome structure and gene order, with a total length of 158–159 kb and 122 genes. Phylogenetic analyses of whole plastomes, non-coding regions and protein-coding genes produced almost the same topological relationships. In contrast to the well-delimitated species boundary inferred from the nuclear ITS sequence variations, three of the four species are non-monophyletic in the plastome trees, which is consistent with previous studies based on a few chloroplast markers.ConclusionsThe high incongruence between the ITS and plastome trees may suggest the widespread occurrences of hybrid introgression and incomplete lineage sorting during the divergence of these species. In addition, the plastomes with more informative sites compared with a few chloroplast markers still failed to resolve the phylogenetic relationships of the four species, and further studies involving population genomic data may be needed to better understand their evolutionary histories.

Highlights

The genus Ostrya (Betulaceae) contains eight species and four of them are distributed in China
The chloroplast genome structures of all the four Ostrya species were consistent with mostly known angiosperms with a typical quadripartite structure consisting of a pair of inverted repeats regions (IRa and IRb: 26,059–26,069 bp) divided by a large single-copy region (LSC: 88,007–88,229 bp) and a small single-copy region (SSC: 18,721–18,975 bp) (Fig. 1 and Table 1)
Expansion of Inverted repeat region (IR) regions into rps19 at the IRb/LSC boundary region occurred in all Ostrya taxa and the pseudogene ycf1 was located at the junction of SSC/IRa, which gave rise to the incomplete duplication of protein-coding gene within IRs

Summary

Introduction

The genus Ostrya (Betulaceae) contains eight species and four of them are distributed in China. Studies based on limited informative sites of several chloroplast markers failed to resolve interspecific delimitation and relationships among the four Chinese species. Ostrya is a small genus belongs to the birch family Betulaceae and merely consists of eight species native in southern Europe, southwest and eastern Asia, and North and Central America [1,2,3]. These small deciduous trees, commonly called as hophornbeam or ironwood, are well known for their hard and heavy woods. In this study, we re-investigate phylogenetic relationships of the four Chinese Ostrya species based on plastomes. The aims of our study are to: 1) investigate whether the three plastome datasets result in consistent phylogenies and whether they can discern the four species and 2) test if phylogeny based on plastome datasets congruent with the ITS tree

Objectives

Methods

Results

Discussion

Conclusion