Comparative Genomics and Phylogenetic Analysis Revealed the Chloroplast Genome Variation and Interspecific Relationships of Corylus (Betulaceae) Species.

Zhen Yang,Qinghua Ma,Tiantian Zhao,Lisong Liang,Guixi Wang

doi:10.3389/fpls.2018.00927

Abstract

Corylus L. is an economically and phylogenetically important genus in the family Betulaceae. Taxonomic and phylogenetic relationships of Corylus species have long been controversial for lack of effective molecular markers. In this study, the complete chloroplast (cp) genomes of six Corylus species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the six Corylus species. The results indicated that Corylus cp genomes were typical of the standard double-stranded DNA molecule, ranging from 160,445 base pairs (bp) (C. ferox var. thibetca) to 161,621 bp (C. yunnanensis) in length. Each genome contained a pair of inverted repeats (IRs), a large single-copy (LSC) region and a small single-copy (SSC) region. Each of the six cp genomes possessed 113 unique genes arranged in the same order, including 80 protein-coding, 29 tRNA, and 4 rRNA genes. C. yunnanensis contained the highest number of repeat sequences, and the richest SSRs in six cp genomes were A/T mononucleotides. Comparative analyses of six Corylus cp genomes revealed four hotspot regions (trnH-psbA, rpoB-trnC, trnF-ndhJ, and rpl32-trnL) that could be used as potential molecular markers. Phylogenetic analyses of the complete chloroplast genomes and 80 protein-coding genes exhibited nearly identical topologies that strongly supported the monophyly of Corylus and simultaneously revealed the generic relationships among Betulaceae. The availability of these genomes can offer valuable genetic information for further taxonomy, phylogeny, and species delimitation in Corylus or even Betulaceae plants.

Highlights

Corylus, comprising 16–20 species, is a transitionally and phylogenetically important genus in the family Betulaceae
All six cp genomes showed a typical quadripartite structure that consisted of a pair of inverted repeats (IRs) regions (26,561–27,118 bp) separated by the large single-copy (LSC) (88,409– 88,628 bp) and small single-copy (SSC) (18,769–18,857 bp) regions, which was similar to the majority of land plant cp genomes
The cp genome of all Corylus species encoded an identical set of 132 genes, including 88 protein-coding genes, 36 tRNA genes, and 8 rRNA genes (Table 1)

Summary

Introduction

Corylus, comprising 16–20 species, is a transitionally and phylogenetically important genus in the family Betulaceae. Except for abundant phenotypes and species diversity, increasing attention has been paid to this genus, as it includes several economically important species for their commercial and ornamental values. One of the most economic values of Corylus is the nuts sales from several. Chloroplast Genomics of Corylus species such as C. avellana in Europe and hybrid variety (C. heterophylla × C. avellana) in China. Another economically important species is C. heterophylla, which is cultivated and utilized as human food in China. Many other species of the genus Corylus have potential breeding value, such as C. kweichowensis. Corylus species are of important ornamental values, especially C. colurna, C. avellana, and C. chinensis

Objectives

Methods

Results

Conclusion