Complete chloroplast genome of Hordeum brevisubulatum: Genome organization, synonymous codon usage, phylogenetic relationships, and comparative structure analysis.

Guangxin Cui,JinHua Li,Xiaoli Wang,Huirong Duan,Hongbo Wang,Xinqiang Zhu,Xiaoxing Wei,Chunmei Wang,Hongshan Yang,Genlou Sun

doi:10.1371/journal.pone.0261196

Abstract

BackgroundHordeum brevisubulatum, known as fine perennial forage, is used for soil salinity improvement in northern China. Chloroplast (cp) genome is an ideal model for assessing its genome evolution and the phylogenetic relationships. We de novo sequenced and analyzed the cp genome of H. brevisubulatum, providing a fundamental reference for further studies in genetics and molecular breeding.ResultsThe cp genome of H. brevisubulatum was 137,155 bp in length with a typical quadripartite structure. A total of 130 functional genes were annotated and the gene of accD was lost in the process of evolution. Among all the annotated genes, 16 different genes harbored introns and the genes of ycf3 and rps12 contained two introns. Parity rule 2 (PR2) plot analysis showed that majority of genes had a bias toward T over A in the coding strand in all five Hordeum species, and a slight G over C in the other four Hordeum species except for H. bogdanil. Additionally, 52 dispersed repeat sequences and 182 simple sequence repeats were identified. Moreover, some unique SSRs of each species could be used as molecular markers for further study. Compared to the other four Hordeum species, H. brevisubulatum was most closely related to H. bogdanii and its cp genome was relatively conserved. Moreover, inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions were relatively conserved compared to non-coding regions. Main divergence was presented at the SSC/IR border.ConclusionsThis research comprehensively describes the architecture of the H. brevisubulatum cp genome and improves our understanding of its cp biology and genetic diversity, which will facilitate biological discoveries and cp genome engineering.

Highlights

Soil salinity is a serious threat to plant growth
Parity rule 2 (PR2) plot analysis showed that majority of genes had a bias toward T over A in the coding strand in all five Hordeum species, and a slight G over C in the other four Hordeum species except for H. bogdanil
Inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions were relatively conserved compared to non-coding regions

Summary

Introduction

Soil salinity is a serious threat to plant growth. the breeding of salt-tolerant plants plays a vital role in the exploitation and utilization of saline land [1]. The first cultivar of H. brevisubulatum, ‘Junxu No.1’, was approved in China in 2003 [5] It took nearly 10 years to breed this variety by conventional breeding methods, which included chemical mutagenesis, fine individual selection and cultivation, variety comparison testing, regional testing, and promotion testing. H. brevisubulatum has been studied as a model to understand the salt-tolerance mechanisms of barley cereal crops, the genetic relationship between barley and H. brevisubulatum is still unclear. This knowledge would enable scientists to exploit H. brevisubulatum germplasm and accelerate the pace of breeding [9]. We de novo sequenced and analyzed the cp genome of H. brevisubulatum, providing a fundamental reference for further studies in genetics and molecular breeding.

Methods

Results

Conclusion