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

Abstract

Background Hordeum 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. Results The 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. Conclusions This 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.

A comparison of 25 complete chloroplast genomes between sister mangrove species Kandelia obovata and Kandelia candel geographically separated by the South China Sea

“…In addition, the fragment from 8,966 to 52,067 bp was in inverse order in the LSC region, which was different from the reported cp genome of K. obovata (Chen et al, 2019;Yang et al, 2019). This inversion has been previously reported in other cp genomes (Wei et al, 2020;Cui et al, 2021;Kim & Cheon, 2021;Wang et al, 2021).…”

Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes of Clematis nannophylla

“…In this study, we compared the cp genome structure of ve Clematis species using mVISTA (using Clematis fruticosa as a reference) and found that the non-coding region was more prone to mutations than the coding region. Furthermore, the variation in the SC region was higher than that in the IR region, which is similar to the results of previous plant studies [25,51,53]. psbA-atpA, atpI-rpoC2, rpoB-psbD, psbE-petG, clpP, and rpoC2 were the most highly variable regions detected in C. nannophylla.…”

“…The expansion and contraction of the IR region boundaries are common evolutionary events in most angiosperms, which may lead to variations in cp genome length, gene replication or reduction, and the origin of pseudogenes [47,48]. This study found that IR expansion and contraction of C. nannophylla showed great similarity with other plants of Clematis, and these regional genotypes and distribution locations are similar [25]. However, only minor differences were observed near the IRb/SSC boundaries.…”

“…Chloroplasts have a unique genome and gene expression system that plays a crucial role in metabolism as a source of energy that supports plant life [24]. The complete C. nannophylla cp genome showed great similarities to the majority of angiosperms in terms of GC content and quadripartite architecture, including two inverted repeats (IRs), a large singlecopy region (LSC), and a small single-copy region (SSC), which is common in plants [24][25][26].…”

Structural characterization of four Rhododendron spp. chloroplast genomes and comparative analyses with other azaleas

“…The chloroplast genome is a typical double-stranded circular multi-copy DNA molecule in cells. Plant chloroplast (cp) genomes are very conserved and can be divided into four segments, namely two inverted repeat (IRa and IRb) regions, a large single copy (LSC) region, and a small single copy (SSC) region separating IR regions (Wicke et al, 2011;Cui et al, 2021). The expansion or contraction of the IR regions often results in the variation in length of the chloroplast genome (Chung et al, 2006).…”