Comparative Analysis of the Complete Chloroplast Genomes in IAllium/I Section IBromatorrhiza/I Species : Phylogenetic Relationship and Adaptive Evolution

With the development of molecular sequencing approaches, many taxonomic and phylogenetic problems of the genus Allium L. have been solved; however, the phylogenetic relationships of some subgenera or sections, such as section Bromatorrhiza, remain unresolved, which has greatly impeded our full under...

Full description

Saved in:
Bibliographic Details
Published inGenes Vol. 13; no. 7
Main Authors Chen, Junpei, Xie, Dengfeng, He, Xingjin, Yang, Yi, Li, Xufeng
Format Journal Article
LanguageEnglish
Published MDPI AG 19.07.2022
Subjects
Allium
Analysis
Chloroplasts
Environmental aspects
Evolutionary biology
Genetic aspects
Growth
Phylogeny
China
Online AccessGet full text

Cover

More Information
Summary:With the development of molecular sequencing approaches, many taxonomic and phylogenetic problems of the genus Allium L. have been solved; however, the phylogenetic relationships of some subgenera or sections, such as section Bromatorrhiza, remain unresolved, which has greatly impeded our full understanding of the species relationships among the major clades of Allium. In this study, the complete chloroplast (cp) genomes of nine species in the Allium sect. Bromatorrhiza were determined using the Illumina paired-end sequencing, the NOVOPlasty de novo assembly strategy, and the PGA annotation method. The results showed that the cp genome exhibited high conservation and revealed a typical circular tetrad structure. Among the sect. Bromatorrhiza species, the gene content, SSRs, codon usage, and RNA editing site were similar. The genome structure and IR regions’ fluctuation were investigated while genes, CDSs, and non-coding regions were extracted for phylogeny reconstruction. Evolutionary rates (Ka/Ks values) were calculated, and positive selection analysis was further performed using the branch-site model. Five hypervariable regions were identified as candidate molecular markers for species authentication. A clear relationship among the sect. Bromatorrhiza species were detected based on concatenated genes and CDSs, respectively, which suggested that sect. Bromatorrhiza is monophyly. In addition, there were three genes with higher Ka/Ks values (rps2, ycf1, and ycf2), and four genes (rpoC2, atpF, atpI, and rpl14) were further revealed to own positive selected sites. These results provide new insights into the plastome component, phylogeny, and evolution of Allium species.
ISSN:2073-4425
2073-4425
DOI:10.3390/genes13071279