Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae)

Abstract

Astragalus is the largest genus in Leguminosae. Several molecular studies have investigated the potential adulterants of the species within this genus; nonetheless, the evolutionary relationships among these species remain unclear. Herein, we sequenced and annotated the complete chloroplast genomes of three Astragalus species—Astragalus adsurgens, Astragalus mongholicus var. dahuricus, and Astragalus melilotoides using next-generation sequencing technology and plastid genome annotator (PGA) tool. All species belonged to the inverted repeat lacking clade (IRLC) and had similar sequences concerning gene contents and characteristics. Abundant simple sequence repeat (SSR) loci were detected, with single-nucleotide repeats accounting for the highest proportion of SSRs, most of which were A/T homopolymers. Using Astragalus membranaceus var. membranaceus as reference, the divergence was evident in most non-coding regions of the complete chloroplast genomes of these species. Seven genes (atpB, psbD, rpoB, rpoC1, trnV, rrn16, and rrn23) showed high nucleotide variability (Pi), and could be used as DNA barcodes for Astragalus sp. cemA and rpl33 were found undergoing positive selection by the section patterns in the coded protein. Phylogenetic analysis showed that Astragalus is a monophyletic group closely related to the genus Oxytropis within the tribe Galegeae. The newly sequenced chloroplast genomes provide insight into the unresolved evolutionary relationships within Astragalus spp. and are expected to contribute to species identification.

Comparative chloroplast genome analyses of 23 species in Swertia L. (Gentianaceae) with implications for its phylogeny

“…The plastid genome annotator tool was used for the functional annotation of Swertia L. chloroplast genomes; the start codon, stop codon, and other problematic sites in the annotation result were adjusted manually ( Qu et al, 2019 ; Tian et al, 2021 ). The annotated chloroplast genome data were exported in Gb format, and the chloroplast genome maps of the four Swertia L. species were drawn using OGDRAW ( Marc et al, 2013 ) software.…”

Complete chloroplast genomes of eight Artemisia species: Comparative analysis, molecular identification, and phylogenetic analysis

“…The highly variable regions of the chloroplast genome can be used to discriminate between closely related species, and applied to plant identification and phylogenetic analysis (Tian et al . 2021). We compared chloroplast genomes of nine Artemisia species using mVISTA software and the A. argyi chloroplast genome as reference.…”

The Complete Chloroplast Genome Sequence of Four Plant Species, Their SSR Identification and Phylogenetic Analysis

“…However, these sequences have insufficient information to differentiate the closely related taxa, especially some without knowing their taxonomic relationships. At higher taxonomic levels (family), conserved sequences and protein-coding regions of the chloroplast genome can be employed for phylogenetic analysis and domestication studies in plants [10,12,13].…”

“…Most chloroplast genome comprises specific four regions, i.e., large and small single copies and two inverted repeats [12]. Complete four regions in chloroplast commonly mean related full biological functions in related species.…”

“…What's more, the specific regions showed regular length individually, which indicated there was no loss of significant long fragments. Usually, the chloroplast genome contained 120~130 genes, and that length fall ranged from 107-218 kb [12]. Within these four chloroplast genomes, 124, 130, 129, and 131 genes were identified, and the whole genomes were 152, 624 bp, 153,296 bp, 156,309 bp, and 158, 953 bp in length, correspondingly.…”