Complete Chloroplast Genome of Corethrodendron fruticosum (Papilionoideae: Fabaceae): Comparative and Phylogenetic Analysis

Abstract

Corethrodendron fruticosum is an endemic forage grasses in China with high ecological value. In this study, the complete chloroplast genome of C. fruticosum was sequenced using Illumina paired-end sequencing. The C. fruticosum chloroplast genome was 123,100 bp and comprised 105 genes, including 74 protein-coding genes, 4 rRNA-coding genes, and 27 tRNA-coding genes. The genome had a GC content of 34.53%, with 50 repetitive sequences and 63 simple repeat repetitive sequences that did not contain reverse repeats. The simple repeats included 45 single-nucleotide repeats, which accounted for the highest proportion and primarily comprised A/T repeats. A comparative analysis of C. fruticosum, C. multijugum, and four Hedysarum species revealed that the six genomes were highly conserved, with differentials primarily located in the conserved non-coding regions. Moreover, the accD and clpP genes in the coding regions exhibited high nucleotide variability. Accordingly, these genes may serve as molecular markers for the classification and phylogenetic analysis of Corethrodendron species. Phylogenetic analysis further revealed that C. fruticosum and C. multijugum appeared in different clades than the four Hedysarum species. The newly sequenced chloroplast genome provides further insights into the phylogenetic position of C. fruticosum, which is useful for the classification and identification of Corethrodendron.

Phylogenomic analysis of Bupleurum in Western Sichuan, China, including an overlooked new species

“…The rpl32-trnL, petA-psbJ gene have also been reported to show very high nucleotide per site diversity in several genera (Dong et al,FIGURE 4 Comparison of the six Bupleurum species cp genomes using the mVISTA alignment program, with B. chinense as a reference. Chao et al 10.3389/fpls.2023.1294670 Frontiers in Plant Science frontiersin.org Tan et al, 2020;Wang et al, 2022;Niu et al, 2023), and indeed the Pi values of the rpl32-trnL spacer regions of these six Bupleurum species were also much higher than the other regions in the present study, so rpl32-trnL together with petA-psbJ, trnK-rps16, and ycf1 were considered as having potential to be used as high-resolution DNA barcodes to identify species of Bupleurum.…”

“…There is evidence supporting the ycf 1 gene as one of the core plastid DNA barcodes in land plants ( Neubig et al., 2009 ; Franck et al., 2012 ; Dong et al., 2015 ). The rpl 32- trn L, pet A- psb J gene have also been reported to show very high nucleotide per site diversity in several genera ( Dong et al., 2012 ; Tan et al., 2020 ; Wang et al., 2022 ; Niu et al., 2023 ), and indeed the Pi values of the rpl 32- trn L spacer regions of these six Bupleurum species were also much higher than the other regions in the present study, so rpl 32- trn L together with pet A- psb J, trn K- rps 16, and ycf 1 were considered as having potential to be used as high-resolution DNA barcodes to identify species of Bupleurum .…”