The chloroplasts genomic analyses of Caragana arborescens and Caragana opulens

Abstract

Abstract Background Numerous species within the genus Caragana have high ecological and medicinal value. In this genus, however, species identification based on morphological characteristics is quite complicated; this issue can be resolved by analyzing the complete plastid genomes. Results We obtained the chloroplast genomes of two species using lllumina sequencing technology: Caragana arborescens and Caragana opulens, with lengths of 129,473 bp and 132,815 bp, respectively. The absence of inverted repeat sequences in the two species allowed them to be ascribed to the inverted repeat-lacking clade (IRLC). They comprise a total of 111 distinct genes (4 rRNA, 31 tRNA, and 76 protein-coding genes). In addition, 16 genes containing introns were identified in two genomes, the majority of which contained a single intron. C. arborescens and C. opulens were found to contain 129 and 229 repeats, as well as 277 and 265 simple repeats, respectively. The codon usage bias analysis revealed that the two Caragana species exhibit similar codon usage patterns. rpoC2-rps2, accD-cemA, rps18-clpP, rpoA-rpl36, and rpl2-rpl23 were identified as the five regions most likely to be mutated based on analysis of nucleotide diversity (Pi). Analysis of sequence divergence revealed that certain intergenic regions (matK-rbcL, psbM-petN, atpA-psbI, petA-psbL, psbE-petL, and rps7-rps12) are highly variable. Phylogenetic analysis showed that C. arborescens and C. opulens were related and clustered together as the other four Caragana species. And the genus Astragalus and Caragana were relatively closely related. Conclusions In our research, the chloroplast genomes of C. arborescens and C. opulens were sequenced and their genomic structural characteristics were compared. We have also confirmed that both plants lack IR regions, which resulted in unclear boundary analysis, and that two plants could be classified as IRLC. This study provides a foundation for future phylogenetic research and the development of molecular markers for Caragana plants.