Comparative analyses of the complete chloroplast genomes of four Caragana species, a specific genus distributed in arid and semi-arid area.

Caragana species, perennial deciduous shrubs of Leguminosae, are significant to illustrate the synchronous evolution of floristics, vegetation, and climate change in arid Central Asia, cold arid alpine Qinghai-Tibetan plateau (QTP), and mesophytic East Asia. The objective of this study was to assemble and annotate the complete cp genome of four Caragana species, including C. opulens, C. roborovskyi, C. stenophylla, C. tibetica, and to compare their various characteristics with previously published data of Caragana species. High-quality DNA was paired-end sequenced utilizing the Illumina NovaSeq platform, followed by de novo assembly with the NOVOPlasty. The four cp genomes of Caragana lacked the IR region and ranged in length from 129,303 to 132,895 bp. The cp genome encoded 112-113 genes, consisting of 77 protein coding genes, 31-32 tRNA genes and four rRNA genes. Similar to other IRLC species, the genes rpl22 and rps16, as well as the intron of rpl2 and rps12 were found to be absent. A total of 77-94 simple sequence repeats (SSRs) were identified with the proportion of SSRs ≥ 10 bp ranging from 55.32 to 66.23%. Comparative analyses indicated that five genes (clpP, matK, rbcL, rpoC and ycf1) underwent positive selection during evolution, and 13 hypervariable regions were recommended as potential molecular markers for distinguishing Caragana species. Phylogenetic analyses showed that the Caragana species were classified into two distinct clades and exhibited a close relationship with Hedysareae. These findings will greatly facilitate the further exploration of the phylogenetic development and adaptive evolution of Caragana species and also IRLC at the genomic scale.