Decoding the complete chloroplast genome of Cissus quadrangularis: insights into molecular structure, comparative genome analysis and mining of mutational hotspot regions

Cissus quadrangularis L., a member of the Vitaceae family, is an important medicinal plant with widespread application in Indian traditional medicines. C. quadrangularis L. whole chloroplast genome of 160,404 bp was assembled using a genome skimming approach from the whole genome library. The assembled chloroplast genome contained a large single-copy region (88,987 bp), a small single-copy region (18,621 bp), and pairs of inverted repeat regions (26,398 bp). It also comprised 133 genes, including 37 tRNAs, eight rRNAs, and 88 protein-coding genes. Aside from that, we annotated three genes atpH, petB, and psbL, as well as one duplicated copy of the ycf1 gene in C. quadrangularis L. that had previously been missing from the annotation of compared Cissus chloroplast genomes. Five divergent hotspot regions such as petA_psbJ (0.1237), rps16_trnQ-UUG (0.0913), psbC_trnS-UGA (0.0847), rps15_ycf1 (0.0788), and rps2_rpoC2 (0.0788) were identified in the investigation that could aid in future species discrimination. Surprisingly, we found the overlapping genes ycf1 and ndhF on the IRb/SSC junction, rarely seen in angiosperms. The results of the phylogenetic study showed that the genomes of the Cissus species under study formed a single distinct clade. The detailed annotations given in this study could be useful in the future for genome annotations of Cissus species. The current findings of the study have the potential to serve as a useful resource for future research in the field of population genetics and the evolutionary relationships in the Cissus genus.

Supplementary information: The online version contains supplementary material available at 10.1007/s12298-023-01312-w.