Complete chloroplast-based analysis reveals the emergence of candidate new species and revised divergence time in Vincetoxicum

Abstract Background The taxonomic understanding of Vincetoxicum remains unresolved due to the lack of genetic information for Vincetoxicum inamoenum . Vincetoxicum sp. was recently identified as a morphologically distinct putative new species related to V. inamoenum , increasing the necessity for a more accurate reconstruction of the taxonomic history of Vincetoxicum based on molecular and phylogenetic evidence from V. inamoenum and V. sp. Objective To assemble the complete chloroplast genomes of V . inamoenum and V . sp., elucidate their genetic divergence from 12 Vincetoxicum species, and determine the phylogenetic relationship and divergence time of the candidate new species of Vincetoxicum . Methods Complete chloroplast genomes of V. inamoenum and V . sp. were assembled. Repeat sequences, nucleotide diversity, and selective pressure between V. inamoenum and V . sp. were analyzed using 12 previously reported Vincetoxicum species. Phylogenetic analysis was performed to determine the phylogenetic position and divergence time. Results The chloroplast genomes of V. inamoenum and V . sp. were 160,787 and 160,849 base pairs long, respectively. Highly variable regions were identified between the two Vincetoxicum species ( accD-psaI ) and among the 14 Vincetoxicum species ( trnH-psbA ). The psaI , rpl33 and ycf2 genes exhibited positive selection. The phylogenetic tree showed that V. inamoenum and V . sp. formed a sister group and reconstructed the phylogenetic relationships within Vincetoxicum . Divergence time estimation indicated that V. inamoenum and V. sp. diverged approximately 1.182 million years ago (95% Highest Posterior Density: 0.181–2.751). Conclusions Distinct genetic differences and divergence time indicate that V . sp. is a putative new species and provide a more comprehensive and accurate understanding of the genomic diversity and phylogenetic insight into Vincetoxicum .