Comparative analysis of complete chloroplast genomes of five Anemone species and phylogenetic analysis within Tribe Anemoneae (Ranunculaceae)

Anemone plants (Ranunculaceae) are perennial, low-growing herbs that have a long history of traditional medicinal use. However, the phylogenetic relationship of Anemone species and the comprehensive study of the tribe Anemoneae have not been thoroughly examined due to the lack of available molecular resources. In this study, we conducted a comprehensive sequencing and characterization of the complete chloroplast genomes of Anemone species. These genomes exhibited typical quadripartite structures, ranging in length from 156,659 to 162,991 bp. We also identified several highly divergent intergenic regions (trnQ-UUG–psbK, trnfM-CAU–psbC, trnT-GGU–trnC-GCA, trnG-UCC–trnL-UAA, ndhC–trnM-CAU, psbE–petL, trnW-CCA–rpl33, rps12–trnV-GAC, and trnL-UAG–ndhF) and genes (rps16, ndhD, and ycf1) that could potentially serve as phylogenetic markers. We conducted phylogenetic analyses on 125 species from the tribe Anemoneae using chloroplast genome sequences. We obtained consistent topological structures and strong support for the backbone of phylogenetic relationships by employing maximum likelihood and Bayesian inference methods. Our findings suggest that Hepatica forms a monophyletic group, while Anemone s.l. is paraphyletic, based on the phylogenetic trees. Furthermore, the Hepatica + Anemone clade and the Anemoclema + Clematis clade exhibit a sister relationship. Overall, these results provide valuable genetic resources for the identification and phylogenetic studies of Anemone species.