Comparative phylogenomic study of East Asian endemic genus, Corchoropsis Siebold & Zucc. (Malvaceae s.l.), based on complete plastome sequences

Abstract

Background Endemic plants are key to understanding the evolutionary history and enhancing biodiversity within their unique regions, while also offering significant economic potential. The East Asian endemic genus Corchoropsis Siebold & Zucc., classified within the subfamily Dombeyoideae of Malvaceae s.l., comprises three species. Results This study characterizes the complete plastid genomes (plastomes) of C . crenata var. crenata Siebold & Zucc. and C . crenata var. hupehensis Pamp., which range from 160,093 to 160,724 bp. These genomes contain 78 plastid protein-coding genes, 30 tRNA, and four rRNA, except for one pseudogene, inf A. A total of 316 molecular diagnostic characters (MDCs) specific to Corchoropsis were identified. In addition, 91 to 92 simple sequence repeats (SSRs) in C . crenata var. crenata and 75 in C . crenata var. hupehensis were found. Moreover, 49 long repeats were identified in both the Chinese C . crenata var. crenata and C . crenata var. hupehensis , while 52 were found in the South Korean C . crenata var. crenata . Our phylogenetic analyses, based on 78 plastid protein-coding genes, reveal nine subfamilies within the Malvaceae s.l. with high support values and confirm Corchoropsis as a member of Dombeyoideae. Molecular dating suggests that Corchoropsis originated in the Oligocene, and diverged during the Miocene, influenced by the climate shift at the Eocene–Oligocene boundary. Conclusions The research explores the evolutionary relationships between nine subfamilies within the Malvaceae s.l. family, specifically identifying the position of the Corchoropsis in the Dombeyoideae. Utilizing plastome sequences and fossil data, the study establishes that Corchoropsis first appeared during the Eocene and experienced further evolutionary divergence during the Miocene, paralleling the evolutionary patterns observed in other East Asian endemic species. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-024-10725-0.