Evolutionary dynamics of Senna: Perspectives from plastome evolution and phylogenomics

Genus Senna (Caesalpinioideae, Fabaceae) comprises about 350 species mainly distributed in the American continent. Despite the sequencing and assembly of the chloroplast genome of some of the species in the genus, the chloroplast genome sequence and structural variation have not been evaluated, and the evolutionary relationship within the genus is still lacking. In this study, we sampled different species of the genus representing the six sections to examine the variation in the genome and phylogenetic relationships. The chloroplast genome of Senna has a typical quadripartite structure with a size ranging from 148, 437 bp to 162, 426 bp. There are gene losses in some species of the genus, the earliest diverged species lost 9 protein-coding genes which were recovered in the latter diverged lineages. No inversion was detected in the genome but there is a significant level of sequence variation, gene number, and genome size, that provide valuable information on the evolution of the genus. The following regions are the most variable regions in the genus and can be used as DNA barcodes for the identification of the species: Psba, ndhH, trnT-trnL, trnG-trnR, rps18-rpl20, and trnI-rrn16. The phylogenomic analysis revealed a well-resolved phylogenetic relationship of the genus, supporting the monophyly of the genus. The phylogenetic tree reported the phylogenetic positions and sister relationships of some species for the first time. Our result revealed that section Chameafistula is paraphyletic and calls for the revision of the infrageneric classification of the genus.