Comparative and phylogenomic plastome analysis of the Physalideae tribe (Solanaceae)

The tribe Physalideae comprises two monophyletic subtribes, Iochrominae and Physalidinae, along with the polyphyletic Withaninae. However, consensus regarding phylogenetic relationships within and between subtribes remains elusive. To contribute to a better understanding of the evolutionary history and relationships among Physalideae species, we sequenced, assembled, and annotated the chloroplast genome of 15 species, reannotated 40 plastomes of Physalideae species available from GenBank, and conducted a comprehensive comparative phylogenomic analysis of the plastomes. The analyzed complete plastomes exhibit a quadripartite structure, with Iochrominae having a larger average size, followed by intermediate sizes in Physalidinae, and the smallest in Withaninae. The number of functional genes ranged from 112 to 114 per species, with Physalidinae consistently having 114. Plastome identity was generally high, with variation more pronounced in the Large Single Copy (LSC) and Small Single Copy (SSC) regions than in the Inverted Repeat (IR) and in non-coding regions compared to coding regions. We identify nine genes under positive selection, and their differential expression could optimize processes related to photosynthesis and ribosome self-replication. Phylogenomic analyses confirm that Iochrominae and Physalidinae are monophyletic. Withaninae may be monophyletic if the genera Cuatresia and Tubocapsicum are excluded from this subtribe. Within the tribe Physalideae, we observe no relation between plastome size, number of functional genes, or identity of positively selected genes with geographic distribution or life history traits. This decoupling suggests that distinct evolutionary forces are occurring within each species or groups of species.