Novel perspectives on plastome evolution in Onagraceae

Previous systematic studies have generated abundant information on plants in family Onagraceae Juss., making this taxonomic group a model for understanding plant evolution. The chloroplast genome is widely used to provide valuable insights into how plant lineages evolved. In the present study, we employed shotgun sequencing to assemble new plastomes from Onagraceae. Plastomes of ten species and one genus, <i>Fuchsia</i>, are reported for the first time. We characterize and compare the plastome features of six genera (<i>Chamaenerion, Circaea</i>, <i>Epilobium</i>, <i>Fuchsia</i>, <i>Ludwigia</i>, and <i>Oenothera</i>), allowing us to reconstruct their phylogenies and explore inter- and infra-generic evolutionary relationships, inverted repeat (IR) expansion, plastome size increases, and correlations among repeat elements, genetic variations, and evolutionary events. Our findings indicate that each of the tribes and subfamilies we assessed exhibits unique plastome features. Our phylogenetic tree supports previous findings, but also reveals that some clades need further systematic analyses. We show that increased plastome size within subfamily Onagroideae coincides with IR expansion, which is not the case for subfamily Ludwigioideae. In addition, our results indicate that higher repeat numbers and greater genetic variation can serve as indicators of evolutionary events, such as gene loss and gain, IR boundary shifts, and inversions, but they may not have arisen universally across all members of Onagraceae. Our study provides some novel insights into plastome evolution in the Onagraceae. Further studies should aim to elucidate how plastome size has evolved in Ludwigioideae and explore the evolutionary roles of regions in Onagraceae plastomes exhibiting high repeat numbers and genetic variations.