Plastome evolution and phylogenomic insights into the evolution of the African submerged endemic genus Lagarosiphon (Hydrocharitaceae)

The genus Lagarosiphon, a remarkable group of fully submerged plants within the family Hydrocharitaceae, is native to tropical Africa. However, the phylogenetic relationships among its species have long remained elusive due to a lack of molecular data. In this study, we assembled and compared the plastomes of three Lagarosiphon species from Africa. By integrating additional data from public databases, we reconstructed the phylogeny and evolutionary history of the genus. Our results revealed that the plastomes of Lagarosiphon were conserved but exhibited notable length variation, likely due to the accumulation of dispersed repeats. Furthermore, we found that nucleotide diversity in the intergenic spacer regions was significantly higher than in the protein-coding genes. Such regions as ycf1, infA, rpl23-trnI-CAU, and ycf1-ndhF were recognized as mutation hotspots, highlighting their potential as important markers for future population genetics and phylogenetic studies. Phylogenomic analysis strongly supported Lagarosiphon as a monophyly, with the most recent common ancestor estimated to have occurred around 29.95 Ma. The diversification of this genus in Africa is likely a response to rapid climatic and geological changes during the Miocene. Our study provides valuable molecular resources for the taxonomic and phylogenomic investigation of the genus Lagarosiphon.