Phylogenomics and adaptive evolution of hydrophytic umbellifers (tribe Oenantheae, Apioideae) revealed from chloroplast genomes

Abstract

Background Tribe Oenantheae consists mainly of aquatic species within the Apioideae. The unique morphology and habitat distinguish this group from other Apioideae groups. However, the genomic information of these group species has not been widely developed, and the molecular mechanisms of adaptive evolution remain unclear. Results We provide comparative analyses on 30 chloroplast genomes of this tribe representing five genera to explore the molecular variation response to plant adaptations. The Oenantheae chloroplast genomes presented typical quadripartite structures, with sizes ranging from 153,024 bp to 155,006 bp. Gene content and order were highly conserved with no significant expansion or contraction observed. Seven regions ( rps16 intron –trnK , rpoB – trnC , trnE – trnT – psbD , petA – psbJ , ndhF – rpl32 – trnL , ycf1a – rps15 , and ycf1a gene) were identified as remarkable candidate DNA markers for future studies on species identification, biogeography, and phylogeny of tribe Oenantheae. Our study elucidated the relationships among the genera of tribe Oenantheae and subdivided the genera of Sium and Oenanthe . However, relationships among the Oenanthe I clade remain to be further clarified. Eight positively selected genes ( accD , rbcL , rps8 , ycf1a , ycf1b , ycf2 , ndhF , and ndhK ) were persuasively detected under site models tests, and these genes might have played roles in Oenantheae species adaptation to the aquatic environments. Conclusions Our results provide sufficient molecular markers for the subsequent molecular studies of the tribe Oenantheae, and promote the understanding of the adaptation of the Oenantheae species to aquatic environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12870-024-05863-2.