A comprehensive phylogenomic study of the monocot order Commelinales, with a new classification of Commelinaceae

Premise Resolving relationships within order Commelinales has posed quite a challenge, as reflected in its unstable infra-familial classification. Thus, we investigated: (1) relationships across families and genera of Commelinales; (2) phylogenetic placement of never-before sequenced genera; (3) integration of plastome data from off-target reads with existing plastome datasets; and (4) how do the novel inferencescoincide with infra-familial classification Methods We generated two large datasets (nuclear and plastome) by means of target sequence capture using the Angiosperms353 probe set, with additional sequences mined from publicly available transcriptomes and full plastomes. A third extended-plastid dataset was considered, including all species with sequences in public repositories. Species trees were inferred under a multispecies coalescent framework from individual gene trees, and also usingmaximum likelihood analyzes from concatenated and partitioned data. Results The nuclear, plastome, and extended-plastid datasets include 52, 53, and 58 genera, respectively, and up to 290 species of Commelinales, representing the most comprehensive molecular sampling made for the order to date, which includes seven never-before sequenced genera. Conclusions We inferred robust phylogenies supporting the monophyly of Commelinales and its five constituent families, and we recovered a Pontederiaceae-Haemodoraceae and a Hanguanaceae-Commelinaceae, as previously reported. The placement of Philydraceae remains contentious. Relationships within the two largest families, Commelinaceae and Haemodoraceae, are resolved. Based on the latter results, we confirm the subfamilial classification of Haemodoraceae and propose a new classification for Commelinaceae, which includes synonymization of Tapheocarpa in Commelina.