Plastid genomes and phylogenomic relationships in Cheilosoideae, a poorly known early-diverging subfamily of Euphorbiaceae.

Cheilosoideae is the smallest and earliest-diverging of the four subfamilies of Euphorbiaceae, with seven species grouped in two morphologically similar paleotropical genera, Cheilosa and Neoscortechinia. The subfamily is distinguished by its unusual echinate pollen but their relationships remain poorly understood, with limited taxon sampling in prior evolutionary analyses. The present study, using newly generated whole plastome and nuclear ribosomal DNA (nrDNA) datasets, provides new insights into their molecular and morphological evolution. Our findings on the seven assembled Cheilosoideae plastomes reveal typical tetrad structure and length variation, with sizes ranging from 160,197 bp to 163,210 bp. Structural variations among plastomes generated distinct hotspots of repetitive sequences, particularly within tandem repeats and SSRs. Our phylogenetic analyses based on the plastome dataset resolved the four subfamilies (Cheilosoideae, Acalyphoideae, Crotonoideae, and Euphorbioideae) of Euphorbiaceae in successive sister relationships, although this result was partly inconsistent with an alternative topology based on the nrDNA dataset. Our study provides the first species-level phylogenetic framework for the Cheilosoideae. Both plastid and nuclear analyses strongly support an unexpected, slightly nested position of Cheilosa within a paraphyletic Neoscortechinia. Biogeographic analyses infer that Cheilosoideae probably originated from Southeast Asia and diversified since Middle Miocene (ca. 12.77 Ma). These results offer novel perspectives on the evolutionary history and biogeographic origins of Cheilosoideae within the Euphorbiaceae.