Beyond the trinity: unraveling a fourth clade in the PEBP gene family in plants

Proposal for a new fourth PEBP gene group (SFT-like) in a genomic context different from 21 the other three. FT/TFL groups evolved from MFT, but then became sub-, neo-functionalized. The phosphatidylethanolamine-binding protein (PEBP) gene family plays crucial roles in plant development, principally involved in flowering time regulation and seed development. Traditionally, PEBP genes are classified into three clades: MOTHER OF FT AND TFL1 (MFT), FLOWERING LOCUS T (FT), and TERMINAL FLOWER 1 (TFL). We used phylogenomic and microsynteny network analyses to explore the PEBP family across 275 plant genomes from different lineages. The phylogenetic tree of the identified 3707 PEBP proteins allows us to visualize a fourth clade within the PEBP family. This new clade, named SFT (Sibling of FT/TFL), is closely related to the MFT clade but sister to the branch point of FT/TFL subfamilies, suggesting a long-standing evolutionary divergence. In addition, the SFT subfamily is in a different genomic context, whereas FT and TFL share a common origin with MFT. Motif analyzes show differences between this new clade and those already reported, suggesting functions other than flowering or seed development. The Ka/Ks analysis also suggests that SFT clade had fewer duplication events, so these genes could have an important function for the plant that had not yet been elucidated. These findings offer new insights into the evolutionary history and functional diversification of PEBP genes in plants. This study provides an update on the classification of the PEBP family. By understanding the syntenic relationships and evolutionary dynamics within the PEBP family, this research sets the stage for future functional studies on PEBP genes in plant biology, particularly the recently identified SFT clade.