Background: Plants contain numerous Su(var) 3-9 homologues (SUVH) and related (SUVR) genes, some of which await functional characterization. Although there have been studies on the evolution of plant Su(var) 3-9 SET genes, a systematic evolutionary study including major land plant groups has not been reported. Large-scale phylogenetic and evolutionary analyses can help to elucidate the underlying molecular mechanisms and contribute to improve genome annotation.

Results: Putative orthologs of plant Su(var) 3-9 SET protein sequences were retrieved from major representatives of land plants. A novel clustering that included most members analyzed, henceforth referred to as core Su(var) 3-9 homologues and related (cSUVHR) gene clade, was identified as well as all orthologous groups previously identified. Our analysis showed that plant Su(var) 3-9 SET proteins possessed a variety of domain organizations, and can be classified into five types and ten subtypes. Plant Su(var) 3-9 SET genes also exhibit a wide range of gene structures among different paralogs within a family, even in the regions encoding conserved PreSET and SET domains. We also found that the majority of SUVH members were intronless and formed three subclades within the SUVH clade.

Conclusions: A detailed phylogenetic analysis of the plant Su(var) 3-9 SET genes was performed. A novel deep phylogenetic relationship including most plant Su(var) 3-9 SET genes was identified. Additional domains such as SAR, ZnF_C2H2 and WIYLD were early integrated into primordial PreSET/SET/PostSET domain organization. At least three classes of gene structures had been formed before the divergence of Physcomitrella patens (moss) from other land plants. One or multiple retroposition events might have occurred among SUVH genes with the donor genes leading to the V-2 orthologous group. The structural differences among evolutionary groups of plant Su(var) 3-9 SET genes with different functions were described, contributing to the design of further experimental studies.