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Background  Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though  PEBP  family genes have been well studied in  Arabidopsis  and other model species, less is known about these genes in perennial trees.    Results  To understand the evolution of  PEBP  genes and their functional roles in flowering control, we identified 56  PEBP  members belonging to three gene clades ( MFT -like,  FT -like, and  TFL1 -like) and five lineages ( FT ,  BFT ,  CEN ,  TFL1 , and  MFT ) across nine  Rosaceae  perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among  Rosaceae  PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of  FT -like and  TFL1 -like genes from the  MFT -like gene clade. Spatial and temporal expression analyses revealed the essential role of  FT  in regulating floral bud breaking and blooming in  P. mume . By employing a weighted gene co-expression network approach, we inferred a putative  FT  regulatory module required for dormancy release and blooming in  P. mume .    Conclusions  We have characterized the  PEBP  family genes in nine  Rosaceae  species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of  PEBP  genes and their functions in regulating floral bud development and blooming among  Rosaceae  tree species.

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume