Molecular characterization and expression of PPDs in strawberry
To gain insights into the existence of non-JAZ TIFY proteins in strawberry, we characterized inferred amino acid sequences containing conserved domains for TIFY and Jas. In this sense, we identified two PEAPOD (PPD) genes in F. vesca genome using AtPPD ortholog protein sequences as queries (S1 Table), named as FvPPD1-1 and FvPPD1-2 according to the gene nomenclature proposed for the Rosaceae [44]. We compared exon-intron structures between F. vesca and A. thaliana PPD genes and observed that FvPPD1-1 and FvPPD1-2 have an extra intron and longer introns in comparison to those of A. thaliana orthologs (Panel A in S5 Fig). FvPPDs proteins showed conserved position of PPD, TIFY and degenerated Jas domains respect to those present in AtPPD proteins (Panel B in S5 Fig) along with a high identity sequence as we observed from multiple sequence alignment analysis (Panel C in S5 Fig). Additionally, we constructed a phylogenetic tree that showed evolutionary relationships between FvPPDs and A. thaliana, M. x domestica, V. vinifera and S. lycopersicum orthologs (Panel D in S5 Fig). TIFY family was characterized in O. sativa, however PPDs were not reported [45]. FvPPD1-1 and FvPPD1-2 were clustered along with MdPPDs and VvPPD1 in group II (Panel D in S5 Fig). Finally, we determined the relative expression levels of FaPPD1-1, displaying a decreasing pattern during fruit development and ripening (Panel E in S5 Fig) as we observed for most of the JA signalling-related genes in strawberry.