Evolution ofSHORT VEGETATIVE PHASE(SVP) genes in Rosaceae: Implications of lineage-specific gene duplication events and function diversifications with respect to their roles in processes other than bud dormancy

MADS-box genes that are homologous toArabidopsis SHORT VEGETATIVE PHASE(SVP) have been shown to play key roles in the regulation of bud dormancy in perennial species, particularly in the deciduous fruit trees of Rosaceae. However, their evolutionary profiles in Rosaceae have not yet been analyzed systematically. Here, TheSVPgenes were found to be significantly expanded in Rosaceae when compared with annual species from Brassicaceae. Phylogenetic analysis showed that RosaceaeSVPgenes could be classified into five clades, namely, SVP1, SVP2-R1, SVP2-R2, SVP2-R3 and SVP3. The SVP1 clade genes were retained in most of the species, whereas the SVP2-R2 and SVP2-R3 clades were found to be Maleae- and Amygdaleae-specific (Both of the lineages belong to Amygdaloideae), respectively, and SVP2-R1 was Rosoideae-specific in Rosaceae. Furthermore, 10 lineage-specific gene duplication (GD) events (GD1-10) were proposed for the expansion ofSVPgenes, suggesting that the expansion and divergence of RosaceaeSVPgenes were mainly derived by lineage-specific manner during evolution. Moreover, tandem and segmental duplications were the major reasons for the expansion ofSVPgenes, and interestingly, tandem duplications, a well-known evolutionary feature ofSVPgenes, were found to be mainly Amygdaloideae-specific. Sequence alignment, selection pressure, andcis-acting element analysis suggested large functional innovations and diversification ofSVPgenes in different lineages of Rosaceae. Finally, the different growth cycle ofRosa multifloraand their novel expression patterns ofRmSVPgenes provided new insights into the functional diversification ofSVPgenes in terms of their roles in processes other than bud dormancy.