Evolution of SHORT 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

Abstract

MADS-box genes that are homologous to Arabidopsis 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, The SVP genes were found to be significantly expanded in Rosaceae when compared with annual species from Brassicaceae. Phylogenetic analysis showed that Rosaceae SVP genes 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 of SVP genes, suggesting that the expansion and divergence of Rosaceae SVP genes were mainly derived by lineage-specific manner during evolution. Moreover, tandem and segmental duplications were the major reasons for the expansion of SVP genes, and interestingly, tandem duplications, a well-known evolutionary feature of SVP genes, were found to be mainly Amygdaloideae-specific. Sequence alignment, selection pressure, and cis-acting element analysis suggested large functional innovations and diversification of

Unraveling the role of MADS transcription factor complexes in apple tree dormancy using sequential DAP-seq

“…DAM TFs are phylogenetically related to SVP from Arabidopsis and, therefore, are often referred to as SVP-like TFs. Eudicots’ SVP-like proteins have been classified in three different clades, probably originated from a whole genome triplication [84,85]. Apple DAM TFs, together with other DAM proteins from peach, plum and pear, belong to a Rosaceae-specific clade that is separated from the cluster containing the Arabidopsis SVP, which also includes MdSVPa and MdSVPb [11,84,85].…”

“…Eudicots’ SVP-like proteins have been classified in three different clades, probably originated from a whole genome triplication [84,85]. Apple DAM TFs, together with other DAM proteins from peach, plum and pear, belong to a Rosaceae-specific clade that is separated from the cluster containing the Arabidopsis SVP, which also includes MdSVPa and MdSVPb [11,84,85]. It has been proposed that these two groups were originated by a lineage-specific whole genome duplication event [84,85].…”

“…Apple DAM TFs, together with other DAM proteins from peach, plum and pear, belong to a Rosaceae-specific clade that is separated from the cluster containing the Arabidopsis SVP, which also includes MdSVPa and MdSVPb [11,84,85]. It has been proposed that these two groups were originated by a lineage-specific whole genome duplication event [84,85]. The divergence between DAM and SVP TFs is partially caused by structural changes in the DNA-binding MADS domain [86,87], suggesting functional diversification between these two groups.…”

“…This seems not to be the case at least for the FLC-like TF studied in this work, as its expression pattern suggests a role related to ecodormancy and independent of cold requirement (Figure 2D, [5,46]). Moreover, during the evolution of the Rosaceae, SVP -like genes were expanded and several FLC -like genes were lost [84], favorizing the neofunctionalization of some SVP -like genes to take dormancy-related roles, and thus originating the MdDAM TFs. Indeed, in some non-Brassicaceae species, the FLC-like function is performed by distinct MADS TFs.…”

“…The oligomerization between MADS TFs is facilitated by their K domain (Keratin-like domain, a predicted coiled-coil) [33]. Interestingly, Rosaceae SVP-like TFs are highly variable in the K domain, which present a large number of potential positive selection sites [33,84]. Therefore, evolutionary forces might have contributed not only to originate a dormancy-specific group of TFs but also to combinatorial complexes that modulate the progression of dormancy in Rosaceae species.…”