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 SVP genes in different lineages of Rosaceae. Finally, the different growth cycle of Rosa multiflora and their novel expression patterns of RmSVP genes provided new insights into the functional diversification of SVP genes in terms of their roles in processes other than bud dormancy.

中文翻译：

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蔷薇科植物生长期（SVP）基因的进化：谱系特异性基因复制事件和功能多样化与其在芽休眠以外过程中的作用有关

与拟南芥短生植物阶段（SVP）同源的MADS-box基因已显示在多年生物种特别是酒渣鼻落叶果树的芽休眠调节中起关键作用。但是，尚未对它们在蔷薇科中的进化概况进行系统的分析。在这里，与来自十字花科的一年生物种相比，在蔷薇科中发现SVP基因显着扩增。系统发育分析表明，蔷薇科SVP基因可以分为五个进化枝，即SVP1，SVP2-R1，SVP2-R2，SVP2-R3和SVP3。SVP1进化枝基因保留在大多数物种中，而SVP2-R2和SVP2-R3进化枝分别是马来亚和扁桃体特有的（两个谱系都属于扁桃体），而SVP2-R1是蔷薇科。特定于蔷薇科。此外，提出了10个沿袭特异性基因复制（GD）事件（GD1–10）用于SVP基因的扩增，这表明蔷薇科SVP基因的扩增和分化主要是通过进化过程中沿袭特异性的方式产生的。此外，串联和分段重复是SVP扩展的主要原因有趣的是，SVP基因的一个众所周知的进化特征是串联重复，主要是扁桃体特有的。序列比对，选择压力和顺式作用元件分析表明，在蔷薇科不同谱系中，SVP基因具有重大的功能创新和多样化。最后，Rosa multiflora的不同生长周期及其新颖的RmSVP基因表达模式，为SVP基因在芽休眠以外的过程中发挥了作用提供了新的见解。