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
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
复制标题
蔷薇科短营养期（SVP）基因的进化：谱系特异性基因复制事件和功能多样化对其在芽休眠以外过程中的作用的影响
DOI：
10.1002/tpg2.20053
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发表时间：
2020-09-17
期刊：
影响因子：
4.2
通讯作者：
Wang, Changquan
中科院分区：
文献类型：
--
作者：
Liu, Jinyi;Ren, Min;Wang, Changquan
MADS-box基因与拟南芥短营养期（SVP）基因同源，在多年生植物尤其是蔷薇科落叶果树芽休眠调控中发挥重要作用。然而，它们在蔷薇科的进化概况尚未得到系统的分析。在这里，与菊科一年生植物相比，蔷薇科植物中的SVPs基因被发现显著扩增。系统发育分析表明，蔷薇科植物SVP基因可分为5个分支，即SVP 1、SVP 2-R1、SVP 2-R2、SVP 2-R3和SVP 3。SVP 1进化枝基因在大多数物种中保留，而SVP 2-R2和SVP 2-R3进化枝分别被发现是马来族和扁桃族特有的（这两个谱系都属于扁桃亚科），而SVP 2-R1是蔷薇科蔷薇亚科特有的。此外，还发现了10个谱系特异性的基因重复（GD）事件（GD 1 -10），表明蔷薇科植物的SVP基因在进化过程中主要以谱系特异性的方式扩展和分化。此外，串联重复和片段重复是SVPs基因扩增的主要原因，有趣的是，串联重复，一个众所周知的SVPs基因的进化特征，被发现主要是扁桃科特有的。序列比对、选择压力和顺式作用元件分析表明，SVP基因在蔷薇科不同谱系中具有较大的功能创新和多样性。最后，不同的生长周期的多花蔷薇和他们的新的表达模式的RmSVP基因提供了新的见解SVP基因的功能多样性方面的作用，在其他过程中芽休眠。
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.