Evolution of Brassica genome post-polyploidization reveals asymmetrical genome fractionation and copy number variation. Herein, we describe the impact of promoter divergence among SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1) homeologs on expression and function in Brassica spp. SOC1, a regulated floral pathway integrator, is conserved as 3 redundant homeologs in diploid Brassicas. Even with high sequence identity within coding regions (92.8-100%), the spatio-temporal expression patterns of 9 SOC1 homologs in B. juncea and B. nigra indicates regulatory divergence. While LF and MF2 SOC1 homeologs are upregulated during floral transition, MF1 is barely expressed. Also, MF2 homeolog levels do not decline post-flowering, unlike LF. To investigate the underlying source of divergence, we analyzed the sequence and phylogeny of all reported (22) and isolated (21) upstream regions of Brassica SOC1. Full length upstream regions (4712-19189 bp) reveal 5 ubiquitously conserved ancestral Blocks, harboring binding sites of 18 TFs (TFBSs) characterized in Arabidopsis thaliana. The orthologs of these TFBSs are differentially conserved among Brassica SOC1 homeologs, imparting expression divergence. No crucial TFBSs are exclusively lost from LF_SOC1 promoter, while MF1_SOC1 has lost NF-Y binding site crucial for SOC1 activation by CONSTANS. MF2_SOC1 homeologs have lost important TFBSs (SEP3, AP1 and SMZ), responsible for SOC1 repression post-flowering. BjuAALF_SOC1 promoter (proximal 2 kb) shows ubiquitous reporter expression in B. juncea cv. Varuna transgenics, while BjuAAMF1_SOC1 promoter shows absence of reporter expression, validating the impact of TFBS divergence. Conservation of the original primary protein sequence is discovered in B. rapa homeologs (46) of 18 TFs. Co-regulation pattern of these TFs appeared similar for B. rapa LF and MF2 SOC1 homeologs; MF1 shows significant variation. Strong regulatory association is recorded for AP1, AP2, SEP3, FLC and CONSTANS/NF-Y, highlighting their importance in homeolog-specific SOC1 regulation. Correlation of B. juncea AP1, AP2 and FLC expression with SOC1 homeologs also complies with the TFBS differences. We thus conclude that redundant SOC1 loci contribute differentially to cumulative expression of SOC1 due to divergent selection of ancestral TFBSs.

中文翻译：

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由于启动子中进化保守的转录因子结合位点的分配，芸苔属SOC1的同源物（开花时间的中央调节剂）受到差异调节。

芸苔属基因组多倍体化的进化揭示了不对称的基因组分级分离和拷贝数变异。在这里，我们描述了过表达的CONSTANS1（SOC1）同源基因抑制子之间的启动子差异对芸苔属植物的表达和功能的影响。SOC1，一种受调节的花卉途径整合剂，在二倍体芸苔属植物中被保存为3个多余的同源物。即使在编码区内具有较高的序列同一性（92.8-100％），芥菜和黑芥菜中9个SOC1同源物的时空表达模式也表明调节差异。虽然LF和MF2 SOC1同源基因在花期过渡期间被上调，但MF1几乎没有表达。而且，与LF不同，MF2同源蛋白水平不会在花后下降。为了调查差异的根源，我们分析了芸苔属SOC1的所有报道的（22）和孤立的（21）上游区域的序列和系统发育。全长上游区域（4712-19189 bp）揭示了5个普遍保守的祖先区，具有拟南芥特有的18个TF（TFBS）的结合位点。这些TFBS的直系同源基因在芸苔属SOC1同源基因中差异保守，从而导致表达差异。没有重要的TFBS从LF_SOC1启动子中完全丢失，而MF1_SOC1丢失了对CONSTANS激活SOC1至关重要的NF-Y结合位点。MF2_SOC1同系物丢失了重要的TFBS（SEP3，AP1和SMZ），它们负责开花后SOC1的抑制。BjuAALF_SOC1启动子（近2 kb）显示在芥菜芽孢杆菌cv中普遍存在报告基因表达。Varuna转基因，而BjuAAMF1_SOC1启动子显示没有报告子表达，验证TFBS差异的影响。在18个TF的B. rapa同源基因（46）中发现了原始一级蛋白序列的保守性。这些TF的共同调控模式对于菜芥LF和MF2 SOC1同源物似乎相似; MF1显示出明显的变化。记录到AP1，AP2，SEP3，FLC和CONSTANS / NF-Y有很强的调节关联，突显了它们在特定同源物SOC1调节中的重要性。芥菜假单胞菌AP1，AP2和FLC表达与SOC1同源基因的相关性也符合TFBS差异。因此，我们得出结论，由于祖先TFBS的选择不同，冗余SOC1基因座对SOC1的累积表达有不同的贡献。这些TF的共同调控模式对于菜芥LF和MF2 SOC1同源物似乎相似; MF1显示出明显的变化。记录到AP1，AP2，SEP3，FLC和CONSTANS / NF-Y有很强的调节关联，突显了它们在特定同源物SOC1调节中的重要性。芥菜芽孢杆菌AP1，AP2和FLC表达与SOC1同源基因的相关性也符合TFBS差异。因此，我们得出结论，由于祖先TFBS的选择不同，冗余SOC1基因座对SOC1的累积表达有不同的贡献。这些TF的共同调控模式对于菜芥LF和MF2 SOC1同源物似乎相似; MF1显示出明显的变化。记录到AP1，AP2，SEP3，FLC和CONSTANS / NF-Y有很强的调节关联，突显了它们在特定同源物SOC1调节中的重要性。芥菜芽孢杆菌AP1，AP2和FLC表达与SOC1同源基因的相关性也符合TFBS差异。因此，我们得出结论，由于祖先TFBS的选择不同，冗余SOC1基因座对SOC1的累积表达有不同的贡献。AP2和FLC带有SOC1同源基因的表达也符合TFBS的差异。因此，我们得出结论，由于祖先TFBS的选择不同，冗余SOC1基因座对SOC1的累积表达有不同的贡献。AP2和FLC带有SOC1同源基因的表达也符合TFBS的差异。因此，我们得出结论，由于祖先TFBS的选择不同，冗余SOC1基因座对SOC1的累积表达有不同的贡献。