Data_Sheet_1_Transcriptome Analysis Reveals Putative Target Genes of APETALA3-3 During Early Floral Development in Nigella damascena L..xlsx

Even though petals are homoplastic structures, their identity consistently involves genes of the APETALA3 (AP3) lineage. However, the extent to which the networks downstream of AP3 are conserved in species with petals of different evolutionary origins is unknown. In Ranunculaceae, the specificity of the AP3-III lineage offers a great opportunity to identify the petal gene regulatory network in a comparative framework. Using a transcriptomic approach, we investigated putative target genes of the AP3-III ortholog NdAP3-3 in Nigella damascena at early developmental stages when petal identity is determined, and we compared our data with that from selected eudicot species. We generated a de novo reference transcriptome to carry out a differential gene expression analysis between the wild-type and mutant NdAP3-3 genotypes differing by the presence vs. absence of petals at early stages of floral development. Among the 1,620 genes that were significantly differentially expressed between the two genotypes, functional annotation suggested a large involvement of nuclear activities, including regulation of transcription, and enrichment in processes linked to cell proliferation. Comparing with Arabidopsis data, we found that highly conserved genes between the two species are enriched in homologs of direct targets of the AtAP3 protein. Integrating AP3-3 binding site data from another Ranunculaceae species, Aquilegia coerulea, allowed us to identify a set of 18 putative target genes that were conserved between the three species. Our results suggest that, despite the independent evolutionary origin of petals in core eudicots and Ranunculaceae, a small conserved set of genes determines petal identity and early development in these taxa.

尽管花瓣是同质结构，但其身份的确定始终涉及APETALA3 (AP3)谱系的基因。然而，在花瓣具有不同进化起源的物种中，AP3下游网络的保守程度尚不清楚。在毛茛科中，AP3-III谱系的特异性为在比较框架下识别花瓣基因调控网络提供了极佳的机会。采用转录组学方法，我们研究了在花瓣身份确定的关键发育阶段，拟南芥中AP3-III直系同源基因NdAP3-3的潜在靶基因，并将其与选定的双子叶植物物种的数据进行了比较。我们生成了一组新的参考转录组，以对野生型和突变型NdAP3-3基因型（在花蕾发育早期阶段花瓣的有无）进行差异基因表达分析。在两个基因型之间存在显著差异表达的1,620个基因中，功能注释表明核活动（包括转录调控）的广泛参与以及与细胞增殖相关的过程的富集。与拟南芥数据相比，我们发现两个物种之间高度保守的基因富集在AtAP3蛋白的直接靶基因的同源物中。整合来自另一毛茛科物种，蓝花鸢尾（Aquilegia coerulea）的AP3-3结合位点数据，使我们能够鉴定出一组在三个物种中保守的18个潜在靶基因。我们的结果表明，尽管核心双子叶植物和毛茛科花瓣的进化起源独立，但一小部分保守的基因集合决定了这些类群中花瓣的身份和早期发育。