WRKY 转录因子 (TF) 在植物发育中发挥着重要作用。然而,尚未研究它们对地中海国家重要水果品种无花果 ( Ficus carica L.) 的影响。在这项研究中,我们从基因结构、蛋白质结构域和基序、理化特性、系统发育关系和选择压力方面广泛检查了全基因组F. carica WRKY ( FcWRKYs ) 基因补体(47 个基因)。根据编码蛋白的结构特性,我们将FcWRKY基因分为三个主要组(I、II 和 III),第二组进一步分为五个亚组(a-e)。亚组 IId FcWRKY 蛋白被发现含有植物锌簇 (Plant-zn-clust) 结构域和 Ca 2+依赖性钙调蛋白 (CaM) 结合结构域 (CaMBD)。总的来说,我们发现了十个保守基序,其中七个可能与单个群体或少数群体的 WRKY 功能特异性相关。系统发育相关的成员具有相似的外显子-内含子结构,与 IIc、IId、IIe 和 III(亚)组(亚组)相比,I、IIa、IIb(亚)组的外显子平均数量(约 5)更高(约 3)。使用桑WRKY基因互补体 ( MnWRKYs )的比较系统发育揭示了两个物种共有的 38 对直系同源基因,它们在 84.3 至 2530 万年前 (Mya) 之间分化,并且一直在第三组基因较弱的纯化选择下进化,这表明该组在扩大 WRKY TF 的自适应阵列中发挥着重要作用。RNA-seq结果显示,在所有果实发育阶段的果皮中高表达的基因属于I组和IIb、IIc、IId和IIe亚组,表明这些成员在果皮发育中发挥的作用。RT-qPCR 验证了这一图谱,并进一步表明,与浅紫色品种相比,在突尼斯深色品种“Zidi”的颜色采集过程中,三个基因FcWRKY25 (IIc)、FcWRKY31 (IIb) 和FcWRKY39 (IIc) 明显过度表达。 “Soltani”,提出这三个基因是果实成熟过程中无花果皮中生化化合物变化的潜在贡献者。我们的研究提供的知识框架将成为可能与水果品质相关的候选基因功能探索的宝贵资产。
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Genome-Level Investigation of WRKY Transcription Factors and Their Potential Roles in Fruit Peel Ripening and Coloration in the Common Fig (Ficus carica L.)
WRKY transcription factors (TFs) play significant roles in plant development. However, they have not yet been studied in terms of the impact they have on the common fig (Ficus carica L.), a significant fruit species in Mediterranean countries. In this study, we extensively examined the full-genome F. carica WRKY (FcWRKYs) gene complement (47 genes), in terms of gene structure, protein domains and motifs, physicochemical properties, phylogenetic relationships and selection pressure. Based on the structural properties of the encoded proteins, we grouped the FcWRKY genes into three main groups (I, II and III), with the second group being further divided into five subgroups (a–e). Subgroup IId FcWRKY proteins were discovered to contain the Plant zinc cluster (Plant-zn-clust) domain and Ca2+-dependent Calmodulin (CaM)-binding domain (CaMBD). In total, we discovered ten conserved motifs, seven of which may be associated with WRKY functional specificities attributable to a single group or a small number of groups. Phylogenetically related members shared similar exon–intron structure, with the average number of exons being higher (~ 5) in (sub)groups I, IIa, IIb compared to IIc, IId, IIe and III (~ 3). Comparative phylogeny using the mulberry WRKY gene complement (MnWRKYs) revealed 38 pairs of orthologous genes shared by both species, which diverged from 84.3 to 25.3 million years ago (Mya) and have been evolving under purifying selection that was weaker on group III genes, suggesting an important role of this group in the enlargement of the adaptive array of WRKY TFs. RNA-seq results revealed that genes that were highly expressed in the peel across all fruit developmental stages belonged to group I and subgroups IIb, IIc, IId and IIe, suggesting the role played by these members in fruit peel development. RT-qPCR validated this profile and further showed that three genes FcWRKY25 (IIc), FcWRKY31 (IIb), and FcWRKY39 (IIc) are clearly more overexpressed during color acquisition in the Tunisian dark cultivar ‘Zidi’, in comparison with the light purple cultivar ‘Soltani’, presenting these three genes as potential contributors to the changes in biochemical compounds in the fig peel during fruit maturation. The knowledge framework provided by our study will be a valuable asset in the functional exploration of candidate genes that may be associated with fruit quality.