WRKY is a group of transcription factors (TFs) that play a vital role in plant growth, development, and stress tolerance. To date, none of jute WRKY (CcWRKY) genes have been identified, even if jute (Corchorus capsularis) is one of the most important natural fiber crops in the world. Little information about the WRKY genes in jute is far from sufficient to understand the molecular mechanism of bast fiber biosynthesis. A total of 244,489,479 clean reads were generated using Illumina paired-end sequencing. De novo assembly yielded 90,982 unigenes with an average length of 714 bp. By sequence similarity searching for known proteins, 48,896 (53.74%) unigenes were annotated. To mine the CcWRKY TFs and identify their potential function, the search for CcWRKYs against the transcriptome data of jute was performed, and a total of 43 CcWRKYs were identified in this study. The gene structure, phylogeny, conserved domain and three-dimensional structure of protein were analyzed by bioinformatics tools of GSDS2.0, MEGA7.0, DNAMAN5.0, WebLogo 3 and SWISS-MODEL respectively. Phylogenetic analysis showed that 43 CcWRKYs were divided into three groups: I, II and III, containing 9, 28, and 6 members respectively, according to the WRKY conserved domain features and the evolution analysis with Arabidopsis thaliana. Gene structure analysis indicated that the number of exons of these CcWRKYs varied from 3 to 11. Among the 43 CcWRKYs, 10, 2, 2, and 14 genes showed higher expression in leaves, stem sticks, stem barks, and roots at the vigorous vegetative growth stage, respectively. Moreover, the expression of 21 of 43 CcWRKYs was regulated significantly with secondary cell wall biosynthesis genes using FPKM and RT-qPCR by GA3 stress to a typical GA3 sensitive dwarf germplasm in comparison to an elite cultivar in jute. The Cis-element analysis showed that promoters of these 21 CcWRKYs had 1 to 4 cis-elements involved in gibberellin-responsiveness, suggesting that they might regulate the development of bast fiber in response to GA3 stress. A total of 43 CcWRKYs were identified in jute for the first time. Analysis of phylogenetic relationship and gene structure revealed that these CcWRKYs might have a functional diversity. Expression analysis showed 21 TFs as GA3 stress responsive genes. The identification of these CcWRKYs and the characterization of their expression pattern will provide a basis for future clarification of their functions in bast fiber development in jute.

中文翻译：

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转录组的从头组装和全基因组鉴定揭示了参与黄麻纤维形成的GA3胁迫响应性WRKY转录因子。

WRKY是一组转录因子（TF），在植物生长，发育和胁迫耐受性中起着至关重要的作用。迄今为止，即使黄麻（Corchorus荚膜猴）是世界上最重要的天然纤维作物之一，也未鉴定出黄麻WRKY（CcWRKY）基因。关于黄麻中WRKY基因的信息很少，不足以了解韧皮纤维生物合成的分子机制。使用Illumina的双末端测序，总共产生了244,489,479个干净的读数。从头组装产生90,982个单基因，平均长度为714 bp。通过序列相似性搜索已知的蛋白质，注释了48,896（53.74％）个单基因。为了挖掘CcWRKY TF并确定其潜在功能，针对黄麻的转录组数据进行了搜索CcWRKY，本研究共鉴定出43个CcWRKY。分别通过GSDS2.0，MEGA7.0，DNAMAN5.0，WebLogo 3和SWISS-MODEL等生物信息学工具分析了蛋白质的基因结构，系统发育，保守结构域和三维结构。系统进化分析表明，根据WRKY保守域特征和拟南芥的进化分析，将43个CcWRKYs分为三类：I，II和III，分别包含9、28和6个成员。基因结构分析表明，这些CcWRKY的外显子数量从3到11不等。在43个CcWRKY中，有10、2、2和14个基因在有营养的叶片，茎杆，茎皮和根中表达较高。分别处于成长期。此外，与黄麻优良品种相比，GA3胁迫典型的GA3敏感矮种质，利用FPKM和RT-qPCR通过二次细胞壁生物合成基因显着调节43个CcWRKYs中21个的表达。Cis元素分析表明，这21个CcWRKYs的启动子具有1至4个与赤霉素反应有关的顺式元件，表明它们可能响应GA3应激而调节韧皮纤维的发育。首次在黄麻中鉴定出总共43个CcWRKY。系统发育关系和基因结构分析表明，这些CcWRKYs可能具有功能多样性。表达分析显示21个TFs为GA3应激反应基因。