Bi Changwei, Xu Yiqing, Ye Qiaolin, Yin Tongming, Ye Ning
College of Information Science and Technology, Nanjing Forestry University , Nanjing, Jiangsu , China.
College of Forest Resources and Environment, Nanjing Forestry University , Nanjing, Jiangsu , China.
PeerJ. 2016 Sep 7;4:e2437. doi: 10.7717/peerj.2437. eCollection 2016.
WRKY proteins are the zinc finger transcription factors that were first identified in plants. They can specifically interact with the W-box, which can be found in the promoter region of a large number of plant target genes, to regulate the expressions of downstream target genes. They also participate in diverse physiological and growing processes in plants. Prior to this study, a plenty of WRKY genes have been identified and characterized in herbaceous species, but there is no large-scale study of WRKY genes in willow. With the whole genome sequencing of Salix suchowensis, we have the opportunity to conduct the genome-wide research for willow WRKY gene family. In this study, we identified 85 WRKY genes in the willow genome and renamed them from SsWRKY1 to SsWRKY85 on the basis of their specific distributions on chromosomes. Due to their diverse structural features, the 85 willow WRKY genes could be further classified into three main groups (group I-III), with five subgroups (IIa-IIe) in group II. With the multiple sequence alignment and the manual search, we found three variations of the WRKYGQK heptapeptide: WRKYGRK, WKKYGQK and WRKYGKK, and four variations of the normal zinc finger motif, which might execute some new biological functions. In addition, the SsWRKY genes from the same subgroup share the similar exon-intron structures and conserved motif domains. Further studies of SsWRKY genes revealed that segmental duplication events (SDs) played a more prominent role in the expansion of SsWRKY genes. Distinct expression profiles of SsWRKY genes with RNA sequencing data revealed that diverse expression patterns among five tissues, including tender roots, young leaves, vegetative buds, non-lignified stems and barks. With the analyses of WRKY gene family in willow, it is not only beneficial to complete the functional and annotation information of WRKY genes family in woody plants, but also provide important references to investigate the expansion and evolution of this gene family in flowering plants.
WRKY蛋白是最早在植物中发现的锌指转录因子。它们能够特异性地与W-box相互作用，W-box存在于大量植物靶基因的启动子区域，从而调控下游靶基因的表达。它们还参与植物的多种生理和生长过程。在本研究之前，已经在草本物种中鉴定并表征了大量WRKY基因，但尚未对柳树中的WRKY基因进行大规模研究。随着苏柳全基因组测序的完成，我们有机会对柳树WRKY基因家族进行全基因组研究。在本研究中，我们在柳树基因组中鉴定出85个WRKY基因，并根据它们在染色体上的特定分布将其重新命名为SsWRKY1至SsWRKY85。由于其多样的结构特征，这85个柳树WRKY基因可进一步分为三个主要组（I-III组），其中II组有五个亚组（IIa-IIe）。通过多序列比对和人工搜索，我们发现了WRKYGQK七肽的三种变体：WRKYGRK、WKKYGQK和WRKYGKK，以及正常锌指基序的四种变体，它们可能执行一些新的生物学功能。此外，来自同一亚组的SsWRKY基因具有相似的外显子-内含子结构和保守基序结构域。对SsWRKY基因的进一步研究表明，片段重复事件（SDs）在SsWRKY基因的扩增中发挥了更突出的作用。利用RNA测序数据对SsWRKY基因的不同表达谱分析表明，在嫩根、幼叶、营养芽、未木质化茎和树皮这五个组织中存在多种表达模式。通过对柳树WRKY基因家族的分析，不仅有助于完善木本植物中WRKY基因家族的功能和注释信息，也为研究该基因家族在开花植物中的扩增和进化提供重要参考。
