Genome-wide Identification And Analysis Of WRKY Gene Family And MicroRNA In Cucumis Sativus

WRKY proteins are a large family of transcriptional regulators in higher plant. They are involved in many biological processes, such as plant development, metabolism, and responses to biotic and abiotic stresses. Prior to the present study, only one full-length cucumber WRKY protein had been reported. The recent publication of the draft genome sequence of cucumber allowed us to conduct a genome-wide search for cucumber WRKY proteins, and to compare these positively identified proteins with their homologs in model plants, such as Arabidopsis.We identified a total of55WRKY genes in the cucumber genome. According to structural features of their encoded proteins, the cucumber WRKY (CsWRKY) genes were classified into three groups (group1-3). Analysis of expression profiles of CsWRKY genes indicated that48WRKY genes display differential expression either in their transcript abundance or in their expression patterns under normal growth conditions, and23WRKY genes were differentially expressed in response to at least one abiotic stresses (cold, drought or salinity). The expression profile of stress-inducible CsWRKY genes were correlated with those of their putative Arabidopsis WRKY (AtWRKY) orthologs, except for the group3WRKY genes. Interestingly, duplicated group3AtWRKY genes appear to have been under positive selection pressure during evolution. In contrast, there was no evidence of recent gene duplication or positive selection pressure among CsWRKY group3genes, which may have led to the expressional divergence of group3orthologs.In plants, the interaction of Dicer-like proteins (DCLs), Argonautes (AGOs) and RNA-dependent RNA polymerases (RDRs) mediate the RNA silencing pathways triggered by small RNAs (siRNA and miRNA), which regulate gene expression by mediating gene silencing at transcriptional and post-transcriptional level. miRNA play a key role in development, abiotic stress responses or pathogen responses in plants.In this study, we conducted a genome-wide analysis to the members of the RNA silencing pathways in cucumber including miRNA, DCLs, AGOs and RDRs. We identified a total of four, six and seven DCLs, AGOS and RDRs proteins respectively in cucumber genome. Comparison and evolution analysis indicated that limited role played by the recent duplication events in the generation of DCLs, AGOS and RDRs proteins. However, the orthologs of some Arabidopsis AGOs (AtAGOs) seems have lost in cucumber genome. We further used deep-sequencing to identify the conserved and various cucumber tissues. A total of26conserved miRNA families were identified in cucumber. Due to the absence of recent duplication events, these cucumber miRNAs loci in gnome were much less than that of Arabidopsis. In addition, we also identified a total of127cucumber-special miRNA in cucumber genome. Interestingly, there was little similarity between cucumber-special miRNA with melon-special miRNA, although the divergence of these two allies of cucurbitaceae was less than4Myr. Finally,68target mRNAs of conseratived and54target mRNAs of new cucumber-specific miRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Furtherly, we used resequence data of cucumber to investigate the genetic diversity of miRNA locus. Our results indicated that the genetic diversity of conserative miRNA locus were lower than that of new miRNA significantly, and the genetic diversity of miRNA locus are lower than that of the sequence around of miRNA locus. Compared with the wild cucumber, the genetic diversity of domestical cucumber decreased significantly. We also detected the miRNA164and it's target genes under domestic selection.