| Cucumber(Cucumis sativus L.) is the main vegetables in China and one of the ten major vegetables in the world. Post-transcriptional control of gene expression can be achieved through RNA interference when the activities of DCL, AGO and RDR proteins are significant. DCL, AGO and RDR comprise the core components of RNA-induced silencing complexes, which trigger RNA silencing. Bioinformatics analysis of CsAGOs, CsDCLs, CsRDRs, including the basic information about Dicer-like, Argonaute and RDR proteins in cucumber and primer sequences used for real-time quantitative PCR; physical locations; domain distribution; distribution of 10 conserved motifs; intron–exon organization; selection pressure analysis; Heat-map of the expression pattern and phylogenetic relationships of cucumber and other species Dicer-like, Argonaute and RDR genes. In the same time, we study the sequence characterization analysis and expression of AGO, RDR, DCL gene under abiotic stresses in cucumber. The main results are summarized as follow:1. Seven CsAGOs, five CsDCLs and eight CsRDRs genes are distributed on six chromosomes, with variable distribution. The three conserved domains, DUF, PAZ and Piwi, are present in all CsAGO proteins. Most CsDCL proteins have six types of conserved domains. Finally, all CsRDR proteins contain the conserved Rd RP domain. Ten major motifs were detected in all CsDCL proteins. Only three of the seven CsAGO proteins contain all ten major motifs, most CsRDR proteins contain all ten motifs. The intron–exon organization shows that most CsAGOs have more than six introns, and most CsRDRs have three introns. By contrast, all CsDCLs have more than 20 introns.2. Orthologs of CsAGO, CsDCL and CsRDR proteins were identified in apple, peach, wild strawberry, maize and foxtail millet. Among seven CsAGO genes, the ollinearity pattern of four AGO genes with peach, five with wild strawberry and three with foxtail millet. Meanwhile, of the five CsDCL genes, two are present in peach, four in maize and fourin foxtail millet, while there is no gene is found in apple and wild strawberry. Similarly, CsRDR genes showed the syntenic relationship with four RDR genes with peach. Based on phylogenetic analysis, CsAGO gene families were categorized into five clades, while CsDCL and CsRDR gene families were categorized into four clades.3. Heat-map of the expression patterns indicate that CsAGO1 a and CsAGO4 expressed highly in all the six tissues. Tissue-specific higher expression of CsAGO1 b, CsAGO1 c and CsAGO7 was observed inleaf. In particular, all CsDCLs were predominantly expressed in tendril at lower levels, whereas all the CsDCLs showed moderate expression in other tissues. Among CsRDRs, higher expression of CsRDR1 a and CsRDR1 b were evidenced in most of the tissues especially in root, while CsRDR1 d and CsRDR1 e showed a relatively lower expression in most tissues.4. Total RNA were extracted from five organs of cucumber under salinity, dehydration, cold, heat and hormone treatments. Then we analyzed the expression of seven AGO, five DCL and eight RDR genes using q RT-PCR after reverse transcription. CsDCLs, CsAGOs and CsRDRs were similarly expressed in response to salinity, cold, heat and ABA treatments. Most of the genes were expressed at higher levels in flowers or stems than in other organs, whereas most CsAGOs were highly expressed in roots and most CsDCLs expressed highly in flowers during dehydration treatment. In addition, almost all CsRDRs were relatively higher upregulation in roots or flowers, while few CsRDRs expressed highly in stems.In conclusion, Genome-wide analysis and the expression of CsDCLs, CsAGOs and CsRDRs family genes under abiotic stress are analyzed in cucumber, which provides basic information and insights into the putative roles of these genes in abiotic stress. The results of this study will serve as a basis for further functional characterization of these gene families, and will also facilitate further studies of gene silencing pathways. |
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