Comprehensive Analysis of Dicer-Like, Argonaute, and RNA-dependent RNA Polymerase Gene Families in Grapevine (Vitis Vinifera)

Abstract

Regulation of gene expression is associated with RNA interference (RNAi) at the posttranscriptional level and chromatin modification in transcriptional silencing during plant development. Dicer-like (DCL) and Argonaute (AGO) proteins, along with RNA-dependent RNA polymerase (RDR), play integral roles in these processes. Many members of the DCL, AGO, and RDR gene families have been characterized in Arabidopsis, rice, maize, and tomato. However, little is known about these genes in grapevine. Here, we implemented a comprehensive bioinformatics analysis of the DCL, AGO, and RDR gene families in grapevine. In this study, a total of four VvDCL, thirteen VvAGO, and five VvRDR genes were identified in grapevine. These genes were categorized into four groups for each family based on phylogenetic analysis. Twenty-two genes were distributed across 11 chromosomes. We detected five segmental or tandem duplication events, which suggested their conserved functions during evolution. In each subfamily, protein motif composition was relatively conserved. The digital EST expression analyses provided a first glimpse of the expression patterns of DCL, AGO, and RDR gene in grapevine. It is worth mentioning that one gene, VvAGO10a, only expressed in the stem, which suggested that VvAGO10a may function in the regulation of siRNAs in the grapevine stem. Gene expression patterns during berry development and under different abiotic stresses were investigated utilizing microarray data. Thus, these detailed investigations provide a foundation for transcriptional silencing-associated gene families in grapevine for future functional genomics studies.