Comprehensive In Silico Analysis of RNA Silencing‐Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.)

Abstract

Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are known as the three major gene families that act as the critical components of RNA interference or silencing mechanisms through the noncoding small RNA molecules (miRNA and siRNA) to regulate the expressions of protein-coding genes in eukaryotic organisms. However, most of their characteristics including structures, chromosomal location, subcellular locations, regulatory elements, and gene networking were not rigorously studied. Our analysis identified 7 TaDCL, 39 TaAGO, and 16 TaRDR genes as RNA interference (RNAi) genes from the wheat genome. Phylogenetic analysis of predicted RNAi proteins with the RNAi proteins of Arabidopsis and rice showed that the predicted proteins of TaDCL, TaAGO, and TaRDR groups are clustered into four, eight, and four subgroups, respectively. Domain, 3D protein structure, motif, and exon-intron structure analyses showed that these proteins conserve identical characteristics within groups and maintain differences between groups. The nonsynonymous/synonymous mutation ratio Ka / Ks < 1 suggested that these protein sequences conserve some purifying functions. RNAi genes networking with TFs revealed that ERF, MIKC-MADS, C2H2, BBR-BPC, MYB, and Dof are the key transcriptional regulators of the predicted RNAi-related genes. The cis-regulatory element (CREs) analysis detected some important CREs of RNAi genes that are significantly associated with light, stress, and hormone responses. Expression analysis based on an online database exhibited that almost all of the predicted RNAi genes are expressed in different tissues and organs. A case-control study from the gene expression level showed that some RNAi genes significantly responded to the drought and heat stresses. Overall results would therefore provide an excellent basis for in-depth molecular investigation of these genes and their regulatory elements for wheat crop improvement against different stressors.

Identification and Expression Analysis of Key Gene Families in RNA Silencing and Their Responses to Heat Stress in Wheat (<em>Triticum aestivum</em>)

“…TaAGO18 subfamily was aligned with Z. mays and O. sativa. AGO18 ortholog proteins in the phylogenetic study, suggesting that both had comparable activities, similar results were reported in prior reports [32,33] .…”

“…However, there are slight variations between the TaDCL and their orthologues: (1) While rice and maize DCL1 PAZ and Dicer-dimer domains alter somewhat from those of TaDCL1, TaDCL1's domain organization is extremely similar to that of AtDCL1. This change may have taken place following the split between the rice and maize ancestor and the common ancestor of wheat and barley (roughly 60 million years ago) [14]; (2) the PAZ domain in monocot DCL2s (including wheat and barley) may have a modified structure, indicating a different folding and RNA binding [32,36]; and (3) upon analysis, we discovered a highly conserved DCL catalytic core within all DCLs (Figure 2b). Although dsRNA binding may change between DCL orthologs and paralogs, (4) unlike dicots, monocots have developed a fifth DCL, DCL5 [14].…”

“…These three gene families' members play key roles in the synthesis of sRNAs and the efficient silencing of their targets. In previous report analysis [32,33] RNA silencing gene family characterization in wheat using computational analysis. However, in the current study we have extended the comprehensive knowledge of RNA silencing gene in terms of stress responsive experimental validation.…”

Argonaute 1 and 5 proteins play crucial roles in the defence against cucumber green mottle mosaic virus in watermelon

“…The 11 ClRDR proteins were divided into four clades. Among the four groups, group I contained seven members, named ClRDR1a, ClRDR1b, ClRDR1c, ClRDR1d, ClRDR1e, ClRDR1f, and ClRDR1g (Figure S2b), which is consistent with the number of RDR1 proteins found in Triticum aestivum (Akond et al, 2022). However, four RDR1 proteins were identified in strawberry, which were also diploid (Jing et al, 2023), we speculate that this difference may be due to variation among different species.…”

Genome-wide identification, characterization and expression analysis of AGO, DCL, and RDR families in Chenopodium quinoa

“…To date, several studies have shown that the sizes of AGO , DCL , and RDR gene families vary among species. For example, Arabidopsis 14 , rice 15 , maize 16 , millet 17 , grapevine 18 , tomato 19 , wheat 20 , soybean 21 , pepper 22 , cucumber 23 , barley 24 , sugarcane 25 , sweet orange 6 , and tea 26 genomes encode ten, 19, 18, 19, 13, 15, 39, 21, 12, seven, 11, 21, eight, and 18 AGO genes; four, five, five, eight, four, seven, seven, seven, four, five, five, four, four, and five DCL genes; six, eight, five, 11, five, six, 16, seven, six, eight, seven, 11, four, and nine RDR genes, respectively. These studies have also shown that these gene families are highly conserved in plants, although little is known about the corresponding genes in quinoa.…”