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

Article


Akond, Zobaer, Rahman, Hafizur, Ahsan, Md. Asif, Mosharaf, Md. Parvez, Alam, Munirul and Mollah, Md. Nurul Haque. 2022. "Comprehensive In Silico Analysis of RNA Silencing-Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.)." BioMed Research International. 2022. https://doi.org/10.1155/2022/4955209
Article Title

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

ERA Journal ID3417
Article CategoryArticle
AuthorsAkond, Zobaer, Rahman, Hafizur, Ahsan, Md. Asif, Mosharaf, Md. Parvez, Alam, Munirul and Mollah, Md. Nurul Haque
Journal TitleBioMed Research International
Journal Citation2022
Article Number4955209
Number of Pages26
Year2022
Place of PublicationUnited Kingdom
ISSN1110-7243
1110-7251
2314-6133
2314-6141
Digital Object Identifier (DOI)https://doi.org/10.1155/2022/4955209
Web Address (URL)https://www.hindawi.com/journals/bmri/2022/4955209/
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.

KeywordsCase-Control Studies; Gene Expression Regulation, Plant; Genes, Plant; Hormones; MicroRNAs; Phylogeny; Plant Proteins; RNA Interference; RNA, Small Interfering; RNA-Dependent RNA Polymerase; Stress, Physiological; Triticum
Contains Sensitive ContentDoes not contain sensitive content
Byline AffiliationsUniversity of Rajshahi, Bangladesh
Bangladesh Agricultural Research Institute, Bangladesh
School of Business
International Centre for Diarrheal Disease Research (ICDDRB), Bangladesh
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