In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.)

Article


Mosharaf, Md. Parvez, Rahman, Hafizur, Ahsan, Md. Asif, Akond, Zobaer, Ahmed, Fee Faysal, Islam, Md. Mazharul, Moni, Mohammad Ali and Mollah, Md. Nurul Haque. 2020. "In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.)." PLoS One. 15 (12 December). https://doi.org/10.1371/journal.pone.0228233
Article Title

In silico identification and characterization of AGO, DCL and RDR gene families and their associated regulatory elements in sweet orange (Citrus sinensis L.)

ERA Journal ID39745
Article CategoryArticle
AuthorsMosharaf, Md. Parvez, Rahman, Hafizur, Ahsan, Md. Asif, Akond, Zobaer, Ahmed, Fee Faysal, Islam, Md. Mazharul, Moni, Mohammad Ali and Mollah, Md. Nurul Haque
Journal TitlePLoS One
Journal Citation15 (12 December)
Article Numbere0228233
Number of Pages33
Year2020
PublisherPublic Library of Science (PLoS)
Place of PublicationUnited States
ISSN1932-6203
Digital Object Identifier (DOI)https://doi.org/10.1371/journal.pone.0228233
Web Address (URL)https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0228233
Abstract

RNA interference (RNAi) plays key roles in post-transcriptional and chromatin modification levels as well as regulates various eukaryotic gene expressions which are involved in stress responses, development and maintenance of genome integrity during developmental stages. The whole mechanism of RNAi pathway is directly involved with the gene-silencing process by the interaction of Dicer-Like (DCL), Argonaute (AGO) and RNA-dependent RNA polymerase (RDR) gene families and their regulatory elements. However, these RNAi gene families and their sub-cellular locations, functional pathways and regulatory components were not extensively investigated in the case of economically and nutritionally important fruit plant sweet orange (Citrus sinensis L.). Therefore, in silico characterization, gene diversity and regulatory factor analysis of RNA silencing genes in C. sinensis were conducted by using the integrated bioinformatics approaches. Genome-wide comparison analysis based on phylogenetic tree approach detected 4 CsDCL, 8 CsAGO and 4 CsRDR as RNAi candidate genes in C. sinensis corresponding to the RNAi genes of model plant Arabidopsis thaliana. The domain and motif composition and gene structure analyses for all three gene families exhibited almost homogeneity within the same group members. The Gene Ontology enrichment analysis clearly indicated that the predicted genes have direct involvement into the gene-silencing and other important pathways. The key regulatory transcription factors (TFs) MYB, Dof, ERF, NAC, MIKC_MADS, WRKY and bZIP were identified by their interaction network analysis with the predicted genes. The cis-acting regulatory elements associated with the predicted genes were detected as responsive to light, stress and hormone functions. Furthermore, the expressed sequence tag (EST) analysis showed that these RNAi candidate genes were highly expressed in fruit and leaves indicating their organ specific functions. Our genome-wide comparison and integrated bioinformatics analyses provided some necessary information about sweet orange RNA silencing components that would pave a ground for further investigation of functional mechanism of the predicted genes and their regulatory factors.

KeywordsArgonaute Proteins; Citrus sinensis; Computer Simulation; Expressed Sequence Tags; Fruit; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; Genome, Plant; Multigene Family; Phylogeny; Plant Proteins; Regulatory Sequences, Nucleic Acid; Ribonuclease III; RNA Interference; RNA-Dependent RNA Polymerase; Transcription Factors
Contains Sensitive ContentDoes not contain sensitive content
Byline AffiliationsUniversity of Rajshahi, Bangladesh
Bangladesh Agricultural Research Institute, Bangladesh
Jashore University of Science and Technology, Bangladesh
University of Sydney
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