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

Md Parvez Mosharaf,Hafizur Rahman,Md Asif Ahsan,Fee Faysal Ahmed,Mohammad Ali Moni,Md Nurul Haque Mollah,Zobaer Akond,Md Mazharul Islam,Branislav T Šiler

doi: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.

Highlights

IntroductionWide range of biological functions including genome rearrangement, antiviral defense, heterochromatin formation and development patterning and timing are fine-tuned by generally two types of small RNA (sRNA; including 21–24 nucleotides), named microRNA (miRNA) and short interfering RNA (siRNA) [1,2,3]
In multicellular eukaryotes, wide range of biological functions including genome rearrangement, antiviral defense, heterochromatin formation and development patterning and timing are fine-tuned by generally two types of small RNA, named microRNA and short interfering RNA [1,2,3]
To identify the best candidates of RNA interference (RNAi) related pathway in C. sinensis similar to the A. thaliana, all the previously downloaded sequences were gone through various kinds of analysis (Fig 1)

Summary

Introduction

Wide range of biological functions including genome rearrangement, antiviral defense, heterochromatin formation and development patterning and timing are fine-tuned by generally two types of small RNA (sRNA; including 21–24 nucleotides), named microRNA (miRNA) and short interfering RNA (siRNA) [1,2,3] These sRNA molecules are involved in both transcriptional and post-transcriptional gene silencing as well as natural immunity system [2, 4,5,6,7]. The specification to the endonucleasecontaining, RNA-induced silencing complex (RISC) is provided by these sRNAs which facilitate the AGO proteins with RNaseH-type activities to degrade the target homologous RNAs with the sequence complementary to the small RNAs [14, 15] These are involved in the transcriptional gene silencing by the implementation of chromatin reformation [16, 17]

Methods

Results

Conclusion