Abstract
RNA silencing is mediated through RNA interference (RNAi) pathway gene families, i.e., Dicer-Like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) and their cis-acting regulatory elements. The RNAi pathway is also directly connected with the post-transcriptional gene silencing (PTGS) mechanism, and the pathway controls eukaryotic gene regulation during growth, development, and stress response. Nevertheless, genome-wide identification of RNAi pathway gene families such as DCL, AGO, and RDR and their regulatory network analyses related to transcription factors have not been studied in many fruit crop species, including banana (Musa acuminata). In this study, we studied in silico genome-wide identification and characterization of DCL, AGO, and RDR genes in bananas thoroughly via integrated bioinformatics approaches. A genome-wide analysis identified 3 MaDCL, 13 MaAGO, and 5 MaRDR candidate genes based on multiple sequence alignment and phylogenetic tree related to the RNAi pathway in banana genomes. These genes correspond to the Arabidopsis thaliana RNAi silencing genes. The analysis of the conserved domain, motif, and gene structure (exon-intron numbers) for MaDCL, MaAGO, and MaRDR genes showed higher homogeneity within the same gene family. The Gene Ontology (GO) enrichment analysis exhibited that the identified RNAi genes could be involved in RNA silencing and associated metabolic pathways. A number of important transcription factors (TFs), e.g., ERF, Dof, C2H2, TCP, GATA and MIKC_MADS families, were identified by network and sub-network analyses between TFs and candidate RNAi gene families. Furthermore, the cis-acting regulatory elements related to light-responsive (LR), stress-responsive (SR), hormone-responsive (HR), and other activities (OT) functions were identified in candidate MaDCL, MaAGO, and MaRDR genes. These genome-wide analyses of these RNAi gene families provide valuable information related to RNA silencing, which would shed light on further characterization of RNAi genes, their regulatory elements, and functional roles, which might be helpful for banana improvement in the breeding program.
Highlights
We identified three genes encoding DCL proteins (MaDCLs), 13 thirteen genes encoding AGO proteins (MaAGOs), and five genes encoding RNA-dependent RNA polymerase (RDR) proteins (MaRDRs) in the banana genome database based on the HMM profile analysis
3 DCL, 13 AGO, and 5 RDR RNA interference (RNAi) pathway genes were identified in the banana genome
Regulatory network and sub-network analysis were identified important transcription factors (TFs); ERF, Dof, C2H2, TCP, GATA and MIKC_MADS families, which are associated with MaDCL, MaAGO, and MaRDR genes
Summary
Small RNAs (sRNAs) are considered novel riboregulators These small regulatory RNAs are mainly of two types; microRNAs (miRNAs) and short interfering RNAs (siRNAs), both of which consist of 21–24 nucleotide and are generated from the synthesis processes of doublestranded RNAs (dsRNA) [1,2]. They play key roles in gene silencing by controlling messenger RNA (mRNA) stability, both (pre and post) translation process, or target epigenetic modifications to specific genome positions in plants, animals, and fungi [3]. DCL, AGO, and RDR genes are the main components of the sRNAs biogenesis process and RNAi pathway, triggering the gene silencing activities [10,11]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
