TY - JOUR T1 - <em>In Silico</em> Identification, Characterization and Diversity Analysis of RNAi Genes and their Associated Regulatory Elements in Sweet Orange (<em>Citrus sinensis L</em>) JF - bioRxiv DO - 10.1101/2020.01.13.904128 SP - 2020.01.13.904128 AU - Md. Parvez Mosharaf AU - Md. Asif Ahsan AU - Hafizur Rahman AU - Zobaer Akond AU - Fee Faysal Ahmed AU - Md. Mazharul Islam AU - Mohammad Ali Moni AU - Md. Nurul Haque Mollah Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/01/13/2020.01.13.904128.abstract N2 - RNA interference (RNAi) plays key roles in post-transcriptional and chromatin modification levels as well as regulates various eukaryotic gene expressions which 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. However, the genes of these three RNAi families are largely unknown yet in sweet orange (Citrus sinensis), though it is an economically important fruit plant all over the world. Therefore, a comprehensive investigation for genome-wide identification, characterization and diversity analysis of RNA silencing genes in C. sinensis was conducted and identified 4 CsDCL, 8 CsAGO and 4 CsRDR as RNAi genes. To characterize and validate the predicted genes of RNAi families, various bioinformatics analysis was conducted. Phylogenetic analysis clustered the predicted CsDCLs, CsAGOs and CsRDRs genes into four, six and four subgroups with the relevant genes of Arabidopsis respectively. The domain and motif composition analysis, the gene structure for all three-gene families exhibited almost homogeneity within the same group members while showed significant differences in between groups. The GO enrichment analysis results clearly indicated that the predicted genes have direct involvement into the RNAi process as expected in C. sinensis. Moreover, Cis-regulatory elements and regulatory transcription factor analysis of the reported RNAi genes demonstrated the diverse connection to the huge biological functions and regulatory pathways. The expressed sequence tag (EST) analysis showed that these genes are highly expressed in fruit and leaves which indicate that these reported genes have great involvement in C. sinensis food, flowering and fruit production. The expression analysis of the reported RNAi genes might be more useful to explore the most effective RNAi genes in C. sinensis for further biotechnological application.AGOArgonauteBLASTBasic Local Alignment Search Toolbpbase pairDCLDicer-LikeGOGene OntologyGSDSGene Structure Display ServerHMMHidden Markov ModelMEMEMultiple Em for Motif ElicitationmiRNAmicroRNAPTGSpost-transcriptional gene silencingRDRRNA, dependent RNA polymeraseRNAiRNA interferenceRISCRNA-induced silencing complexsRNAsmall RNAsiRNAshort interfering RNATFtranscription factorTGStranscriptional gene silencing ER -