Genome-wide identification, organization and phylogenetic analysis of Dicer-like, Argonaute and RNA-dependent RNA Polymerase gene families and their expression analysis during reproductive development and stress in rice

Meenu Kapoor,Sanjay Kapoor,Jitendra P Khurana,Tenisha Lama,Aashima Nijhawan,Akhilesh K Tyagi,Rita Arora

doi:10.1186/1471-2164-9-451

Abstract

BackgroundImportant developmental processes in both plants and animals are partly regulated by genes whose expression is modulated at the post-transcriptional level by processes such as RNA interference (RNAi). Dicers, Argonautes and RNA-dependent RNA polymerases (RDR) form the core components that facilitate gene silencing and have been implicated in the initiation and maintenance of the trigger RNA molecules, central to process of RNAi. Investigations in eukaryotes have revealed that these proteins are encoded by variable number of genes with plants showing relatively higher number in each gene family. To date, no systematic expression profiling of these genes in any of the organisms has been reported.ResultsIn this study, we provide a complete analysis of rice Dicer-like, Argonaute and RDR gene families including gene structure, genomic localization and phylogenetic relatedness among gene family members. We also present microarray-based expression profiling of these genes during 14 stages of reproductive and 5 stages of vegetative development and in response to cold, salt and dehydration stress. We have identified 8 Dicer-like (OsDCLs), 19 Argonaute (OsAGOs) and 5 RNA-dependent RNA polymerase (OsRDRs) genes in rice. Based on phylogeny, each of these genes families have been categorized into four subgroups. Although most of the genes express both in vegetative and reproductive organs, 2 OsDCLs, 14 OsAGOs and 3 OsRDRs were found to express specifically/preferentially during stages of reproductive development. Of these, 2 OsAGOs exhibited preferential up-regulation in seeds. One of the Argonautes (OsAGO2) also showed specific up-regulation in response to cold, salt and dehydration stress.ConclusionThis investigation has identified 23 rice genes belonging to DCL, Argonaute and RDR gene families that could potentially be involved in reproductive development-specific gene regulatory mechanisms. These data provide an insight into probable domains of activity of these genes and a basis for further, more detailed investigations aimed at understanding the contribution of individual components of RNA silencing machinery during reproductive phase of plant development.

Highlights

Important developmental processes in both plants and animals are partly regulated by genes whose expression is modulated at the post-transcriptional level by processes such as RNA interference (RNAi)
The present investigation has been carried out with the aim to obtain comprehensive expression overview of all the members of rice Dicer-like, Argonaute and RNA-dependent RNA polymerases (RDR) gene families to gain insight into the domains of activity of these genes and to provide a firm foundation for further, more detailed investigations aimed at understanding the contribution of individual components of RNA silencing machinery in regulating gene expression during reproductive development of plants
Identification and structural organization of rice Dicerlike, Argonaute and RDR genes Name search using the keywords, Dicer, PAZ, PIWI, Argonaute and RNA-dependent RNA polymerase and Hidden Markov Model (HMM) analysis resulted in the identification of 8 genes encoding Dicer-like (OsDCL) proteins, 19 for Argonautes (OsAGO) and 5 genes for RDR (OsRDR) in the rice genome (TIGR rice pseudomolecule release 5)

Summary

Introduction

Important developmental processes in both plants and animals are partly regulated by genes whose expression is modulated at the post-transcriptional level by processes such as RNA interference (RNAi). Small RNAs have been widely implicated in varied developmental events and as guide RNAs in many gene silencing pathways [1,2,3,4,5,6] These RNAs are usually generated by the activities of Dicers, Argonautes and RNAdependent RNA polymerases (RDRs), which are sometimes referred to as the core proteins mediating RNA interference. One strand of these RNAs associates with the silencing effector complexes through the Argonaute proteins This confers sequence-specific guide functions to these complexes that find target RNAs with sequences complementary to the small RNAs. Silencing/repression of the target genes occurs by either blocking translation or cleavage of the target mRNA. These small RNAs could mediate transcriptional gene silencing by recruitment of histone and/or DNA methyltransferases to regulatory sequences of the target genes [8,9]

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