title: 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.
abstract: BACKGROUND
  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). 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  This 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.
authors.affiliation: Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi-110021, India. kapoors@genomeindia.org
authors.forename: Meenu
authors.initials: M
authors.lastname: Kapoor
authors.forename: Rita
authors.initials: R
authors.lastname: Arora
authors.forename: Tenisha
authors.initials: T
authors.lastname: Lama
authors.forename: Aashima
authors.initials: A
authors.lastname: Nijhawan
authors.forename: Jitendra P
authors.initials: JP
authors.lastname: Khurana
authors.forename: Akhilesh K
authors.initials: AK
authors.lastname: Tyagi
authors.forename: Sanjay
authors.initials: S
authors.lastname: Kapoor
mesh_terms: D000595:Amino Acid Sequence; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D012324:RNA-Dependent RNA Polymerase / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D043244:Ribonuclease III / Q000145:classification / Q000235:genetics / Q000378:metabolism; D012260:Ribonucleases / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D012639:Seeds / Q000235:genetics; D016415:Sequence Alignment
chemical_list: D010940:Plant Proteins; D012324:RNA-Dependent RNA Polymerase; D012260:Ribonucleases; D043244:Ribonuclease III