title: Phylogenetic distribution of plant snoRNA families.
abstract: Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention.
  
  
  
  In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families.
  
  
  
  The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation.
authors.affiliation: Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany.|Institut für Informatik, Halle (Saale), D-06120, Germany.
authors.forename: Deblina
authors.initials: D
authors.lastname: Patra Bhattacharya
authors.affiliation: Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Canzler
authors.affiliation: Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Kehr
authors.affiliation: Young Investigators Group Bioinformatics & Transcriptomics, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, D-04318, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Hertel
authors.affiliation: Institut für Informatik, Halle (Saale), D-06120, Germany.|German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany.
authors.forename: Ivo
authors.initials: I
authors.lastname: Grosse
authors.affiliation: Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany. studla@bioinf.uni-leipzig.de.|Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103, Germany. studla@bioinf.uni-leipzig.de.|Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, D-04103, Germany. studla@bioinf.uni-leipzig.de.|Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, Leipzig, A-1090, Germany. studla@bioinf.uni-leipzig.de.|Center for RNA in Technology and Health, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Copenhagen, Denmark. studla@bioinf.uni-leipzig.de.|Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA. studla@bioinf.uni-leipzig.de.|German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany. studla@bioinf.uni-leipzig.de.
authors.forename: Peter F
authors.identifier: 0000-0002-5016-5191
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods; D017124:Conserved Sequence; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D005810:Multigene Family; D010802:Phylogeny; D010944:Plants / Q000145:classification* / Q000235:genetics*; D018749:RNA, Plant / Q000235:genetics*; D020537:RNA, Small Nucleolar / Q000235:genetics*
chemical_list: D018749:RNA, Plant; D020537:RNA, Small Nucleolar
keywords: Evolution; Small RNAs; snoRNA targets; snoRNAs