title: Conservation and losses of non-coding RNAs in avian genomes.
abstract: Here we present the results of a large-scale bioinformatics annotation of non-coding RNA loci in 48 avian genomes. Our approach uses probabilistic models of hand-curated families from the Rfam database to infer conserved RNA families within each avian genome. We supplement these annotations with predictions from the tRNA annotation tool, tRNAscan-SE and microRNAs from miRBase. We identify 34 lncRNA-associated loci that are conserved between birds and mammals and validate 12 of these in chicken. We report several intriguing cases where a reported mammalian lncRNA, but not its function, is conserved. We also demonstrate extensive conservation of classical ncRNAs (e.g., tRNAs) and more recently discovered ncRNAs (e.g., snoRNAs and miRNAs) in birds. Furthermore, we describe numerous "losses" of several RNA families, and attribute these to either genuine loss, divergence or missing data. In particular, we show that many of these losses are due to the challenges associated with assembling avian microchromosomes. These combined results illustrate the utility of applying homology-based methods for annotating novel vertebrate genomes.
authors.affiliation: School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
authors.forename: Paul P
authors.initials: PP
authors.lastname: Gardner
authors.affiliation: Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany; ecSeq Bioinformatics, Brandvorwerkstr.43, D-04275 Leipzig, Germany.
authors.forename: Mario
authors.initials: M
authors.lastname: Fasold
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, Cambridge, CB10 1SD, UK.
authors.forename: Sarah W
authors.initials: SW
authors.lastname: Burge
authors.affiliation: Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
authors.forename: Maria
authors.initials: M
authors.lastname: Ninova
authors.affiliation: Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
authors.forename: Jana
authors.initials: J
authors.lastname: Hertel
authors.affiliation: Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.
authors.forename: Stephanie
authors.initials: S
authors.lastname: Kehr
authors.affiliation: School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
authors.forename: Tammy E
authors.initials: TE
authors.lastname: Steeves
authors.affiliation: Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.
authors.forename: Sam
authors.initials: S
authors.lastname: Griffiths-Jones
authors.affiliation: Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany; Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany; Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria; Center for RNA in Technology and Health, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark; Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, USA; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
mesh_terms: D000818:Animals; D001717:Birds / Q000235:genetics*; D002645:Chickens / Q000235:genetics; D019295:Computational Biology; D017124:Conserved Sequence; D018628:Gene Dosage; D014644:Genetic Variation; D016678:Genome; D006801:Humans; D008322:Mammals / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics; D058977:Molecular Sequence Annotation; D005810:Multigene Family; D011544:Pseudogenes; D020537:RNA, Small Nucleolar / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D050436:Regulatory Elements, Transcriptional; D013045:Species Specificity
chemical_list: D035683:MicroRNAs; D020537:RNA, Small Nucleolar; D022661:RNA, Untranslated
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