Conservation and losses of avian non-coding RNA loci

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dc.contributor.authorGardner, P.P.
dc.contributor.authorFasold, M.
dc.contributor.authorBurge, S.W.
dc.contributor.authorNinova, M.
dc.contributor.authorHertel, J.
dc.contributor.authorKehr, S.
dc.contributor.authorSteeves, T.E.
dc.contributor.authorGriffiths-Jones, S.
dc.contributor.authorStadler, P.F.
dc.date.accessioned2015-04-13T22:10:31Z
dc.date.available2015-04-13T22:10:31Z
dc.date.issued2014en
dc.description.abstractHere we present the results of a large-scale bioinformatic 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 show that a number of lncRNA-associated loci are conserved between birds and mammals, including several intriguing cases where the reported mammalian lncRNA function is not conserved in birds. 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 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.en
dc.identifier.citationGardner, P.P., Fasold, M., Burge, S.W., Ninova, M., Hertel, J., Kehr, S., Steeves, T.E., Griffiths-Jones, S., Stadler, P.F. (2014) Conservation and losses of avian non-coding RNA loci. Quantitative Biology, (early access online).en
dc.identifier.urihttp://hdl.handle.net/10092/10306
dc.language.isoen
dc.publisherUniversity of Canterbury. Biological Sciencesen
dc.relation.urihttp://arxiv.org/abs/1406.7140en
dc.rights.urihttps://hdl.handle.net/10092/17651en
dc.subject.anzsrcFields of Research::31 - Biological sciences::3105 - Genetics::310510 - Molecular evolutionen
dc.subject.anzsrcFields of Research::31 - Biological sciences::3105 - Genetics::310509 - Genomicsen
dc.titleConservation and losses of avian non-coding RNA locien
dc.typeJournal Article
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