Conservation and losses of non-coding RNAs in avian genomes

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 pre...

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Bibliographic Details
Published in:PloS one 2015-03, Vol.10 (3), p.e0121797-e0121797
Main Authors: Gardner, Paul P, Fasold, Mario, Burge, Sarah W, Ninova, Maria, Hertel, Jana, Kehr, Stephanie, Steeves, Tammy E, Griffiths-Jones, Sam, Stadler, Peter F
Format: Article
Language:English
Subjects:
Analysis
Animals
Annotations
Bioinformatics
Birds
Birds - genetics
Chickens - genetics
Chromosomes
Computational Biology
Computer science
Conservation
Conserved Sequence
Divergence
Gene Dosage
Gene expression
Gene loci
Genetic Variation
Genome
Genomes
Genomics
Homology
Humans
Interdisciplinary aspects
Life sciences
Loci
Mammals - genetics
Mathematical models
MicroRNA
MicroRNAs
MicroRNAs - genetics
miRNA
Missing data
Molecular Sequence Annotation
Multigene Family
Non-coding RNA
Probabilistic models
Protection and preservation
Pseudogenes
Regulatory Elements, Transcriptional
Ribonucleic acid
RNA
RNA, Small Nucleolar - genetics
RNA, Untranslated - genetics
Species Specificity
Transfer RNA
tRNA
Vertebrates
Wildlife conservation
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0121797