ArticlePloS one2015
Conservation and losses of non-coding RNAs in avian genomes.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- A conservedRNA biology · 2023Article
- Microsyntenic Clusters Reveal Conservation of lncRNAs in Chordates Despite Absence of Sequence Conservation.Biology · 2019Article
- Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation.GigaScience · 2019Article
- Evolutionary Patterns of Non-Coding RNA in Cardiovascular Biology.Non-coding RNA · 2019Review
- Article
- Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes.BMC evolutionary biology · 2017Article
- Article
- Genome-wide profiling of chicken dendritic cell response to infectious bursal disease.BMC genomics · 2016Article
- Article
- Evolution to the rescue: using comparative genomics to understand long non-coding RNAs.Nature reviews. Genetics · 2016Review
- Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes.BMC genomics · 2015Article
- Functional classification of 15 million SNPs detected from diverse chicken populations.DNA research : an international journal for rapid publication of reports on genes and genomes · 2015Article
- Third Report on Chicken Genes and Chromosomes 2015.Cytogenetic and genome research · 2015Article
- Annotating RNA motifs in sequences and alignments.Nucleic acids research · 2015Article
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Authors and funding
9 authors.
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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.
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