Conservation and losses of avian non-coding RNA loci
Type of content
UC permalink
Publisher's DOI/URI
Thesis discipline
Degree name
Publisher
Journal Title
Journal ISSN
Volume Title
Language
Date
Authors
Abstract
Here 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.
Description
Citation
Keywords
Ngā upoko tukutuku/Māori subject headings
ANZSRC fields of research
Fields of Research::31 - Biological sciences::3105 - Genetics::310509 - Genomics