A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes.
Journal
NAR genomics and bioinformatics
ISSN: 2631-9268
Titre abrégé: NAR Genom Bioinform
Pays: England
ID NLM: 101756213
Informations de publication
Date de publication:
Mar 2020
Mar 2020
Historique:
received:
03
07
2019
revised:
21
08
2019
accepted:
10
09
2019
entrez:
15
4
2020
pubmed:
15
4
2020
medline:
15
4
2020
Statut:
ppublish
Résumé
Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies, we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (rna.uni-jena.de/supplements/bats) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology and important host-virus interactions.
Identifiants
pubmed: 32289119
doi: 10.1093/nargab/lqz006
pii: lqz006
pmc: PMC7108008
doi:
Types de publication
Journal Article
Langues
eng
Pagination
lqz006Informations de copyright
© The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics.
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