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A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes

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...

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Autores principales: Mostajo, Nelly F, Lataretu, Marie, Krautwurst, Sebastian, Mock, Florian, Desirò, Daniel, Lamkiewicz, Kevin, Collatz, Maximilian, Schoen, Andreas, Weber, Friedemann, Marz, Manja, Hölzer, Martin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108008/
https://www.ncbi.nlm.nih.gov/pubmed/32289119
http://dx.doi.org/10.1093/nargab/lqz006
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author Mostajo, Nelly F
Lataretu, Marie
Krautwurst, Sebastian
Mock, Florian
Desirò, Daniel
Lamkiewicz, Kevin
Collatz, Maximilian
Schoen, Andreas
Weber, Friedemann
Marz, Manja
Hölzer, Martin
author_facet Mostajo, Nelly F
Lataretu, Marie
Krautwurst, Sebastian
Mock, Florian
Desirò, Daniel
Lamkiewicz, Kevin
Collatz, Maximilian
Schoen, Andreas
Weber, Friedemann
Marz, Manja
Hölzer, Martin
author_sort Mostajo, Nelly F
collection PubMed
description 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.
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spelling pubmed-71080082020-04-02 A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes Mostajo, Nelly F Lataretu, Marie Krautwurst, Sebastian Mock, Florian Desirò, Daniel Lamkiewicz, Kevin Collatz, Maximilian Schoen, Andreas Weber, Friedemann Marz, Manja Hölzer, Martin NAR Genom Bioinform Standard Article 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. Oxford University Press 2019-09-30 /pmc/articles/PMC7108008/ /pubmed/32289119 http://dx.doi.org/10.1093/nargab/lqz006 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Standard Article
Mostajo, Nelly F
Lataretu, Marie
Krautwurst, Sebastian
Mock, Florian
Desirò, Daniel
Lamkiewicz, Kevin
Collatz, Maximilian
Schoen, Andreas
Weber, Friedemann
Marz, Manja
Hölzer, Martin
A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
title A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
title_full A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
title_fullStr A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
title_full_unstemmed A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
title_short A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
title_sort comprehensive annotation and differential expression analysis of short and long non-coding rnas in 16 bat genomes
topic Standard Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108008/
https://www.ncbi.nlm.nih.gov/pubmed/32289119
http://dx.doi.org/10.1093/nargab/lqz006
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