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Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity

High throughput (or ‘next generation’) sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing...

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Autores principales: Gerth, Michael, Hurst, Gregory D.D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510586/
https://www.ncbi.nlm.nih.gov/pubmed/28717593
http://dx.doi.org/10.7717/peerj.3529
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author Gerth, Michael
Hurst, Gregory D.D.
author_facet Gerth, Michael
Hurst, Gregory D.D.
author_sort Gerth, Michael
collection PubMed
description High throughput (or ‘next generation’) sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and ‘contaminating’ material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome. Here, we aimed to assess if these ‘contaminations’ provide information with regard to biologically important microorganisms associated with the individual. To achieve this, we examined whether the short read data from Apis retrieved elements of its well established microbiome. To this end, we screened almost 1,000 short read libraries of honey bee (Apis sp.) DNA sequencing project for the presence of microbial sequences, and find sequences from known honey bee microbial associates in at least 11% of them. Further to this, we screened ∼500 Apis RNA sequencing libraries for evidence of viral infections, which were found to be present in about half of them. We then used the data to reconstruct draft genomes of three Apis associated bacteria, as well as several viral strains de novo. We conclude that ‘contamination’ in short read sequencing libraries can provide useful genomic information on microbial taxa known to be associated with the target organisms, and may even lead to the discovery of novel associations. Finally, we demonstrate that RNAseq samples from experiments commonly carry uneven viral loads across libraries. We note variation in viral presence and load may be a confounding feature of differential gene expression analyses, and as such it should be incorporated as a random factor in analyses.
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spelling pubmed-55105862017-07-17 Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity Gerth, Michael Hurst, Gregory D.D. PeerJ Evolutionary Studies High throughput (or ‘next generation’) sequencing has transformed most areas of biological research and is now a standard method that underpins empirical study of organismal biology, and (through comparison of genomes), reveals patterns of evolution. For projects focused on animals, these sequencing methods do not discriminate between the primary target of sequencing (the animal genome) and ‘contaminating’ material, such as associated microbes. A common first step is to filter out these contaminants to allow better assembly of the animal genome or transcriptome. Here, we aimed to assess if these ‘contaminations’ provide information with regard to biologically important microorganisms associated with the individual. To achieve this, we examined whether the short read data from Apis retrieved elements of its well established microbiome. To this end, we screened almost 1,000 short read libraries of honey bee (Apis sp.) DNA sequencing project for the presence of microbial sequences, and find sequences from known honey bee microbial associates in at least 11% of them. Further to this, we screened ∼500 Apis RNA sequencing libraries for evidence of viral infections, which were found to be present in about half of them. We then used the data to reconstruct draft genomes of three Apis associated bacteria, as well as several viral strains de novo. We conclude that ‘contamination’ in short read sequencing libraries can provide useful genomic information on microbial taxa known to be associated with the target organisms, and may even lead to the discovery of novel associations. Finally, we demonstrate that RNAseq samples from experiments commonly carry uneven viral loads across libraries. We note variation in viral presence and load may be a confounding feature of differential gene expression analyses, and as such it should be incorporated as a random factor in analyses. PeerJ Inc. 2017-07-12 /pmc/articles/PMC5510586/ /pubmed/28717593 http://dx.doi.org/10.7717/peerj.3529 Text en ©2017 Gerth and Hurst 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 use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Evolutionary Studies
Gerth, Michael
Hurst, Gregory D.D.
Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity
title Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity
title_full Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity
title_fullStr Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity
title_full_unstemmed Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity
title_short Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity
title_sort short reads from honey bee (apis sp.) sequencing projects reflect microbial associate diversity
topic Evolutionary Studies
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5510586/
https://www.ncbi.nlm.nih.gov/pubmed/28717593
http://dx.doi.org/10.7717/peerj.3529
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