Sangam: A Confluence of Knowledge Streams

Characterisation of the UK honey bee metagenome

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dc.contributor BBSRC - Biotechnology and Biological Sciences Research Council
dc.contributor Regan, Tim
dc.creator Regan, Tim
dc.creator Freeman, Tom
dc.creator Barnett, Mark
dc.date 2018-10-11T11:06:28Z
dc.date 2018-10-15T04:15:09Z
dc.date.accessioned 2023-02-17T20:54:13Z
dc.date.available 2023-02-17T20:54:13Z
dc.identifier Regan, Tim; Freeman, Tom; Barnett, Mark. (2018). Characterisation of the UK honey bee metagenome, 2016-2017 [dataset]. The Roslin Institute. University of Edinburgh. https://doi.org/10.7488/ds/2453.
dc.identifier https://hdl.handle.net/10283/3197
dc.identifier https://doi.org/10.7488/ds/2453
dc.identifier.uri http://localhost:8080/xmlui/handle/CUHPOERS/244200
dc.description The European honey bee (Apis mellifera) plays a major role in pollination and food production, but is under threat from emerging pathogens and agro-environmental insults. As with other organisms, honey bee health is a complex product of environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of bee genetics and their molecular ecology can help manage modern challenges to bee health and production. Sampling bee and cobiont genomes, we characterised the metagenome of 19 honey bee colonies across Britain. Low heterozygosity was observed in bees from many Scottish colonies, sharing high similarity to the native dark bee, A. mellifera mellifera. Apiaries exhibited high diversity in the composition and relative abundance of individual microbiome taxa. Most non-bee sequences derived from known honey bee commensal bacteria or known pathogens, e.g. Lotmaria passim (Trypanosomatidae), and Nosema spp. (Microsporidia). However, DNA was also detected from numerous additional bacterial, plant (food source), protozoan and metazoan organisms. To classify sequences from cobionts lacking genomic information, we developed a novel network analysis approach clustering orphan contigs, allowing the identification of a pathogenic gregarine. Our analyses demonstrate the power of high-throughput, directed metagenomics in agroecosystems identifying potential threats to honey bees present in their microbiota.
dc.description Contains raw Illumina reads, assembled contigs, annotated clusters of contigs. View ReadMe.txt for description of files.
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dc.language eng
dc.publisher University of Edinburgh. The Roslin Institute
dc.relation https://doi.org/10.1038/s41467-018-07426-0
dc.relation Regan, T, Barnett, MW, Laetsch, DR, Bush, SJ, Wragg, D, Budge, GE, Highet, F, Dainat, B, De Miranda, JR, Watson, M, Blaxter, M & Freeman, TC 2018, 'Characterisation of the British honey bee metagenome' Nature Communications, vol. 9, no. 1. DOI: 10.1038/s41467-018-07426-0
dc.relation https://www.biorxiv.org/content/early/2018/05/18/293647
dc.relation Characterisation of the UK honey bee (Apis mellifera) metagenome. Tim Regan, Mark W Barnett, Dominik R Laetsch, Stephen J Bush, David Wragg, Giles E Budge, Fiona Highet, Benjamin Dainat, Joachim R de Miranda, Mark Blaxter, Tom C Freeman bioRxiv 293647; doi: https://doi.org/10.1101/293647
dc.rights Creative Commons Attribution 4.0 International Public License
dc.subject Metagenomics
dc.subject genomics
dc.subject microbiome
dc.subject Honey bee
dc.subject Apis mellifera
dc.subject Network analysis
dc.subject Network graph
dc.subject Assemblies
dc.subject Biological Sciences::Genetics not elsewhere classified
dc.title Characterisation of the UK honey bee metagenome
dc.type dataset
dc.coverage Scotland
dc.coverage England
dc.coverage UK
dc.coverage UNITED KINGDOM
dc.coverage start=2016-10-01; end=2017-06-01; scheme=W3C-DTF


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1.bam 638.8Mb application/octet-stream View/Open
10.bam 276.4Mb application/octet-stream View/Open
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All_contigs.fasta.gz 49.83Mb application/gzip View/Open
Entire Table with low cov filtered.csv 11.67Mb text/csv View/Open
ReadMe.txt 518bytes text/plain View/Open

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