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Investigating the viral ecology of global bee communities with high-throughput metagenomics

David A. Galbraith, Zachary L. Fuller, Axel Brockmann, Maryann Frazier, Mary W. Gikungu, Karen M. Kapheim, Jeffrey T. Kerby, Sarah D. Kocher, Oleksiy Losyev, Elliud Muli, Harland M. Patch, Joyce M. Sakamoto, Scott Stanley, Anthony D. Vaudo, Christina M. Grozinger
doi: https://doi.org/10.1101/243139
David A. Galbraith
1Pennsylvania State University, Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, University Park, PA, USA
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Zachary L. Fuller
1Pennsylvania State University, Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, University Park, PA, USA
2Pennsylvania State University, Department of Biology, University Park, PA, USA & Columbia University, Department of Biological Sciences, New York, NY, USA
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Axel Brockmann
3Tata Institute of Fundamental Research, National Centre for Biological Sciences, Bangalore, India
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Maryann Frazier
1Pennsylvania State University, Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, University Park, PA, USA
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Mary W. Gikungu
4National Museums of Kenya, Department of Zoology, Nairobi, Kenya
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Karen M. Kapheim
5Utah State University, Department of Biology, Logan, UT, USA & Smithsonian Tropical Research Institute, Panama City, Panama
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Jeffrey T. Kerby
6Dartmouth College, Neukom Institute for Computational Science, Hanover, NH, USA
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Sarah D. Kocher
7Princeton University, Lewis-Sigler Institute for Integrative Genomics, Princeton, NJ, USA
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Oleksiy Losyev
8The National University of Life and Environmental Sciences of Ukraine, Department of Beekeeping, Kyiv, Ukraine
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Elliud Muli
9The International Center of Insect Physiology and Ecology, Nairobi, Kenya
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Harland M. Patch
1Pennsylvania State University, Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, University Park, PA, USA
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Joyce M. Sakamoto
1Pennsylvania State University, Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, University Park, PA, USA
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Scott Stanley
10Pennsylvania State University Children’s Hospital, Division of Pediatric Hematology and Oncology, Hershey, PA, USA
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Anthony D. Vaudo
1Pennsylvania State University, Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, University Park, PA, USA
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Christina M. Grozinger
1Pennsylvania State University, Department of Entomology, Center for Pollinator Research, Huck Institutes of the Life Sciences, University Park, PA, USA
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ABSTRACT

Bee viral ecology is a fascinating emerging area of research: viruses exert a range of effects on their hosts, exacerbate the impacts of other environmental stressors, and, importantly, are readily shared across multiple bee species in a community. However, our understanding of bee viral communities is limited, as it is primarily derived from studies of North American and European Apis mellifera populations. Here, we examined viruses in populations of A. mellifera and 11 other bee species from 9 countries, across 5 continents and Oceania. We developed a novel pipeline to rapidly, inexpensively, and robustly screen for bee viruses. This pipeline includes purification of encapsulated RNA/DNA viruses, sequence-independent amplification, high throughput sequencing, integrated assembly of contigs, and filtering to identify contigs specifically corresponding to viral sequences. We identified sequences corresponding to (+)ssRNA, (-)ssRNA, dsRNA, and ssDNA viruses. Overall, we found 127 contigs corresponding to novel viruses (i.e. previously not observed in bees), with 29 represented by >0.1 % of the reads in a given sample. These viruses and viral families were distributed across multiple regions and species. This study provides a robust pipeline for metagenomics analysis of viruses, and greatly expands our understanding of the diversity of viruses found in bee communities.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted January 04, 2018.
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Investigating the viral ecology of global bee communities with high-throughput metagenomics
David A. Galbraith, Zachary L. Fuller, Axel Brockmann, Maryann Frazier, Mary W. Gikungu, Karen M. Kapheim, Jeffrey T. Kerby, Sarah D. Kocher, Oleksiy Losyev, Elliud Muli, Harland M. Patch, Joyce M. Sakamoto, Scott Stanley, Anthony D. Vaudo, Christina M. Grozinger
bioRxiv 243139; doi: https://doi.org/10.1101/243139
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Investigating the viral ecology of global bee communities with high-throughput metagenomics
David A. Galbraith, Zachary L. Fuller, Axel Brockmann, Maryann Frazier, Mary W. Gikungu, Karen M. Kapheim, Jeffrey T. Kerby, Sarah D. Kocher, Oleksiy Losyev, Elliud Muli, Harland M. Patch, Joyce M. Sakamoto, Scott Stanley, Anthony D. Vaudo, Christina M. Grozinger
bioRxiv 243139; doi: https://doi.org/10.1101/243139

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