Jiggins, F.M.; Longdon, B.

Drosophila C virus genomes, Cambridge (2017)

The resource consists of genome sequence data for the Drosophila C virus that has been serially passaged through different species of Drosophila in the laboratory. The genomes were sequenced and aligned to the reference genome. The frequency of variants at both biallelic and triallelic sites was then calculated. We also generated a phylogeny of the species involved using published data. This data was generated to understand how viruses adapt to new host species by Francis Jiggins and his co workers. The work was carried out between July 2016 and September 2017 and was funded by NERC under award reference NE/L004232/1

Publication date: 2018-01-24

Get the data

This dataset is made available under the terms of the Open Government Licence

This data is available as Comma-separated values (CSV), BAM or Newick

You must cite: Jiggins, F.M.; Longdon, B. (2018). Drosophila C virus genomes, Cambridge (2017). NERC Environmental Information Data Centre. https://doi.org/10.5285/4434a27d-5288-4f2e-88ac-4b1372e4d073

 

© Cambridge University

Where/When

Temporal extent
2016-01-01    to    2017-09-01

Provenance & quality

Each species of Drosophila was infected by dipping a needle in virus suspension. After 3 days the fly was then homogenized and the process repeated for 8-10 passages. At the end of this process, Ribonucleic acid (RNA) was extracted, the viral genome amplified by Polymerase chain reaction (PCR) and Nextera libraries constructed. These were sequenced on n Illumina sequencer, the sequences quality trimmed and aligned to the reference genome to generate the BAM file in this dataset. We then called variants to generate the allele frequency CSV files. Full details of these steps are provided in the supporting documentation. NB: these data are not adequately described in that there are no column descriptions for the csv files.

Supplemental information

This dataset is a supplement to:

Longdon, B., Day, J. P., Alves, J. M., Smith, S. C. L., Houslay, T. M., McGonigle, J. E., … Jiggins, F. M. (2018). Host shifts result in parallel genetic changes when viruses evolve in closely related species. PLOS Pathogens, 14(4), e1006951.

Correspondence/contact details

Dr Francis Jiggins
University of Cambridge
Department of Genetics, Downing Street
Cambridge
Cambridgeshire
CB2 3EH
UK
 fmj1001@cam.ac.uk

Authors

Jiggins, F.M.
University of Cambridge
Longdon, B.
University of Exeter

Other contacts

Custodian
Environmental Information Data Centre
 info@eidc.ac.uk
Publisher
NERC Environmental Information Data Centre
 info@eidc.ac.uk
Rights Holder
University of Cambridge
 enquiries@ceh.ac.uk

Additional metadata

Topic categories
Health
Keywords
DCV,  disease emergence,  drosophila,  Drosophila C virus,  evolution,  host shift,  virus
Funding
Natural Environment Research Council Award: NE/L004232/1
Last updated
13 March 2020 14:28