Drosophila C virus genomes, Cambridge (2017)
https://doi.org/10.5285/4434a27d-5288-4f2e-88ac-4b1372e4d073
Download/Access
This dataset is made available under the terms of the Open Government Licence
By accessing or using this dataset, you agree to the terms of the relevant licence agreement(s). You will ensure that this dataset is cited in any publication that describes research in which the data have been used.
© Cambridge University
Bulk download options
You can use WGET to download data. For example
wget https://catalogue.ceh.ac.uk/datastore/eidchub/4434a27d-5288-4f2e-88ac-4b1372e4d073 --user=YOUR_USERNAME --password=YOUR_PASSWORD --auth-no-challenge
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
View numbers valid from 01 June 2023
Download numbers valid from 20 June 2024
Formats
Comma-separated values (CSV), BAM
Temporal information
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.
Licensing and constraints
This dataset is made available under the terms of the Open Government Licence 
Cite this dataset as:
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
Citations
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. https://doi.org/10.1371/journal.ppat.1006951
Longdon, B., Day, J.P., Alves, J.M., Smith, S.C., Houslay, T.M., McGonigle, J.E., … Jiggins, F.M. (2017). Host shifts result in parallel genetic changes when viruses evolve in closely related species. https://doi.org/10.1101/226175
Correspondence/contact details
Jiggins, F.
University of Cambridge
Department of Genetics, Downing Street
Cambridge
Cambridgeshire
CB2 3EH
UK
fmj1001@cam.ac.uk
Cambridge
Cambridgeshire
CB2 3EH
UK
Other contacts
Publisher
NERC Environmental Information Data Centre
info@eidc.ac.uk
Rights holder
University of Cambridge