Drosophila C virus genomes, Cambridge (2017)

Name: Drosophila C virus genomes, Cambridge (2017)
Published: 2018-01-24

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

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https://doi.org/10.5285/4434a27d-5288-4f2e-88ac-4b1372e4d073

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

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More information

View numbers valid from 01 June 2023 Download numbers valid from 20 June 2024 (information prior to this was not collected)

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

BibTeX RIS

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