Pea aphid (Acyrthosiphon pisum) targeted capture sequence reads

Illumina short-read sequence data from targeted capture of 434 genes, including 150 chemosensory genes, in 104 individuals distributed across eight host races of the pea aphid. This data is NERC-funded but not held by the EIDC. This data is archived in the European Bioinformatics Institute SRA (Sequence Read Archive) with project accession reference PRJEB6325

Publication date: 2015-05-15

Get the data

This record describes NERC-funded data managed by The European Bioinformatics Institute (EMBL-EBI)

Access and use conditions

Conditions unknown

Supplemental information

Other useful information regarding this dataset:

Duvaux, L., Geissmann, Q., Gharbi, K., Zhou, J.-J., Ferrari, J., Smadja, C. M., & Butlin, R. K. (2014). Dynamics of Copy Number Variation in Host Races of the Pea Aphid. Molecular Biology and Evolution, 32(1), 63–80

Quality

Lineage
Sequencing reads sorted by individuals (Edinburgh Genomics tags) have been deposited in the EBI Sequence Read Archive (SRA) with project accession no. PRJEB6325 (individual accession numbers are given in table S4 of journal paper associated with this record). Some intermediate data sets and result files needed to reproduce parts of the results outside our pipeline (e.g. matrix of raw PRbp counts, matrix of raw alpha from the "optimalCaptureSegmentation" analysis, R data frames used in GLMMs, NJ tree showing data per capture pools and sequencing lanes, extended figure 1 including all targeted loci) can be found on DRYAD, doi:10.5061/dryad.jf29v. The analytical framework set up to analyse CNV distribution (including CN estimation from PRbp, GLMMs, RF analyses and general statistics) is publicly available on a git repository https://github.com/lduvaux/Duvaux_et_al_2014, and reusable under the conditions of the General Public License (v3). Other miscellaneous scripts and command lines used to process sequencing results can be made available by the authors on request.

Authors

Duvaux, L.
University of Sheffield
Butlin, R.K.
University of Sheffield

Other contacts

Mediator
EIDC

Keywords

Topic categories
Biota
Environment
Other keywords
speciation
adaptation
targeted resequencing
gene duplication
gene family evolution
chemosensory genes
P450
INSPIRE Theme
Species distribution
Habitats and biotopes
Taxon keywords
Acyrthosiphon pisum

Dataset identifiers

PRJEB6325
https://catalogue.ceh.ac.uk/id/b0a79dab-5497-4387-be58-f65c38aa1448

Metadata

Information maintained by
European Nucleotide Archive
Last updated
2018-05-29T14:44:15