Data from: Population-level consequences of complementary sex determination in a solitary parasitoid

de Boer JG, Groenen MAM, Pannebakker BA, Beukeboom LW, Kraus RHS

Date Published: May 20, 2015

DOI: http://dx.doi.org/10.5061/dryad.jn14s

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Reference genome sequence of Cotesia vestalis: scaffolds and contigs
Description No genome information was available for C. vestalis. In order to build a draft reference genome and to develop SNP assays, we sequenced the entire genome of C. vestalis on a single lane of paired-end sequences (2x100 bp) on an Illumina HiSeq 2000 (Illumina Inc., U.S.A.) instrument. The SNP discovery panel consisted of eight C. vestalis females, one from each of eight fields.Before assembly, Illumina reads were trimmed using an in-house Perl script that trims the sequence as soon as two consecutive bases have a quality score lower than 20. Reads that after trimming had a length smaller than 50 bp were removed from the analysis. To obtain C. vestalis sequence contigs to be used as a pseudo-reference genome, we performed a de novo assembly on the 133 million 100 bp reads using SOAPDENOVO version 1.05 [37]. The assembly was done using a k-mer size of 45 and k-mers that were seen only once were removed (option –d). After contig construction, scaffolding was performed using intra-scaffold closure (option –F) and a minimum length for scaffolding of 50 bp. The total size of the assembly was 152 Mb with a contig N50 size of 761 bp and a scaffold N50 size of 2400 bp.
Download de Boer_Cotesia vestalis scaffold sequence...afSeq (166.3 Mb)
Details View File Details
Title Cotesia vestalis SNP information and sequences
Description From our list of putative SNPs across the C. vestalis genome, we selected 100 SNPs for genotyping assay development. We first selected the 200 largest scaffolds; they varied in length from 17-58Kb and contained a total of 7,878 SNPs. We then removed SNPs with a minor allele frequency (MAF) <0.2, SNPs that had another SNP within 50 bp up- or downstream, and SNPs with more than 2 alleles. The remaining SNPs were binned in MAF bins of 0.2-0.3 (1,908 SNPs), 0.3-0.4 (1,605 SNPs) and 0.4-0.5 (1,156 SNPs). Per MAF bin, SNPs were ranked by SNP quality score. We then selected the SNPs with the highest quality scores, picking 20 SNPs with a MAF between 0.2-0.3 and 40 each with a MAF between 0.3-0.4 and 0.4-0.5, all on different scaffolds. All selected SNPs had a quality score of more than 200 (based on SAMTOOLS), and an average read depth of 61. High-throughput genotyping assays based on allele-specific forward primers were developed for these 100 SNP sequences at KBioscience (now LGC Genomics, Hoddesdon, U.K.).
Download de Boer_SNP info and sequences.xlsx (41.27 Kb)
Details View File Details
Title Genototypes of C vestalis females at 98 SNPs
Description SNP genotypes of 139 Cotesia vestalis females collected in Western Taiwan at 98 polymorphic SNPs
Download de Boer_genotype matrix C vestalis.xlsx (62.11 Kb)
Details View File Details
Title Putative SNPs discovered in genome of Cotesia vestalis
Description Individual paired-end reads were aligned against the artificial Cotesia vestalis reference genome obtained from the de novo genome assembly using BWA. The resulting BAM file was then used for the identification of putative SNPs using SAMTOOLS and varFilter from the samtools.pl utility. We only considered nucleotide substitutions and ignored small indels. SNPs were filtered that had a mapping quality higher than 20, a minimum read depth of 3 and a maximum read depth of 90 (3x the average read depth, a strategy to avoid orthologous SNPs, e.g. in multi copy genes.
Download de Boer_putative SNPs.xlsx (33.45 Mb)
Details View File Details

When using this data, please cite the original publication:

de Boer JG, Groenen MAM, Pannebakker BA, Beukeboom LW, Kraus RHS (2015) Data from: Population-level consequences of complementary sex determination in a solitary parasitoid. BMC Evolutionary Biology 15: 98. http://dx.doi.org/10.1186/s12862-015-0340-2

Additionally, please cite the Dryad data package:

de Boer JG, Groenen MAM, Pannebakker BA, Beukeboom LW, Kraus RHS (2015) Data from: Population-level consequences of complementary sex determination in a solitary parasitoid. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.jn14s
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Submissions have been temporarily disabled.

Search for data

Be part of Dryad

We encourage organizations to: