Reference genome sequence of Cotesia vestalis: scaffolds and contigs

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.