Draft genome assembly for the parsnip webworm Depressaria pastinacella

Genomic DNA from adult Depressaria pastinacella (parsnip webworm) moth was extracted. The W.M. Keck Center for Comparative and Functional Genomics at the University of Illinois at Urbana-Champaign generated the following libraries for sequencing: 180-bp and 1-kb insert shotgun libraries from a single male moth and 5-kb, 10-kb and 20-kb insert mate-pair libraries. The 180-bp and 1-kb insert shotgun libraries were prepared with Illumina's TruSeq DNAseq Sample Prep Kit. The 5-kb mate-pair library was prepared similarly except a custom linker was ligated between the read-ends to facilitate mate-pair recovery. The 10- and 20-kb insert mate-pair libraries were prepared with Illumina’s Nextera Mate-Pairs Sample Prep Kit. All libraries were sequenced for 100 cycles on a HiSeq2000 using the TruSeq SBS Sequencing Kit v.3. Data were analyzed with pipeline version 1.8. The custom 5-kb and Nextera 10-kb and 20-kb mate-pair libraries were filtered for reads containing properly-oriented reads of the appropriate insert size and uniqueness. Raw Illumina reads were trimmed at the 5’ and 3’ ends for nucleotide-bias and low-quality bases using the FASTX Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/). Trimmed reads were error-corrected by Quake counting 19-mers. SOAPdenovo v2.04 (Luo et al. 2012), was employed with K=49 to assemble the 180-bp insert library reads followed by scaffolding with iteratively longer insert mate-pair libraries and use of GapCloser v1.12 (Luo et al. 2012) to close gaps generated in the scaffolding process.