Data from: Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: birth, death, and adaptation

Calla B, Noble K, Johnson RM, Walden KKO, Schuler MA, Robertson HM, Berenbaum MR

Date Published: September 13, 2017

DOI: http://dx.doi.org/10.5061/dryad.kv67m

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Title Draft genome assembly for the parsnip webworm Depressaria pastinacella
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Description 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.
Download Parsnip_webworm_SOAP2_072913_K49_GapCloser.fa.txt (639.1 Mb)
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When using this data, please cite the original publication:

Calla B, Noble K, Johnson RM, O Walden KK, Schuler MA, Robertson HM, Berenbaum MR (2017) Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: birth, death, and adaptation. Molecular Ecology, online in advance of print. http://dx.doi.org/10.1111/mec.14348

Additionally, please cite the Dryad data package:

Calla B, Noble K, Johnson RM, Walden KKO, Schuler MA, Robertson HM, Berenbaum MR (2017) Data from: Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: birth, death, and adaptation. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.kv67m
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