DOI: 10.5061/dryad.kv67m
title: Data from: Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: birth, death, and adaptation

description: Across insect genomes, the size of the cytochrome P450 monooxygenase (CYP)
 gene superfamily varies widely. CYPome size variation has been attributed
 to reciprocal adaptive radiations in insect detoxification genes in
 response to plant biosynthetic gene radiations driven by coevolution
 between herbivores and their chemically defended hostplants.
 Alternatively, variation in CYPome size may be due to random “birth and
 death” processes, whereby exponential increase via gene duplications is
 limited by random decay via gene death or transition via divergence. We
 examined CYPome diversification in the genomes of seven Lepidoptera
 species varying in host breadth from monophagous (Bombyx mori) to highly
 polyphagous (Amyelois transitella). CYPome size largely reflects the size
 of Clan 3, the clan associated with xenobiotic detoxification, and to some
 extent phylogenetic age. Consistently across genomes, families CYP6, CYP9,
 and CYP321 are most diverse and CYP6AB, CYP6AE, CYP6B, CYP9A, and CYP9G
 are most diverse among subfamilies. Higher gene number in subfamilies is
 due to duplications occurring primarily after speciation and
 specialization (“P450 blooms”), and the genes are arranged in clusters,
 indicative of active duplicating loci. In the parsnip webworm, Depressaria
 pastinacella, gene expression levels in large subfamilies are high
 relative to smaller subfamilies. Functional and phylogenetic data suggest
 a correlation between highly dynamic loci (reflective of extensive gene
 duplication, functionalization, and in some cases loss) and the ability of
 enzymes encoded by these genes to metabolize hostplant defenses,
 consistent with an adaptive, nonrandom process driven by ecological
 interactions.
description: Draft genome assembly
 for the parsnip webworm Depressaria pastinacellaGenomic 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.Parsnip_webworm_SOAP2_072913_K49_GapCloser.fa.txt