Data from: Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: birth, death, and adaptation
Calla, Bernarda, University of Illinois at Urbana Champaign
Noble, Katherine, University of Utah
Johnson, Reed M., The Ohio State University
Walden, Kimberly K. O., University of Illinois at Urbana Champaign
Schuler, Mary A., University of Illinois at Urbana Champaign
Robertson, Hugh M., University of Illinois at Urbana Champaign
Berenbaum, May R., University of Illinois at Urbana Champaign
Published Sep 13, 2017 on Dryad.
Cite this dataset
Calla, Bernarda et al. (2017). Data from: Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: birth, death, and adaptation [Dataset]. Dryad. https://doi.org/10.5061/dryad.kv67m
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.
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.