@article{coates_walden_lata_vellichirammal_mitchell_andersson_mckay_lorenzen_grubbs_wang_et al._2023, title={A draft Diabrotica virgifera virgifera genome: insights into control and host plant adaption by a major maize pest insect}, volume={24}, ISSN={1471-2164}, url={http://dx.doi.org/10.1186/s12864-022-08990-y}, DOI={10.1186/s12864-022-08990-y}, abstractNote={Adaptations by arthropod pests to host plant defenses of crops determine their impacts on agricultural production. The larval host range of western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), is restricted to maize and a few grasses. Resistance of D. v. virgifera to crop rotation practices and multiple insecticides contributes to its status as the most damaging pest of cultivated maize in North America and Europe. The extent to which adaptations by this pest contributes to host plant specialization remains unknown.A 2.42 Gb draft D. v. virgifera genome, Dvir_v2.0, was assembled from short shotgun reads and scaffolded using long-insert mate-pair, transcriptome and linked read data. K-mer analysis predicted a repeat content of ≥ 61.5%. Ortholog assignments for Dvir_2.0 RefSeq models predict a greater number of species-specific gene duplications, including expansions in ATP binding cassette transporter and chemosensory gene families, than in other Coleoptera. A majority of annotated D. v. virgifera cytochrome P450s belong to CYP4, 6, and 9 clades. A total of 5,404 transcripts were differentially-expressed between D. v. virgifera larvae fed maize roots compared to alternative host (Miscanthus), a marginal host (Panicum virgatum), a poor host (Sorghum bicolor) and starvation treatments; Among differentially-expressed transcripts, 1,908 were shared across treatments and the least number were between Miscanthus compared to maize. Differentially-expressed transcripts were enriched for putative spliceosome, proteosome, and intracellular transport functions. General stress pathway functions were unique and enriched among up-regulated transcripts in marginal host, poor host, and starvation responses compared to responses on primary (maize) and alternate hosts.Manual annotation of D. v. virgifera Dvir_2.0 RefSeq models predicted expansion of paralogs with gene families putatively involved in insecticide resistance and chemosensory perception. Our study also suggests that adaptations of D. v. virgifera larvae to feeding on an alternate host plant invoke fewer transcriptional changes compared to marginal or poor hosts. The shared up-regulation of stress response pathways between marginal host and poor host, and starvation treatments may reflect nutrient deprivation. This study provides insight into transcriptomic responses of larval feeding on different host plants and resources for genomic research on this economically significant pest of maize.}, number={1}, journal={BMC Genomics}, publisher={Springer Science and Business Media LLC}, author={Coates, Brad S. and Walden, Kimberly K. O. and Lata, Dimpal and Vellichirammal, Neetha Nanoth and Mitchell, Robert F. and Andersson, Martin N. and McKay, Rachel and Lorenzen, Marcé D. and Grubbs, Nathaniel and Wang, Yu-Hui and et al.}, year={2023}, month={Jan} }
 @article{xuan_scheffer_lewis_cassel_liu_wiegmann_2023, title={The phylogeny and divergence times of leaf-mining flies (Diptera: Agromyzidae) from anchored phylogenomics}, volume={184}, ISSN={["1095-9513"]}, DOI={10.1016/j.ympev.2023.107778}, abstractNote={Leaf-mining flies (Diptera: Agromyzidae) are a diverse clade of phytophagous Diptera known largely for their economic impact as leaf- or stem-miners on vegetable and ornamental plants. Higher-level phylogenetic relationships of Agromyzidae have remained uncertain because of challenges in sampling of both taxa and characters for morphology and PCR-based Sanger-era molecular systematics. Here, we used hundreds of orthologous single-copy nuclear loci obtained from anchored hybrid enrichment (AHE) to reconstruct phylogenetic relationships among the major lineages of leaf-mining flies. The resulting phylogenetic trees are highly congruent and well-supported, except for a few deep nodes, when using different molecular data types and phylogenetic methods. Based on divergence time dating using a relaxed clock model-based analysis, leaf-mining flies are shown to have diversified in multiple lineages since the early Paleocene, approximately 65 million years ago. Our study not only reveals a revised classification system of leaf-mining flies, but also provides a new phylogenetic framework to understand their macroevolution.}, journal={MOLECULAR PHYLOGENETICS AND EVOLUTION}, author={Xuan, Jing-Li and Scheffer, Sonja J. and Lewis, Matt and Cassel, Brian K. and Liu, Wan-Xue and Wiegmann, Brian M.}, year={2023}, month={Jul} }