Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.

Author contributions M.K. co-designed and implemented the overall strategy for the creation of the knock-in fly lines, designed and implemented the bioassays, the RT-qPCR experiments and the RMO analysis, performed statistical analyses and co-wrote the manuscript. S.C.G. designed and implemented the overall strategy for the creation of the knock-in fly lines, prepared the sequence data and metadata for the phylogenetic analyses, co-designed all other experiments, and co-wrote the manuscript. F.S. performed the structural modelling and docking site analyses. J.N.P. performed the phylogenetic, ancestral state and co-evolutionary analyses. K.I.V. conducted crosses, genotyping, and feeding experiments, and co-designed the qPCR experiments. J.M.A. and S.L.B. conducted crosses and genotyping, and feeding and sequestration experiments. A.P.H. performed the in vitro physiological experiments and sequestration analyses. T.M. conducted feeding experiments M.A. performed the RMO analysis with M.K., and conducted genotyping and feeding experiments. G.G. completed the RMO and ouabain dietary survival analyses. F.R. supervised the structural modelling and docking site analyses. S.D. oversaw and interpreted in vitro cell line analyses, helped to design the overall project and co-wrote the manuscript. A.A.A. helped to design the overall project, oversaw the in vitro physiological and sequestration experiments, and co-wrote the manuscript. N.K.W. led the overall collaboration, the project design and its integration, creation of fly lines and statistical analyses, and co-wrote the manuscript. Peer review information Nature thanks Joseph W. Thornton and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.Online content Any methods, additional references, Nature Research reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at

SIGNIFICANCE STATEMENTThe origin of land plants >400 million years ago (mya) spurred the diversification of plant-feeding (herbivorous) insects and triggered an ongoing chemical co-evolutionary arms race. Because ancestors of most herbivorous insects first colonized plants >200 mya, the sands of time have buried evidence of how their genomes changed with their diet. We leveraged the serendipitous intersection of two genetic model systems: a close relative of yeast-feeding fruit fly ( Drosophila melanogaste r), the "wasabi fly" ( Scaptomyza flava ), that evolved to consume mustard plants including Arabidopsis thaliana . The yeast-to-mustard dietary transition remodeled the fly's gene repertoire for sensing and detoxifying chemicals. Although many genes were lost, some underwent duplications that encode the most efficient detoxifying enzymes against mustard oils known from animals. Gloss et al. 2019 1ABSTRACT One-quarter of extant Eukaryotic species are herbivorous insects, yet the genomic basis of this extraordinary adaptive radiation is unclear. Recently-derived herbivorous species hold promise for understanding how colonization of living plant tissues shaped the evolution of herbivore genomes. Here, we characterized exceptional patterns of evolution coupled with a recent (<15 mya) transition to herbivory of mustard plants (Brassicaceae, including Arabidopsis thaliana ) in the fly genus Scaptomyza, nested within the paraphyletic genus Drosophila . We discovered a radiation of mustard-specialized Scaptomyza species, comparable in diversity to the Drosophila melanogaster species subgroup. Stable isotope, behavioral, and viability assays revealed these flies are obligate herbivores. Genome sequencing of one species, S. flava, revealed that the evolution of herbivory drove a contraction in gene families involved in chemosensation and xenobiotic metabolism. Against this backdrop of losses, highly targeted gains ("blooms") were found in Phase I and Phase II detoxification gene sub-families, including glutathione S-transferase ( Gst ) and cytochrome P450 ( Cyp450 ) genes. S. flava has more validated paralogs of a single Cyp450 (N=6 for Cyp6g1 ) and Gst (N=5 for GstE5-8 ) than any other drosophilid. Functional studies of the Gst repertoire in S. flava showed that transcription of S. flava GstE5-8 paralogs was differentially regulated by dietary mustard oils, and of 22 heterologously expressed cytosolic S. flava GST enzymes, GSTE5-8 enzymes were exceptionally well-adapted to mustard oil detoxification in vitro . One, GSTE5-8a, was an order of magnitude more efficient at metabolizing mustard oils than GSTs from any other metazoan. The serendipitous intersection of two genetic model organisms, Drosophila and Arabidopsis , helped illuminate how an insect genome was remodeled during the evolutionary transformation to herbivory, identifying mechanisms that facilitated the evolution of the most diverse guild of animal life.

Objective: To examine the effectiveness of a web-based parenting intervention (Internet-Based Interacting Together Everyday: Recovery After Childhood TBI [I-InTERACT]) and an abbreviated version (Express) in reducing executive dysfunction and internalizing problems among young children following traumatic brain injury (TBI). Method: Parents of 113 children (ages 3-9 years) who had sustained a TBI were randomized to 1 of 3 treatment groups: I-InTERACT, Express, or an Internet Resource Comparison (IRC) group. Parents who participated in either I-InTERACT or Express completed self-guided web sessions and received live coaching of their parenting skills via videoconferencing with a therapist. I-InTERACT included additional psychoeducation, stress management, and family communication skills (eg, marriage, grief, pain, and sleep). Analyses of covariance were utilized to compare the groups on parent-reported executive function behaviors (ie, Behavior Rating Inventory of Executive Function) and internalizing symptoms (ie, Child Behavior Checklist) at baseline and 6 months. Results: Parents who participated in Express reported significantly lower levels of executive dysfunction than those in I-InTERACT, β = −0.49; t(2, 73) = −2.47, P = .048, and significantly lower levels of withdrawal than those in the IRC group, β = −0.44; t(2, 74) = −2.22, P = .03. The Express group did not significantly differ from the IRC group on executive function behaviors or the I-InTERACT group on internalizing problems, all P > .05. Children with more problems at baseline, families with lower education levels, and parents with more symptoms of depression benefited most. Conclusion: A brief, online parent training intervention may be efficacious in improving executive dysfunction and internalizing problems following early TBI, particularly among children of lower socioeconomic status or with existing behavioral concerns.