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In many respects, the foundation for modern genomics was built by those studying the vinegar (also called fruit or pomace) fly Drosophila melanogaster and related species in the family Drosophilidae. In addition to establishing new standards for modern large-scale genomics projects and opening avenues for genomic research that were previously only feasible in model organisms across a multitude of species, these projects are creating an opportunity to study genetic variation and address fundamental biological questions at a scope that was simply not possible before. Some often overlapping examples include the Vertebrate Genomes Project ( Rhie et al., 2021), the Bird 10,000 Genomes Project ( Feng et al., 2020), the Zoonomia Project ( Zoonomia Consortium et al., 2020), the Darwin Tree of Life ( Threlfall and Blaxter, 2021), the Earth Biogenome Project ( Lewin et al., 2018), and the 5000 Arthropod Genomes Initiative ( Robinson et al., 2011a). Currently, a number of large consortia are leading well-publicized efforts to assemble the genomes of many taxa throughout the Tree of Life. The rise of long-read sequencing alongside the continuously decreasing costs of next-generation sequencing have served to greatly democratize the process of genome assembly, making it feasible to assemble high-quality genomes at a previously unthinkable scale. 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. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. 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. 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. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. School of Life Science, University of Nevada, United States.Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Stowers Institute for Medical Research, United States.Institute of Entomology, Biology Centre, Academy of Sciences of the Czech Republic, Czech Republic.Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of Würzburg, Germany.Department of Biology, Indiana University, United States.Department of Biology, University of Kentucky, United States.Graduate School of Science and Engineering, Ehime University, Japan.Biological Laboratory, Sapporo College, Hokkaido University of Education, Japan.Hokkaido University Museum, Hokkaido University, Japan.School of Ecology and Environmental Science, Yunnan University, China.University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, Serbia.
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Faculty of Biology, University of Belgrade, Serbia.Department of Biological Sciences, Tokyo Metropolitan University, Japan.Molecular and Cellular Biology Program, University of Washington, United States.Department of Integrative Biology, University of California, Berkeley, United States.Biology Department, University of North Carolina, United States.School of Natural Sciences, Bangor University, United Kingdom.Department of Evolution and Ecology, University of California Davis, United States.Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s Hospital, United States.Department of Genetics, University of North Carolina, United States.Department of Biology, Stanford University, United States.