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.

Biological Laboratory Sapporo College Hokkaido University of Education Sapporo Japan

Biology Department University of North Carolina Chapel Hill United States

Department of Biological Sciences Tokyo Metropolitan University Hachioji Japan

Department of Biology Indiana University Bloomington United States

Department of Biology Stanford University Stanford United States

Department of Biology University of Kentucky Lexington United States

Department of Evolution and Ecology University of California Davis Davis United States

Department of Genetics University of North Carolina Chapel Hill United States

Department of Integrative Biology University of California Berkeley Berkeley United States

Department of Molecular and Integrative Physiology University of Kansas Medical Center Stowers Institute for Medical Research Kansas City United States

Department of Pediatrics Division of Genetic Medicine University of Washington and Seattle Children's Hospital Seattle United States

Faculty of Biology University of Belgrade Belgrade Serbia

Graduate School of Science and Engineering Ehime University Matsuyama Japan

Hokkaido University Museum Hokkaido University Sapporo Japan

Institute of Entomology Biology Centre Academy of Sciences of the Czech Republic Prague Czech Republic

Molecular and Cellular Biology Program University of Washington Seattle United States

Neurobiology and Genetics Theodor Boveri Institute Biocentre University of Würzburg Würzburg Germany

School of Ecology and Environmental Science Yunnan University Kunming China

School of Life Science University of Nevada Las Vegas United States

School of Natural Sciences Bangor University Bangor United Kingdom

University of Belgrade Institute for Biological Research Siniša Stanković National Institute of Republic of Serbia Belgrade Serbia

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Elife. 2022 Mar 18;11:e78579. doi: 10.7554/eLife.78579. PubMed

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Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life

Single-fly assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life