Bernard Y. Kim, Stanford University
Jeremy R. Wang, The University of North Carolina at Chapel Hill
Danny E. Miller, University of Washington
Olga Barmina, University of California, Davis
Emily Delaney, University of California, Davis
Ammon Thompson, University of California, Davis
Aaron A. Comeault, Bangor University
David Peede, The University of North Carolina at Chapel Hill
Emmanuel R.R. D’agostino, The University of North Carolina at Chapel Hill
Julianne Pelaez, University of California, Berkeley
Jessica M. Aguilar, University of California, Berkeley
Diler Haji, University of California, Berkeley
Teruyuki Matsunaga, University of California, Berkeley
Ellie E. Armstrong, Stanford University
Molly Zych, University of Washington
Yoshitaka Ogawa, Tokyo Metropolitan University
Marina Stamenković-Radak, University of Belgrade
Mihailo Jelić, University of Belgrade
Marija Savić Veselinović, University of Belgrade
Marija Tanasković, University of Belgrade
Pavle Erić, University of Belgrade
Jian Jun Gao, Yunnan University
Takehiro K. Katoh, Yunnan University
Masanori J. Toda, Hokkaido University
Hideaki Watabe, Hokkaido University of Education
Masayoshi Watada, Ehime University
Jeremy S. Davis, University of Kentucky
Leonie C. Moyle, Indiana University
Giulia Manoli, University of Würzburg
Enrico Bertolini, University of Würzburg
Vladimír Košťál, Academy of Sciences of the Czech Republic
R. Scott Hawley, University of Kansas
Aya Takahashi, Tokyo Metropolitan University
Corbin D. Jones, University of North Carolina, Chapel Hill
Donald K. Price, University of Nevada, Las VegasFollow
Noah Whiteman, University of California, Berkeley
Artyom Kopp, University of California Davis
Daniel R. Matute, University of North Carolina, Chapel Hill
Dmitri A. Petrov, Stanford University

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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.


Comparative genomics; Drosophila; Genome assembly; Long reads; Nanopore


Genetics and Genomics | Life Sciences

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