eLife (Jul 2021)
Highly contiguous assemblies of 101 drosophilid genomes
- Bernard Y Kim,
- Jeremy R Wang,
- Danny E Miller,
- Olga Barmina,
- Emily Delaney,
- Ammon Thompson,
- Aaron A Comeault,
- David Peede,
- Emmanuel RR D'Agostino,
- Julianne Pelaez,
- Jessica M Aguilar,
- Diler Haji,
- Teruyuki Matsunaga,
- Ellie E Armstrong,
- Molly Zych,
- Yoshitaka Ogawa,
- Marina Stamenković-Radak,
- Mihailo Jelić,
- Marija Savić Veselinović,
- Marija Tanasković,
- Pavle Erić,
- Jian-Jun Gao,
- Takehiro K Katoh,
- Masanori J Toda,
- Hideaki Watabe,
- Masayoshi Watada,
- Jeremy S Davis,
- Leonie C Moyle,
- Giulia Manoli,
- Enrico Bertolini,
- Vladimír Košťál,
- R Scott Hawley,
- Aya Takahashi,
- Corbin D Jones,
- Donald K Price,
- Noah Whiteman,
- Artyom Kopp,
- Daniel R Matute,
- Dmitri A Petrov
Affiliations
- Bernard Y Kim
- ORCiD
- Department of Biology, Stanford University, Stanford, United States
- Jeremy R Wang
- ORCiD
- Department of Genetics, University of North Carolina, Chapel Hill, United States
- Danny E Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s Hospital, Seattle, United States
- Olga Barmina
- Department of Evolution and Ecology, University of California Davis, Davis, United States
- Emily Delaney
- ORCiD
- Department of Evolution and Ecology, University of California Davis, Davis, United States
- Ammon Thompson
- Department of Evolution and Ecology, University of California Davis, Davis, United States
- Aaron A Comeault
- ORCiD
- School of Natural Sciences, Bangor University, Bangor, United Kingdom
- David Peede
- ORCiD
- Biology Department, University of North Carolina, Chapel Hill, United States
- Emmanuel RR D'Agostino
- Biology Department, University of North Carolina, Chapel Hill, United States
- Julianne Pelaez
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States
- Jessica M Aguilar
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States
- Diler Haji
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States
- Teruyuki Matsunaga
- ORCiD
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States
- Ellie E Armstrong
- Department of Biology, Stanford University, Stanford, United States
- Molly Zych
- Molecular and Cellular Biology Program, University of Washington, Seattle, United States
- Yoshitaka Ogawa
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
- Marina Stamenković-Radak
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
- Mihailo Jelić
- ORCiD
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
- Marija Savić Veselinović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
- Marija Tanasković
- University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, Belgrade, Serbia
- Pavle Erić
- ORCiD
- University of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, Belgrade, Serbia
- Jian-Jun Gao
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Takehiro K Katoh
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
- Masanori J Toda
- ORCiD
- Hokkaido University Museum, Hokkaido University, Sapporo, Japan
- Hideaki Watabe
- Biological Laboratory, Sapporo College, Hokkaido University of Education, Sapporo, Japan
- Masayoshi Watada
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Japan
- Jeremy S Davis
- Department of Biology, University of Kentucky, Lexington, United States
- Leonie C Moyle
- Department of Biology, Indiana University, Bloomington, United States
- Giulia Manoli
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of Würzburg, Würzburg, Germany
- Enrico Bertolini
- Neurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of Würzburg, Würzburg, Germany
- Vladimír Košťál
- Institute of Entomology, Biology Centre, Academy of Sciences of the Czech Republic, Prague, Czech Republic
- R Scott Hawley
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Stowers Institute for Medical Research, Kansas City, United States
- Aya Takahashi
- ORCiD
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
- Corbin D Jones
- Biology Department, University of North Carolina, Chapel Hill, United States
- Donald K Price
- School of Life Science, University of Nevada, Las Vegas, United States
- Noah Whiteman
- ORCiD
- Department of Integrative Biology, University of California, Berkeley, Berkeley, United States
- Artyom Kopp
- ORCiD
- Department of Evolution and Ecology, University of California Davis, Davis, United States
- Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill, United States
- Dmitri A Petrov
- ORCiD
- Department of Biology, Stanford University, Stanford, United States
- DOI
- https://doi.org/10.7554/eLife.66405
- Journal volume & issue
-
Vol. 10
Abstract
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.
Keywords
