Highly contiguous assemblies of 101 drosophilid genomes

eLife

Hideaki Watabe¹  Daniel R Matute²  David Peede²  Emmanuel RR D'Agostino²  Corbin D Jones²  Yoshitaka Ogawa³  Aya Takahashi³  Leonie C Moyle⁴  Bernard Y Kim⁵  Ellie E Armstrong⁵  Dmitri A Petrov⁵  Jeremy S Davis⁶  Olga Barmina⁷  Ammon Thompson⁷  Emily Delaney⁷  Artyom Kopp⁷  Jeremy R Wang⁸  Teruyuki Matsunaga⁹  Diler Haji⁹  Julianne Pelaez⁹  Noah Whiteman⁹  Jessica M Aguilar⁹  R Scott Hawley^1,10  Danny E Miller^1,11  Mihailo Jelić^1,12  Marina Stamenković-Radak^1,12  Marija Savić Veselinović^1,12  Masayoshi Watada^1,13  Masanori J Toda^1,14  Vladimír Košťál^1,15  Molly Zych^1,16  Enrico Bertolini^1,17  Giulia Manoli^1,17  Jian-Jun Gao^1,18  Takehiro K Katoh^1,18  Donald K Price^1,19  Aaron A Comeault^2,20  Pavle Erić^2,21  Marija Tanasković^2,21 

[1] 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;

关键词: Drosophila;    Drosophilidae;    comparative genomics;    genome assembly;    nanopore;    long reads;   

DOI  :  10.7554/eLife.66405

来源: DOAJ

【 摘 要 】

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.

【 授权许可】

Unknown