Highly contiguous assemblies of 101 drosophilid genomes

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  • Bernard Y Kim
    Stanford University
  • Jeremy Wang
    University of North Carolina, Chapel Hill
  • Danny E Miller
    University of Washington, Seattle
  • Olga Barmina
    University of California, Davis
  • Emily Kay Delaney
    University of California, Davis
  • Ammon Thompson
    University of California, Davis
  • Aaron Comeault
  • David Peede
    University of North Carolina, Chapel Hill
  • Emmanuel R D'Agostino
    University of North Carolina, 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 Armstrong
    Stanford University
  • Molly Zych
    University of Washington, Seattle
  • Yoshitaka Ogawa
    Tokyo Metropolitan University
  • Marina Stamenković-Radak
    University of Belgrade
  • Mihailo Jelić
    University of Belgrade
  • Marija Savić Veselinović
    University of Belgrade
  • Marija Tanasković
    National Institute of Republic of Serbia
  • Pavle Erić
    National Institute of Republic of Serbia
  • Jian-Jun Gao
    Yunnan University
  • Takehiro K Katoh
    Yunnan University
  • Masanori J Toda
    Hokkaido University
  • Hideaki Watabe
    Hokkaido University
  • Masayoshi Watada
    Ehime University
  • Jeremy S Davis
    University of Kentucky
  • Leonie Moyle
    Indiana University
  • Giulia Manoli
    University of Würzburg
  • Enrico Bertolini
    University of Würzburg
  • Vladimír Koštál
    Academy of Sciences of the Czech Republic
  • R Scott Hawley
    University of Kansas Medical Center
  • Aya Takahashi
    Tokyo Metropolitan University
  • Corbin D Jones
    University of North Carolina, Chapel Hill
  • Donald K Price
    University of Nevada
  • Noah K 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
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.
Original languageEnglish
Article numbere66405
JournalElife
Volume10
DOIs
Publication statusPublished - 19 Jul 2021

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