@article{0a06d04729b944f0ac3f078a6cb5ec95,
title = "Highly contiguous assemblies of 101 drosophilid genomes",
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 = "Comparative Genomics, Drosophila, Genome assembly, Long reads, Nanopore",
author = "Kim, {Bernard Y.} and Wang, {Jeremy R.} and Miller, {Danny E.} and Olga Barmina and Emily Delaney and Ammon Thompson and Comeault, {Aaron A.} and David Peede and D{\textquoteright}agostino, {Emmanuel R.R.} and Julianne Pelaez and Aguilar, {Jessica M.} and Diler Haji and Teruyuki Matsunaga and Armstrong, {Ellie E.} and Molly Zych and Yoshitaka Ogawa and Marina Stamenkovi{\'c}-Radak and Mihailo Jeli{\'c} and Veselinovi{\'c}, {Marija Savi{\'c}} and Marija Tanaskovi{\'c} and Pavle Eri{\'c} and Gao, {Jian Jun} and Katoh, {Takehiro K.} and Toda, {Masanori J.} and Hideaki Watabe and Masayoshi Watada and Davis, {Jeremy S.} and Moyle, {Leonie C.} and Giulia Manoli and Enrico Bertolini and Vladim{\'i}r Ko{\v s}{\v t}{\'a}l and Hawley, {R. Scott} and Aya Takahashi and Jones, {Corbin D.} and Price, {Donald K.} and Noah Whiteman and Artyom Kopp and Matute, {Daniel R.} and Petrov, {Dmitri A.}",
note = "Funding Information: BYK was supported by the NIH under award no. F32GM135998 and Google Cloud Platform Research Credits. DAP, BYK, and EEA were supported by the NIH under award no. R35GM118165. JRW was supported by the NIH under award no. K01DK119582, Amazon Web Services Cloud Credits for Research, and Google Cloud Platform Research Credits. JRW and CDJ were supported by the NSF under award DEB-1457707. DRM was supported by the NIH under award nos. R01GM121750 and R01GM125715. AK, OB, ED, and A. Thompson were supported by the NIH under award no. R35GM122592. NW, JP, JMA, DH, and TM were supported by the NIH under award no. NIGMS GM119816. JP was supported by the NSF GRFP and the Mentored Research Award from UC Berkeley. TM was supported by the Uehara Memorial Foundation under award no. 201931028. MS-R, MJ, and MSV were supported by the Ministry of Education, Science and Technological Development of the Republic of Serbia under grant no. 451-03-68/2020-14/200178. MT and PE were supported by the Ministry of Education, Science and Technological Development of the Republic of Serbia under grant no. 451-03-68/2020-14/200007. JJG was supported by the NFSC under award no. 32060112. MW was supported by the JSPS KAKENHI under award no. JP18K06383. GM and EB were supported by the European Union's Horizon 2020 research and innovation program under award no. 765937-CINCHRON. VK was supported by the Czech Science Foundation under award no. 19-13381S. RSH is an American Cancer Society Research Professor. AT was supported by the JSPS KAKENHI under award no. JP19H03276. DKP was supported by the NSF under award no. 1345247. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Publisher Copyright: {\textcopyright} 2021, eLife Sciences Publications Ltd. All rights reserved.",
year = "2021",
month = jul,
doi = "10.7554/eLife.66405",
language = "English (US)",
volume = "10",
journal = "eLife",
issn = "2050-084X",
publisher = "eLife Sciences Publications",
}