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 R.R. 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

doi:10.7554/eLife.66405

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 R.R. 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 TanaskovićPavle 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

Ecology and Evolutionary Biology

Research output: Contribution to journal › Article › peer-review

33 Scopus citations

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.

Original language	English (US)
Article number	e66405
Journal	eLife
Volume	10
DOIs	https://doi.org/10.7554/eLife.66405
State	Published - Jul 2021

Keywords

Comparative Genomics
Drosophila
Genome assembly
Long reads
Nanopore

ASJC Scopus subject areas

Neuroscience(all)
Biochemistry, Genetics and Molecular Biology(all)
Immunology and Microbiology(all)

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10.7554/eLife.66405

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Kim, B. Y., Wang, J. R., Miller, D. E., Barmina, O., Delaney, E., Thompson, A., Comeault, A. A., Peede, D., D’agostino, E. R. R., Pelaez, J., Aguilar, J. M., Haji, D., Matsunaga, T., Armstrong, E. E., Zych, M., Ogawa, Y., Stamenković-Radak, M., Jelić, M., Veselinović, M. S., ... Petrov, D. A. (2021). Highly contiguous assemblies of 101 drosophilid genomes. eLife, 10, [e66405]. https://doi.org/10.7554/eLife.66405

Kim, BY, Wang, JR, Miller, DE, Barmina, O, Delaney, E, Thompson, A, Comeault, AA, Peede, D, D’agostino, ERR, Pelaez, J, Aguilar, JM, Haji, D, Matsunaga, T, Armstrong, EE, Zych, M, Ogawa, Y, Stamenković-Radak, M, Jelić, M, Veselinović, MS, Tanasković, M, Erić, P, Gao, JJ, Katoh, TK, Toda, MJ, Watabe, H, Watada, M, Davis, JS, Moyle, LC, Manoli, G, Bertolini, E, Košťál, V, Hawley, RS, Takahashi, A, Jones, CD, Price, DK, Whiteman, N, Kopp, A, Matute, DR & Petrov, DA 2021, 'Highly contiguous assemblies of 101 drosophilid genomes', eLife, vol. 10, e66405. https://doi.org/10.7554/eLife.66405

@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",

}

TY - JOUR

T1 - Highly contiguous assemblies of 101 drosophilid genomes

AU - Kim, Bernard Y.

AU - Wang, Jeremy R.

AU - Miller, Danny E.

AU - Barmina, Olga

AU - Delaney, Emily

AU - Thompson, Ammon

AU - Comeault, Aaron A.

AU - Peede, David

AU - D’agostino, Emmanuel R.R.

AU - Pelaez, Julianne

AU - Aguilar, Jessica M.

AU - Haji, Diler

AU - Matsunaga, Teruyuki

AU - Armstrong, Ellie E.

AU - Zych, Molly

AU - Ogawa, Yoshitaka

AU - Stamenković-Radak, Marina

AU - Jelić, Mihailo

AU - Veselinović, Marija Savić

AU - Tanasković, Marija

AU - Erić, Pavle

AU - Gao, Jian Jun

AU - Katoh, Takehiro K.

AU - Toda, Masanori J.

AU - Watabe, Hideaki

AU - Watada, Masayoshi

AU - Davis, Jeremy S.

AU - Moyle, Leonie C.

AU - Manoli, Giulia

AU - Bertolini, Enrico

AU - Košťál, Vladimír

AU - Hawley, R. Scott

AU - Takahashi, Aya

AU - Jones, Corbin D.

AU - Price, Donald K.

AU - Whiteman, Noah

AU - Kopp, Artyom

AU - Matute, Daniel R.

AU - Petrov, Dmitri A.

N1 - 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: © 2021, eLife Sciences Publications Ltd. All rights reserved.

PY - 2021/7

Y1 - 2021/7

N2 - 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.

AB - 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.

KW - Comparative Genomics

KW - Drosophila

KW - Genome assembly

KW - Long reads

KW - Nanopore

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JO - eLife

JF - eLife

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ER -

Highly contiguous assemblies of 101 drosophilid genomes

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