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Highly contiguous assemblies of 101 drosophilid genomes

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Highly contiguous assemblies of 101 drosophilid genomes. / Kim, Bernard Y; Wang, Jeremy; Miller, Danny E et al.
In: Elife, Vol. 10, e66405, 19.07.2021.

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

HarvardHarvard

Kim, BY, Wang, J, Miller, DE, Barmina, O, Delaney, EK, Thompson, A, Comeault, A, Peede, D, D'Agostino, ER, Pelaez, J, Aguilar, JM, Haji, D, Matsunaga, T, Armstrong, E, Zych, M, Ogawa, Y, Stamenković-Radak, M, Jelić, M, Savić Veselinović, M, Tanasković, M, Erić, P, Gao, J-J, Katoh, TK, Toda, MJ, Watabe, H, Watada, M, Davis, JS, Moyle, L, Manoli, G, Bertolini, E, Koštál, V, Hawley, RS, Takahashi, A, Jones, CD, Price, DK, Whiteman, NK, 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

APA

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

CBE

Kim BY, Wang J, Miller DE, Barmina O, Delaney EK, Thompson A, Comeault A, Peede D, D'Agostino ER, Pelaez J, et al. 2021. Highly contiguous assemblies of 101 drosophilid genomes. Elife. 10:Article e66405. https://doi.org/10.7554/eLife.66405

MLA

Kim, Bernard Y et al. "Highly contiguous assemblies of 101 drosophilid genomes". Elife. 2021. 10. https://doi.org/10.7554/eLife.66405

VancouverVancouver

Kim BY, Wang J, Miller DE, Barmina O, Delaney EK, Thompson A et al. Highly contiguous assemblies of 101 drosophilid genomes. Elife. 2021 Jul 19;10:e66405. doi: 10.7554/eLife.66405

Author

Kim, Bernard Y ; Wang, Jeremy ; Miller, Danny E et al. / Highly contiguous assemblies of 101 drosophilid genomes. In: Elife. 2021 ; Vol. 10.

RIS

TY - JOUR

T1 - Highly contiguous assemblies of 101 drosophilid genomes

AU - Kim, Bernard Y

AU - Wang, Jeremy

AU - Miller, Danny E

AU - Barmina, Olga

AU - Delaney, Emily Kay

AU - Thompson, Ammon

AU - Comeault, Aaron

AU - Peede, David

AU - D'Agostino, Emmanuel R

AU - Pelaez, Julianne

AU - Aguilar, Jessica M

AU - Haji, Diler

AU - Matsunaga, Teruyuki

AU - Armstrong, Ellie

AU - Zych, Molly

AU - Ogawa, Yoshitaka

AU - Stamenković-Radak, Marina

AU - Jelić, Mihailo

AU - Savić Veselinović, Marija

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

AU - Manoli, Giulia

AU - Bertolini, Enrico

AU - Koštál, Vladimír

AU - Hawley, R Scott

AU - Takahashi, Aya

AU - Jones, Corbin D

AU - Price, Donald K

AU - Whiteman, Noah K

AU - Kopp, Artyom

AU - Matute, Daniel R

AU - Petrov, Dmitri A

PY - 2021/7/19

Y1 - 2021/7/19

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.

U2 - 10.7554/eLife.66405

DO - 10.7554/eLife.66405

M3 - Article

VL - 10

JO - Elife

JF - Elife

SN - 2050-084X

M1 - e66405

ER -