TY  - JOUR
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 RR
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  - 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 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
PY  - 2021
UR  - https://elifesciences.org/articles/66405
UR  - http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC8337076
UR  - https://radar.ibiss.bg.ac.rs/handle/123456789/4457
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.
PB  - Cambridge: eLife Sciences Publications Ltd
T2  - eLife
T1  - Highly contiguous assemblies of 101 drosophilid genomes.
VL  - 10
DO  - 10.7554/eLife.66405
SP  - e66405
ER  - 

@article{
author = "Kim, Bernard Y and Wang, Jeremy R and Miller, Danny E and Barmina, Olga and Delaney, Emily and Thompson, Ammon and Comeault, Aaron A and Peede, David and D'Agostino, Emmanuel RR and Pelaez, Julianne and Aguilar, Jessica M and Haji, Diler and Matsunaga, Teruyuki and Armstrong, Ellie E and Zych, Molly and Ogawa, Yoshitaka and Stamenković-Radak, Marina and Jelić, Mihailo and Savić Veselinović, Marija and Tanasković, Marija and Erić, Pavle and Gao, Jian-Jun and Katoh, Takehiro K and Toda, Masanori J and Watabe, Hideaki and Watada, Masayoshi and Davis, Jeremy S and Moyle, Leonie C and Manoli, Giulia and Bertolini, Enrico and Košťál, Vladimír and Hawley, R Scott and Takahashi, Aya and Jones, Corbin D and Price, Donald K and Whiteman, Noah and Kopp, Artyom and Matute, Daniel R and Petrov, Dmitri A",
year = "2021",
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.",
publisher = "Cambridge: eLife Sciences Publications Ltd",
journal = "eLife",
title = "Highly contiguous assemblies of 101 drosophilid genomes.",
volume = "10",
doi = "10.7554/eLife.66405",
pages = "e66405"
}

Kim, B. Y., Wang, J. R., Miller, D. E., Barmina, O., Delaney, E., Thompson, A., Comeault, A. A., Peede, D., D'Agostino, E. R., Pelaez, J., Aguilar, J. M., Haji, D., Matsunaga, T., Armstrong, E. E., Zych, M., Ogawa, Y., Stamenković-Radak, M., Jelić, M., Savić Veselinović, M., Tanasković, M., Erić, P., Gao, J., Katoh, T. K., Toda, M. J., Watabe, H., Watada, M., Davis, J. S., Moyle, L. C., Manoli, G., Bertolini, E., Košťál, V., Hawley, R. S., Takahashi, A., Jones, C. D., Price, D. K., Whiteman, N., Kopp, A., Matute, D. R.,& Petrov, D. A.. (2021). Highly contiguous assemblies of 101 drosophilid genomes.. in eLife
Cambridge: eLife Sciences Publications Ltd., 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 ER, Pelaez J, Aguilar JM, Haji D, Matsunaga T, Armstrong EE, Zych M, Ogawa Y, Stamenković-Radak M, Jelić M, Savić Veselinović M, Tanasković M, Erić P, Gao J, 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. Highly contiguous assemblies of 101 drosophilid genomes.. in eLife. 2021;10:e66405.
doi:10.7554/eLife.66405 .

Kim, Bernard Y, Wang, Jeremy R, Miller, Danny E, Barmina, Olga, Delaney, Emily, Thompson, Ammon, Comeault, Aaron A, Peede, David, D'Agostino, Emmanuel RR, Pelaez, Julianne, Aguilar, Jessica M, Haji, Diler, Matsunaga, Teruyuki, Armstrong, Ellie E, Zych, Molly, Ogawa, Yoshitaka, Stamenković-Radak, Marina, Jelić, Mihailo, Savić Veselinović, Marija, Tanasković, Marija, Erić, Pavle, Gao, Jian-Jun, Katoh, Takehiro K, Toda, Masanori J, Watabe, Hideaki, Watada, Masayoshi, Davis, Jeremy S, Moyle, Leonie C, Manoli, Giulia, Bertolini, Enrico, Košťál, Vladimír, Hawley, R Scott, Takahashi, Aya, Jones, Corbin D, Price, Donald K, Whiteman, Noah, Kopp, Artyom, Matute, Daniel R, Petrov, Dmitri A, "Highly contiguous assemblies of 101 drosophilid genomes." in eLife, 10 (2021):e66405,
https://doi.org/10.7554/eLife.66405 . .