Highly contiguous assemblies of 101 drosophilid genomes
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. Rec...
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2021-07-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/66405 |
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Article |
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DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Bernard Y Kim Jeremy R Wang Danny E Miller Olga Barmina Emily Delaney Ammon Thompson Aaron A Comeault David Peede Emmanuel RR 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 |
| spellingShingle |
Bernard Y Kim Jeremy R Wang Danny E Miller Olga Barmina Emily Delaney Ammon Thompson Aaron A Comeault David Peede Emmanuel RR 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 Highly contiguous assemblies of 101 drosophilid genomes eLife Drosophila Drosophilidae comparative genomics genome assembly nanopore long reads |
| author_facet |
Bernard Y Kim Jeremy R Wang Danny E Miller Olga Barmina Emily Delaney Ammon Thompson Aaron A Comeault David Peede Emmanuel RR 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 |
| author_sort |
Bernard Y Kim |
| title |
Highly contiguous assemblies of 101 drosophilid genomes |
| title_short |
Highly contiguous assemblies of 101 drosophilid genomes |
| title_full |
Highly contiguous assemblies of 101 drosophilid genomes |
| title_fullStr |
Highly contiguous assemblies of 101 drosophilid genomes |
| title_full_unstemmed |
Highly contiguous assemblies of 101 drosophilid genomes |
| title_sort |
highly contiguous assemblies of 101 drosophilid genomes |
| publisher |
eLife Sciences Publications Ltd |
| series |
eLife |
| issn |
2050-084X |
| publishDate |
2021-07-01 |
| description |
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. |
| topic |
Drosophila Drosophilidae comparative genomics genome assembly nanopore long reads |
| url |
https://elifesciences.org/articles/66405 |
| work_keys_str_mv |
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doaj-c9a4e43af79a4652bb1b17ca0d8011cd2021-08-04T16:06:54ZengeLife Sciences Publications LtdeLife2050-084X2021-07-011010.7554/eLife.66405Highly contiguous assemblies of 101 drosophilid genomesBernard Y Kim0https://orcid.org/0000-0002-5025-1292Jeremy R Wang1https://orcid.org/0000-0002-0673-9418Danny E Miller2Olga Barmina3Emily Delaney4https://orcid.org/0000-0003-3609-5702Ammon Thompson5Aaron A Comeault6https://orcid.org/0000-0003-3954-2416David Peede7https://orcid.org/0000-0002-4826-0464Emmanuel RR D'Agostino8Julianne Pelaez9Jessica M Aguilar10Diler Haji11Teruyuki Matsunaga12https://orcid.org/0000-0002-6433-622XEllie E Armstrong13Molly Zych14Yoshitaka Ogawa15Marina Stamenković-Radak16Mihailo Jelić17https://orcid.org/0000-0002-1637-0933Marija Savić Veselinović18Marija Tanasković19Pavle Erić20https://orcid.org/0000-0002-0053-1982Jian-Jun Gao21Takehiro K Katoh22Masanori J Toda23https://orcid.org/0000-0003-0158-1858Hideaki Watabe24Masayoshi Watada25Jeremy S Davis26Leonie C Moyle27Giulia Manoli28Enrico Bertolini29Vladimír Košťál30R Scott Hawley31Aya Takahashi32https://orcid.org/0000-0002-8391-7417Corbin D Jones33Donald K Price34Noah Whiteman35https://orcid.org/0000-0003-1448-4678Artyom Kopp36https://orcid.org/0000-0001-5224-0741Daniel R Matute37Dmitri A Petrov38https://orcid.org/0000-0002-3664-9130Department of Biology, Stanford University, Stanford, United StatesDepartment of Genetics, University of North Carolina, Chapel Hill, United StatesDepartment of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s Hospital, Seattle, United StatesDepartment of Evolution and Ecology, University of California Davis, Davis, United StatesDepartment of Evolution and Ecology, University of California Davis, Davis, United StatesDepartment of Evolution and Ecology, University of California Davis, Davis, United StatesSchool of Natural Sciences, Bangor University, Bangor, United KingdomBiology Department, University of North Carolina, Chapel Hill, United StatesBiology Department, University of North Carolina, Chapel Hill, United StatesDepartment of Integrative Biology, University of California, Berkeley, Berkeley, United StatesDepartment of Integrative Biology, University of California, Berkeley, Berkeley, United StatesDepartment of Integrative Biology, University of California, Berkeley, Berkeley, United StatesDepartment of Integrative Biology, University of California, Berkeley, Berkeley, United StatesDepartment of Biology, Stanford University, Stanford, United StatesMolecular and Cellular Biology Program, University of Washington, Seattle, United StatesDepartment of Biological Sciences, Tokyo Metropolitan University, Hachioji, JapanFaculty of Biology, University of Belgrade, Belgrade, SerbiaFaculty of Biology, University of Belgrade, Belgrade, SerbiaFaculty of Biology, University of Belgrade, Belgrade, SerbiaUniversity of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, Belgrade, SerbiaUniversity of Belgrade, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, Belgrade, SerbiaSchool of Ecology and Environmental Science, Yunnan University, Kunming, ChinaSchool of Ecology and Environmental Science, Yunnan University, Kunming, ChinaHokkaido University Museum, Hokkaido University, Sapporo, JapanBiological Laboratory, Sapporo College, Hokkaido University of Education, Sapporo, JapanGraduate School of Science and Engineering, Ehime University, Matsuyama, JapanDepartment of Biology, University of Kentucky, Lexington, United StatesDepartment of Biology, Indiana University, Bloomington, United StatesNeurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of Würzburg, Würzburg, GermanyNeurobiology and Genetics, Theodor Boveri Institute, Biocentre, University of Würzburg, Würzburg, GermanyInstitute of Entomology, Biology Centre, Academy of Sciences of the Czech Republic, Prague, Czech RepublicDepartment of Molecular and Integrative Physiology, University of Kansas Medical Center, Stowers Institute for Medical Research, Kansas City, United StatesDepartment of Biological Sciences, Tokyo Metropolitan University, Hachioji, JapanBiology Department, University of North Carolina, Chapel Hill, United StatesSchool of Life Science, University of Nevada, Las Vegas, United StatesDepartment of Integrative Biology, University of California, Berkeley, Berkeley, United StatesDepartment of Evolution and Ecology, University of California Davis, Davis, United StatesBiology Department, University of North Carolina, Chapel Hill, United StatesDepartment of Biology, Stanford University, Stanford, United StatesOver 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.https://elifesciences.org/articles/66405DrosophilaDrosophilidaecomparative genomicsgenome assemblynanoporelong reads |