Highly contiguous assemblies of 101 drosophilid genomes
- Stanford University, United States
- University of North Carolina, United States
- University of Washington and Seattle Children's Hospital, United States
- UC Davis, United States
- University of California, Davis, United States
- Bangor University, United Kingdom
- University of North Carolina, Chapel Hill, United States
- University of California, Berkeley, United States
- University of Washington, United States
- Tokyo Metropolitan University, Japan
- University of Belgrade, Serbia
- National Institute of Republic of Serbia, Serbia
- Institute for Biological Research, Serbia
- Yunnan University, China
- Hokkaido University, Japan
- Sapporo College, Hokkaido University of Education, Japan
- Ehime University, Japan
- University of Kentucky, United States
- Indiana University, United States
- University of Würzburg, Germany
- Academy of Sciences of the Czech Republic, Czech Republic
- Stowers Institute for Medical Research, United States
- The University of North Carolina at Chapel Hill, United States
- University of Nevada, Las Vegas, United States
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.
Data availability
All sequencing data and assemblies generated by this study are deposited at NCBI SRA and GenBank under NCBI BioProject PRJNA675888. Accession numbers for all data used but not generated by this study are provided in the supporting files. Dockerfiles and scripts for reproducing pipelines and analyses are provided on GitHub (https://github.com/flyseq/drosophila_assembly_pipelines). A detailed wet lab protocol is provided at Protocols.io (https://dx.doi.org/10.17504/protocols.io.bdfqi3mw).
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Nanopore-based assembly of many drosophilid genomesNCBI BioProject, PRJNA675888.
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Sequencing and assembly of 14 Drosophila speciesNCBI BioProject, ID: 427774.
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modENCODE Drosophila reference genome sequencing (fruit flies)NCBI BioProject, ID: 62477.
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Drosophila montium Species Group Genomes ProjectNCBI BioProject, ID: 554346.
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Invertebrate sample from Drosophila repletaNCBI BioProject, ID: 476692.
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Genome sequences of 10 Drosophila speciesNCBI BioProject, ID: 322011.
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Raw genomic sequencing data from 16 Drosophila speciesNCBI BioProject, ID: 550077.
Article and author information
Author details
Teruyuki Matsunaga
Funding
National Institute of General Medical Sciences (F32GM135998)
- Bernard Y Kim
National Institute of General Medical Sciences (R35GM119816)
- Noah K Whiteman
Uehara Memorial Foundation (201931028)
- Teruyuki Matsunaga
Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200178)
- Marina Stamenković-Radak
- Mihailo Jelić
- Marija Savić Veselinović
Ministry of Education, Science and Technological Development of the Republic of Serbia (451-03-68/2020-14/200007)
- Marija Tanasković
- Pavle Erić
National Natural Science Foundation of China (32060112)
- Jian-Jun Gao
Japan Society for the Promotion of Science (JP18K06383)
- Masayoshi Watada
European Union Horizon 2020 Research and Innovation Program (765937-CINCHRON)
- Giulia Manoli
- Enrico Bertolini
Czech Science Foundation (19-13381S)
- Vladimír Košťál
Japan Society for the Promotion of Science (JP19H03276)
- Aya Takahashi
National Science Foundation (1345247)
- Donald K Price
National Institute of General Medical Sciences (R35GM118165)
- Dmitri A Petrov
National Institute of Diabetes and Digestive and Kidney Diseases (K01DK119582)
- Jeremy Wang
National Science Foundation (DEB-1457707)
- Corbin D Jones
National Institute of General Medical Sciences (R01GM121750)
- Daniel R Matute
National Institute of General Medical Sciences (R01GM125715)
- Daniel R Matute
Google Cloud Platform Research Credits
- Bernard Y Kim
Google Cloud Platform Research Credits
- Jeremy Wang
National Institute of General Medical Sciences (R35GM122592)
- Artyom Kopp
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Kim et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Highly contiguous assemblies of 101 drosophilid genomes
eLife 10:e66405.
https://doi.org/10.7554/eLife.66405
Further reading
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- Evolutionary Biology
Euarthropods are an extremely diverse phylum in the modern, and have been since their origination in the early Palaeozoic. They grow through moulting the exoskeleton (ecdysis) facilitated by breaking along lines of weakness (sutures). Artiopodans, a group that includes trilobites and their non-biomineralizing relatives, dominated arthropod diversity in benthic communities during the Palaeozoic. Most trilobites – a hyperdiverse group of tens of thousands of species - moult by breaking the exoskeleton along cephalic sutures, a strategy that has contributed to their high diversity during the Palaeozoic. However, the recent description of similar sutures in early diverging non-trilobite artiopodans means that it is unclear whether these sutures evolved deep within Artiopoda, or convergently appeared multiple times within the group. Here, we describe new well-preserved material of Acanthomeridion, a putative early diverging artiopodan, including hitherto unknown details of its ventral anatomy and appendages revealed through CT scanning, highlighting additional possible homologous features between the ventral plates of this taxon and trilobite free cheeks. We used three coding strategies treating ventral plates as homologous to trilobite-free cheeks, to trilobite cephalic doublure, or independently derived. If ventral plates are considered homologous to free cheeks, Acanthomeridion is recovered sister to trilobites, however, dorsal ecdysial sutures are still recovered at many places within Artiopoda. If ventral plates are considered homologous to doublure or non-homologous, then Acanthomeridion is not recovered as sister to trilobites, and thus the ventral plates represent a distinct feature to trilobite doublure/free cheeks.
