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.
Reviewing Editor
- Graham Coop, University of California, Davis, United States
Version history
- Preprint posted: December 15, 2020 (view preprint)
- Received: January 11, 2021
- Accepted: July 16, 2021
- Accepted Manuscript published: July 19, 2021 (version 1)
- Version of Record published: August 4, 2021 (version 2)
- Version of Record updated: March 18, 2022 (version 3)
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
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CD4+ T cell activation is driven by five-module receptor complexes. The T cell receptor (TCR) is the receptor module that binds composite surfaces of peptide antigens embedded within MHCII molecules (pMHCII). It associates with three signaling modules (CD3γε, CD3δε, and CD3ζζ) to form TCR-CD3 complexes. CD4 is the coreceptor module. It reciprocally associates with TCR-CD3-pMHCII assemblies on the outside of a CD4+ T cells and with the Src kinase, LCK, on the inside. Previously, we reported that the CD4 transmembrane GGXXG and cytoplasmic juxtamembrane (C/F)CV+C motifs found in eutherian (placental mammal) CD4 have constituent residues that evolved under purifying selection (Lee et al., 2022). Expressing mutants of these motifs together in T cell hybridomas increased CD4-LCK association but reduced CD3ζ, ZAP70, and PLCγ1 phosphorylation levels, as well as IL-2 production, in response to agonist pMHCII. Because these mutants preferentially localized CD4-LCK pairs to non-raft membrane fractions, one explanation for our results was that they impaired proximal signaling by sequestering LCK away from TCR-CD3. An alternative hypothesis is that the mutations directly impacted signaling because the motifs normally play an LCK-independent role in signaling. The goal of this study was to discriminate between these possibilities. Using T cell hybridomas, our results indicate that: intracellular CD4-LCK interactions are not necessary for pMHCII-specific signal initiation; the GGXXG and (C/F)CV+C motifs are key determinants of CD4-mediated pMHCII-specific signal amplification; the GGXXG and (C/F)CV+C motifs exert their functions independently of direct CD4-LCK association. These data provide a mechanistic explanation for why residues within these motifs are under purifying selection in jawed vertebrates. The results are also important to consider for biomimetic engineering of synthetic receptors.
