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).
-
Nanopore-based assembly of many drosophilid genomesNCBI BioProject, PRJNA675888.
-
Sequencing and assembly of 14 Drosophila speciesNCBI BioProject, ID: 427774.
-
modENCODE Drosophila reference genome sequencing (fruit flies)NCBI BioProject, ID: 62477.
-
Drosophila montium Species Group Genomes ProjectNCBI BioProject, ID: 554346.
-
Invertebrate sample from Drosophila repletaNCBI BioProject, ID: 476692.
-
Genome sequences of 10 Drosophila speciesNCBI BioProject, ID: 322011.
-
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.
Metrics
-
- 9,647
- views
-
- 1,094
- downloads
-
- 151
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Highly contiguous assemblies of 101 drosophilid genomes
eLife 10:e66405.
https://doi.org/10.7554/eLife.66405
Further reading
-
- Evolutionary Biology
Mammalian gut microbiomes are highly dynamic communities that shape and are shaped by host aging, including age-related changes to host immunity, metabolism, and behavior. As such, gut microbial composition may provide valuable information on host biological age. Here, we test this idea by creating a microbiome-based age predictor using 13,563 gut microbial profiles from 479 wild baboons collected over 14 years. The resulting ‘microbiome clock’ predicts host chronological age. Deviations from the clock’s predictions are linked to some demographic and socio-environmental factors that predict baboon health and survival: animals who appear old-for-age tend to be male, sampled in the dry season (for females), and have high social status (both sexes). However, an individual’s ‘microbiome age’ does not predict the attainment of developmental milestones or lifespan. Hence, in our host population, gut microbiome age largely reflects current, as opposed to past, social and environmental conditions, and does not predict the pace of host development or host mortality risk. We add to a growing understanding of how age is reflected in different host phenotypes and what forces modify biological age in primates.
