One fly–one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster

Adams, Matthew S.; McBroome, Jakob; Maurer, Nicholas; Pepper-Tunick, Evan; Saremi, Nedda F.; Green, Edward; Vollmers, Christopher; Corbett-Detig, Russell

doi:10.1093/nar/gkaa450

Cited by 31 publications

(35 citation statements)

References 43 publications

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“…Additional details of sample collection are provided in the Methods . Future work to improve biological and taxonomic diversity, particularly for species difficult to culture, should employ single fly sequencing and assembly workflows (Adams et al, 2020) .…”

Section: Taxon Samplingmentioning

confidence: 99%

Highly contiguous assemblies of 101 drosophilid genomes

Kim

Wang

Miller

et al. 2020

Preprint

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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 generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of high-quality assemblies for 101 lines of 95 drosophilid species encompassing 14 species groups and 35 sub-groups with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. These assemblies, along with detailed wet lab 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 within this key group.

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Section: Taxon Samplingmentioning

confidence: 99%

Highly contiguous assemblies of 101 drosophilid genomes

Kim

Wang

Miller

et al. 2020

Preprint

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“…For species that are not too small, it can be used to generate long-read data from a fraction of the total DNA. This could be levered to implement approaches combining long-read and Hi-C for even smaller species than a fruit fly [ 4 ]. This can also allow the sequenced specimen to be retained to serve as a voucher, by removing the need to crush the specimen to maximize hmw DNA recovery.…”

Section: Discussionmentioning

confidence: 99%

“…Adams et al. obtained a chromosome-level assembly from a single, laboratory-bred, fruit fly based on a combination of Nanopore long reads, Illumina short reads, and low-input Hi-C sequencing [ 4 ]. However, most metazoans are even smaller than a single mosquito or fruit fly and would not yield the amount of DNA required by the applied protocols.…”

Section: Introductionmentioning

confidence: 99%

Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola)

et al. 2021

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Background Genome sequencing of all known eukaryotes on Earth promises unprecedented advances in biological sciences and in biodiversity-related applied fields such as environmental management and natural product research. Advances in long-read DNA sequencing make it feasible to generate high-quality genomes for many non–genetic model species. However, long-read sequencing today relies on sizable quantities of high-quality, high molecular weight DNA, which is mostly obtained from fresh tissues. This is a challenge for biodiversity genomics of most metazoan species, which are tiny and need to be preserved immediately after collection. Here we present de novo genomes of 2 species of submillimeter Collembola. For each, we prepared the sequencing library from high molecular weight DNA extracted from a single specimen and using a novel ultra-low input protocol from Pacific Biosciences. This protocol requires a DNA input of only 5 ng, permitted by a whole-genome amplification step. Results The 2 assembled genomes have N50 values >5.5 and 8.5 Mb, respectively, and both contain ∼96% of BUSCO genes. Thus, they are highly contiguous and complete. The genomes are supported by an integrative taxonomy approach including placement in a genome-based phylogeny of Collembola and designation of a neotype for 1 of the species. Higher heterozygosity values are recorded in the more mobile species. Both species are devoid of the biosynthetic pathway for β-lactam antibiotics known in several Collembola, confirming the tight correlation of antibiotic synthesis with the species way of life. Conclusions It is now possible to generate high-quality genomes from single specimens of minute, field-preserved metazoans, exceeding the minimum contig N50 (1 Mb) required by the Earth BioGenome Project.

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“…hebetor. Two studies already had provided good cases to obtain a high-quality genome assembly with approximately 100 ng of DNA [6,10]. However, it still might be difficult to obtain ~100 ng DNA from a single individual in many small sized species.…”

Section: Genome Sequencingmentioning

confidence: 99%

“…Kingan et al reported a genome assembly from a single mosquito (about 100 ng genomic DNA), Anopheles coluzzii, sequenced with three PacBio SMRT Cells [6]. Adams et al developed a hybrid method (Illumina, Nanopore and Hi-C) to obtain a chromosome-level genome assembly from a single Drosophila melanogaster (totally ~200ng genomic DNA) [10]. These two studies provided good examples for sequencing a single small insect, but obtaining about 100 ng DNA from a single individual may still be challenging for many small insects such as parasitoid wasps.…”

Section: Introductionmentioning

confidence: 99%

A high-qualityde novogenome assembly from a single parasitoid wasp

Yang

Tian

et al. 2020

Preprint

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Sequencing and assembling a genome with a single individual have several advantages, such as lower heterozygosity and easier sample preparation. However, the amount of genomic DNA of some small sized organisms might not meet the standard DNA input requirement for current sequencing pipelines. Although few studies sequenced a single small insect with about 100 ng DNA as input, it may still be challenging for many small organisms to obtain such amount of DNA from a single individual. Here, we use 20 ng DNA as input, and present a high-quality genome assembly for a single haploid male parasitoid wasp (Habrobracon hebetor) using Nanopore and Illumina. Because of the low input DNA, a whole genome amplification (WGA) method is used before sequencing. The assembled genome size is 131.6 Mb with a contig N50 of 1.63 Mb. A total of 99% Benchmarking Universal Single-Copy Orthologs are detected, suggesting the high level of completeness of the genome assembly. Genome comparison between H. hebetor and its relative Bracon brevicornis shows a high-level genome synteny, indicating the genome of H. hebetor is highly accurate and contiguous. Our study provides an example for de novo assembling a genome from ultra-low input DNA, and will be used for sequencing projects of small sized species and rare samples, haploid genomics as well as population genetics of small sized species.

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One fly–one genome: chromosome-scale genome assembly of a single outbred Drosophila melanogaster

Cited by 31 publications

References 43 publications

Highly contiguous assemblies of 101 drosophilid genomes

Highly contiguous assemblies of 101 drosophilid genomes

Two high-quality de novo genomes from single ethanol-preserved specimens of tiny metazoans (Collembola)

A high-qualityde novogenome assembly from a single parasitoid wasp

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