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Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing

The Drosophila genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, Drosophila melanogaster, many other members in this genus also possess a well-developed set of genetic tools. Indeed, high-quality genomes exist f...

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Autores principales: Miller, Danny E., Staber, Cynthia, Zeitlinger, Julia, Hawley, R. Scott
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Genetics Society of America 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169393/
https://www.ncbi.nlm.nih.gov/pubmed/30087105
http://dx.doi.org/10.1534/g3.118.200160
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author Miller, Danny E.
Staber, Cynthia
Zeitlinger, Julia
Hawley, R. Scott
author_facet Miller, Danny E.
Staber, Cynthia
Zeitlinger, Julia
Hawley, R. Scott
author_sort Miller, Danny E.
collection PubMed
description The Drosophila genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, Drosophila melanogaster, many other members in this genus also possess a well-developed set of genetic tools. Indeed, high-quality genomes exist for several species within the genus, facilitating studies of the function and evolution of cis-regulatory regions and proteins by allowing comparisons across at least 50 million years of evolution. Yet, the available genomes still fail to capture much of the substantial genetic diversity within the Drosophila genus. We have therefore tested protocols to rapidly and inexpensively sequence and assemble the genome from any Drosophila species using single-molecule sequencing technology from Oxford Nanopore. Here, we use this technology to present highly contiguous genome assemblies of 15 Drosophila species: 10 of the 12 originally sequenced Drosophila species (ananassae, erecta, mojavensis, persimilis, pseudoobscura, sechellia, simulans, virilis, willistoni, and yakuba), four additional species that had previously reported assemblies (biarmipes, bipectinata, eugracilis, and mauritiana), and one novel assembly (triauraria). Genomes were generated from an average of 29x depth-of-coverage data that after assembly resulted in an average contig N50 of 4.4 Mb. Subsequent alignment of contigs from the published reference genomes demonstrates that our assemblies could be used to close over 60% of the gaps present in the currently published reference genomes. Importantly, the materials and reagents cost for each genome was approximately $1,000 (USD). This study demonstrates the power and cost-effectiveness of long-read sequencing for genome assembly in Drosophila and provides a framework for the affordable sequencing and assembly of additional Drosophila genomes.
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spelling pubmed-61693932018-10-04 Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing Miller, Danny E. Staber, Cynthia Zeitlinger, Julia Hawley, R. Scott G3 (Bethesda) Genome Report The Drosophila genus is a unique group containing a wide range of species that occupy diverse ecosystems. In addition to the most widely studied species, Drosophila melanogaster, many other members in this genus also possess a well-developed set of genetic tools. Indeed, high-quality genomes exist for several species within the genus, facilitating studies of the function and evolution of cis-regulatory regions and proteins by allowing comparisons across at least 50 million years of evolution. Yet, the available genomes still fail to capture much of the substantial genetic diversity within the Drosophila genus. We have therefore tested protocols to rapidly and inexpensively sequence and assemble the genome from any Drosophila species using single-molecule sequencing technology from Oxford Nanopore. Here, we use this technology to present highly contiguous genome assemblies of 15 Drosophila species: 10 of the 12 originally sequenced Drosophila species (ananassae, erecta, mojavensis, persimilis, pseudoobscura, sechellia, simulans, virilis, willistoni, and yakuba), four additional species that had previously reported assemblies (biarmipes, bipectinata, eugracilis, and mauritiana), and one novel assembly (triauraria). Genomes were generated from an average of 29x depth-of-coverage data that after assembly resulted in an average contig N50 of 4.4 Mb. Subsequent alignment of contigs from the published reference genomes demonstrates that our assemblies could be used to close over 60% of the gaps present in the currently published reference genomes. Importantly, the materials and reagents cost for each genome was approximately $1,000 (USD). This study demonstrates the power and cost-effectiveness of long-read sequencing for genome assembly in Drosophila and provides a framework for the affordable sequencing and assembly of additional Drosophila genomes. Genetics Society of America 2018-08-07 /pmc/articles/PMC6169393/ /pubmed/30087105 http://dx.doi.org/10.1534/g3.118.200160 Text en Copyright © 2018 Miller et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Genome Report
Miller, Danny E.
Staber, Cynthia
Zeitlinger, Julia
Hawley, R. Scott
Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing
title Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing
title_full Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing
title_fullStr Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing
title_full_unstemmed Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing
title_short Highly Contiguous Genome Assemblies of 15 Drosophila Species Generated Using Nanopore Sequencing
title_sort highly contiguous genome assemblies of 15 drosophila species generated using nanopore sequencing
topic Genome Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169393/
https://www.ncbi.nlm.nih.gov/pubmed/30087105
http://dx.doi.org/10.1534/g3.118.200160
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