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DrosOmics: A Browser to Explore -omics Variation Across High-Quality Reference Genomes From Natural Populations of Drosophila melanogaster
The advent of long-read sequencing technologies has allowed the generation of multiple high-quality de novo genome assemblies for multiple species, including well-known model species such as Drosophila melanogaster. Genome assemblies for multiple individuals of the same species are key to discover t...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10089646/ https://www.ncbi.nlm.nih.gov/pubmed/36971243 http://dx.doi.org/10.1093/molbev/msad075 |
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author | Coronado-Zamora, Marta Salces-Ortiz, Judit González, Josefa |
author_facet | Coronado-Zamora, Marta Salces-Ortiz, Judit González, Josefa |
author_sort | Coronado-Zamora, Marta |
collection | PubMed |
description | The advent of long-read sequencing technologies has allowed the generation of multiple high-quality de novo genome assemblies for multiple species, including well-known model species such as Drosophila melanogaster. Genome assemblies for multiple individuals of the same species are key to discover the genetic diversity present in natural populations, especially the one generated by transposable elements, the most common type of structural variant. Despite the availability of multiple genomic data sets for D. melanogaster populations, we lack an efficient visual tool to display different genome assemblies simultaneously. In this work, we present DrosOmics, a population genomic-oriented browser currently containing 52 high-quality reference genomes of D. melanogaster, including annotations from a highly reliable set of transposable elements, and functional transcriptomics and epigenomics data for 26 genomes. DrosOmics is based on JBrowse 2, a highly scalable platform, which allows the visualization of multiple assemblies at once, key to unraveling structural and functional features of D. melanogaster natural populations. DrosOmics is an open access browser and is freely available at http://gonzalezlab.eu/drosomics. |
format | Online Article Text |
id | pubmed-10089646 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-100896462023-04-12 DrosOmics: A Browser to Explore -omics Variation Across High-Quality Reference Genomes From Natural Populations of Drosophila melanogaster Coronado-Zamora, Marta Salces-Ortiz, Judit González, Josefa Mol Biol Evol Resource The advent of long-read sequencing technologies has allowed the generation of multiple high-quality de novo genome assemblies for multiple species, including well-known model species such as Drosophila melanogaster. Genome assemblies for multiple individuals of the same species are key to discover the genetic diversity present in natural populations, especially the one generated by transposable elements, the most common type of structural variant. Despite the availability of multiple genomic data sets for D. melanogaster populations, we lack an efficient visual tool to display different genome assemblies simultaneously. In this work, we present DrosOmics, a population genomic-oriented browser currently containing 52 high-quality reference genomes of D. melanogaster, including annotations from a highly reliable set of transposable elements, and functional transcriptomics and epigenomics data for 26 genomes. DrosOmics is based on JBrowse 2, a highly scalable platform, which allows the visualization of multiple assemblies at once, key to unraveling structural and functional features of D. melanogaster natural populations. DrosOmics is an open access browser and is freely available at http://gonzalezlab.eu/drosomics. Oxford University Press 2023-03-27 /pmc/articles/PMC10089646/ /pubmed/36971243 http://dx.doi.org/10.1093/molbev/msad075 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Resource Coronado-Zamora, Marta Salces-Ortiz, Judit González, Josefa DrosOmics: A Browser to Explore -omics Variation Across High-Quality Reference Genomes From Natural Populations of Drosophila melanogaster |
title | DrosOmics: A Browser to Explore -omics Variation Across High-Quality Reference Genomes From Natural Populations of Drosophila melanogaster |
title_full | DrosOmics: A Browser to Explore -omics Variation Across High-Quality Reference Genomes From Natural Populations of Drosophila melanogaster |
title_fullStr | DrosOmics: A Browser to Explore -omics Variation Across High-Quality Reference Genomes From Natural Populations of Drosophila melanogaster |
title_full_unstemmed | DrosOmics: A Browser to Explore -omics Variation Across High-Quality Reference Genomes From Natural Populations of Drosophila melanogaster |
title_short | DrosOmics: A Browser to Explore -omics Variation Across High-Quality Reference Genomes From Natural Populations of Drosophila melanogaster |
title_sort | drosomics: a browser to explore -omics variation across high-quality reference genomes from natural populations of drosophila melanogaster |
topic | Resource |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10089646/ https://www.ncbi.nlm.nih.gov/pubmed/36971243 http://dx.doi.org/10.1093/molbev/msad075 |
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