EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic Neighbourhoods

Conservation of gene neighbourhood over evolutionary distances is generally indicative of shared regulation or functional association among genes. This concept has been broadly exploited in prokaryotes but its use on eukaryotic genomes has been limited to specific functional classes, such as biosynt...

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Autores: Marcet Houben, Marina, Collado Cala, Ismael, Fuentes Palacios, Diego, Gómez, Alicia D., Molina, Manuel, Garisoain Zafra, Andrés, Chorostecki, Uciel, Gabaldón, Toni
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Institución:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/207992
Acceso en línea:https://hdl.handle.net/2445/207992
Access Level:acceso abierto
Palabra clave:Genomes
Genòmica
Genomics
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spelling EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic NeighbourhoodsMarcet Houben, MarinaCollado Cala, IsmaelFuentes Palacios, DiegoGómez, Alicia D.Molina, ManuelGarisoain Zafra, AndrésChorostecki, UcielGabaldón, ToniGenomesGenòmicaGenomesGenomicsConservation of gene neighbourhood over evolutionary distances is generally indicative of shared regulation or functional association among genes. This concept has been broadly exploited in prokaryotes but its use on eukaryotic genomes has been limited to specific functional classes, such as biosynthetic gene clusters. We here used an evolutionary-based gene cluster discovery algorithm (EvolClust) to pre-compute evolutionarily conserved gene neighbourhoods, which can be searched, browsed and downloaded in EvolClustDB. We inferred ∼35,000 cluster families in 882 different species in genome comparisons of five taxonomically broad clades: Fungi, Plants, Metazoans, Insects and Protists. EvolClustDB allows browsing through the cluster families, as well as searching by protein, species, identifier or sequence. Visualization allows inspecting gene order per species in a phylogenetic context, so that relevant evolutionary events such as gain, loss or transfer, can be inferred. EvolClustDB is freely available, without registration, at http://evolclustdb.org/.Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.Elsevier BV2023info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/207992Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésReproducció del document publicat a: https://doi.org/10.1016/j.jmb.2023.168013Journal Of Molecular Biology, 2023, vol. 435, num. 14, p. 168013-NAhttps://doi.org/10.1016/j.jmb.2023.168013cc by-nc (c) Marcet Houben, M. et al., 2024http://creativecommons.org/licenses/by-nc/3.0/es/info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/2079922026-05-27T06:46:51Z
dc.title.none.fl_str_mv EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic Neighbourhoods
title EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic Neighbourhoods
spellingShingle EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic Neighbourhoods
Marcet Houben, Marina
Genomes
Genòmica
Genomes
Genomics
title_short EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic Neighbourhoods
title_full EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic Neighbourhoods
title_fullStr EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic Neighbourhoods
title_full_unstemmed EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic Neighbourhoods
title_sort EvolClustDB: Exploring Eukaryotic Gene Clusters with Evolutionarily Conserved Genomic Neighbourhoods
dc.creator.none.fl_str_mv Marcet Houben, Marina
Collado Cala, Ismael
Fuentes Palacios, Diego
Gómez, Alicia D.
Molina, Manuel
Garisoain Zafra, Andrés
Chorostecki, Uciel
Gabaldón, Toni
author Marcet Houben, Marina
author_facet Marcet Houben, Marina
Collado Cala, Ismael
Fuentes Palacios, Diego
Gómez, Alicia D.
Molina, Manuel
Garisoain Zafra, Andrés
Chorostecki, Uciel
Gabaldón, Toni
author_role author
author2 Collado Cala, Ismael
Fuentes Palacios, Diego
Gómez, Alicia D.
Molina, Manuel
Garisoain Zafra, Andrés
Chorostecki, Uciel
Gabaldón, Toni
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Genomes
Genòmica
Genomes
Genomics
topic Genomes
Genòmica
Genomes
Genomics
description Conservation of gene neighbourhood over evolutionary distances is generally indicative of shared regulation or functional association among genes. This concept has been broadly exploited in prokaryotes but its use on eukaryotic genomes has been limited to specific functional classes, such as biosynthetic gene clusters. We here used an evolutionary-based gene cluster discovery algorithm (EvolClust) to pre-compute evolutionarily conserved gene neighbourhoods, which can be searched, browsed and downloaded in EvolClustDB. We inferred ∼35,000 cluster families in 882 different species in genome comparisons of five taxonomically broad clades: Fungi, Plants, Metazoans, Insects and Protists. EvolClustDB allows browsing through the cluster families, as well as searching by protein, species, identifier or sequence. Visualization allows inspecting gene order per species in a phylogenetic context, so that relevant evolutionary events such as gain, loss or transfer, can be inferred. EvolClustDB is freely available, without registration, at http://evolclustdb.org/.Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.
publishDate 2023
dc.date.none.fl_str_mv 2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/207992
url https://hdl.handle.net/2445/207992
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.1016/j.jmb.2023.168013
Journal Of Molecular Biology, 2023, vol. 435, num. 14, p. 168013-NA
https://doi.org/10.1016/j.jmb.2023.168013
dc.rights.none.fl_str_mv cc by-nc (c) Marcet Houben, M. et al., 2024
http://creativecommons.org/licenses/by-nc/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc by-nc (c) Marcet Houben, M. et al., 2024
http://creativecommons.org/licenses/by-nc/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Elsevier BV
publisher.none.fl_str_mv Elsevier BV
dc.source.none.fl_str_mv Articles publicats en revistes (Institut de Recerca Biomèdica (IRB Barcelona))
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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