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Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes

Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world’s inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 ± 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic “contexts”...

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Autores principales: Seitzer, Phillip, Jeanniard, Adrien, Ma, Fangrui, Van Etten, James L., Facciotti, Marc T., Dunigan, David D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6213493/
https://www.ncbi.nlm.nih.gov/pubmed/30347809
http://dx.doi.org/10.3390/v10100576
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author Seitzer, Phillip
Jeanniard, Adrien
Ma, Fangrui
Van Etten, James L.
Facciotti, Marc T.
Dunigan, David D.
author_facet Seitzer, Phillip
Jeanniard, Adrien
Ma, Fangrui
Van Etten, James L.
Facciotti, Marc T.
Dunigan, David D.
author_sort Seitzer, Phillip
collection PubMed
description Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world’s inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 ± 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic “contexts”, the organization of biological information into units of a scale larger than a gene. Despite a general loss of synteny between virus types, we informatically detected a highly conserved genomic context defined by groups of three or more genes that we have termed “gene gangs”. Unlike previously described local genomic contexts, the definition of gene gangs requires only that member genes be consistently co-localized and are not constrained by strand, regulatory sites, or intervening sequences (and therefore represent a new type of conserved structural genomic element). An analysis of functional annotations and transcriptomic data suggests that some of the gene gangs may organize genes involved in specific biochemical processes, but that this organization does not involve their coordinated expression.
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spelling pubmed-62134932018-11-09 Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes Seitzer, Phillip Jeanniard, Adrien Ma, Fangrui Van Etten, James L. Facciotti, Marc T. Dunigan, David D. Viruses Article Chloroviruses (family Phycodnaviridae) are dsDNA viruses found throughout the world’s inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330 ± 40 kbp each) representing three virus types were analyzed for evidence of evolutionarily conserved local genomic “contexts”, the organization of biological information into units of a scale larger than a gene. Despite a general loss of synteny between virus types, we informatically detected a highly conserved genomic context defined by groups of three or more genes that we have termed “gene gangs”. Unlike previously described local genomic contexts, the definition of gene gangs requires only that member genes be consistently co-localized and are not constrained by strand, regulatory sites, or intervening sequences (and therefore represent a new type of conserved structural genomic element). An analysis of functional annotations and transcriptomic data suggests that some of the gene gangs may organize genes involved in specific biochemical processes, but that this organization does not involve their coordinated expression. MDPI 2018-10-20 /pmc/articles/PMC6213493/ /pubmed/30347809 http://dx.doi.org/10.3390/v10100576 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Seitzer, Phillip
Jeanniard, Adrien
Ma, Fangrui
Van Etten, James L.
Facciotti, Marc T.
Dunigan, David D.
Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
title Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
title_full Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
title_fullStr Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
title_full_unstemmed Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
title_short Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes
title_sort gene gangs of the chloroviruses: conserved clusters of collinear monocistronic genes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6213493/
https://www.ncbi.nlm.nih.gov/pubmed/30347809
http://dx.doi.org/10.3390/v10100576
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