Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.

Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it rem...

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Autores principales:	Pierre Lefeuvre, Gilles Cellier, Benoît Remenant, Frédéric Chiroleu, Philippe Prior
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/114ab91c6c014b6293c638b4bc875aa3
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spelling	oai:doaj.org-article:114ab91c6c014b6293c638b4bc875aa32021-11-18T07:44:12ZConstraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.1932-620310.1371/journal.pone.0063155https://doaj.org/article/114ab91c6c014b6293c638b4bc875aa32013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23723974/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.Pierre LefeuvreGilles CellierBenoît RemenantFrédéric ChiroleuPhilippe PriorPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 5, p e63155 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Pierre Lefeuvre Gilles Cellier Benoît Remenant Frédéric Chiroleu Philippe Prior Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.
description	Because it is suspected that gene content may partly explain host adaptation and ecology of pathogenic bacteria, it is important to study factors affecting genome composition and its evolution. While recent genomic advances have revealed extremely large pan-genomes for some bacterial species, it remains difficult to predict to what extent gene pool is accessible within or transferable between populations. As genomes bear imprints of the history of the organisms, gene distribution pattern analyses should provide insights into the forces and factors at play in the shaping and maintaining of bacterial genomes. In this study, we revisited the data obtained from a previous CGH microarrays analysis in order to assess the genomic plasticity of the R. solanacearum species complex. Gene distribution analyses demonstrated the remarkably dispersed genome of R. solanacearum with more than half of the genes being accessory. From the reconstruction of the ancestral genomes compositions, we were able to infer the number of gene gain and loss events along the phylogeny. Analyses of gene movement patterns reveal that factors associated with gene function, genomic localization and ecology delineate gene flow patterns. While the chromosome displayed lower rates of movement, the megaplasmid was clearly associated with hot-spots of gene gain and loss. Gene function was also confirmed to be an essential factor in gene gain and loss dynamics with significant differences in movement patterns between different COG categories. Finally, analyses of gene distribution highlighted possible highways of horizontal gene transfer. Due to sampling and design bias, we can only speculate on factors at play in this gene movement dynamic. Further studies examining precise conditions that favor gene transfer would provide invaluable insights in the fate of bacteria, species delineation and the emergence of successful pathogens.
format	article
author	Pierre Lefeuvre Gilles Cellier Benoît Remenant Frédéric Chiroleu Philippe Prior
author_facet	Pierre Lefeuvre Gilles Cellier Benoît Remenant Frédéric Chiroleu Philippe Prior
author_sort	Pierre Lefeuvre
title	Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.
title_short	Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.
title_full	Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.
title_fullStr	Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.
title_full_unstemmed	Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.
title_sort	constraints on genome dynamics revealed from gene distribution among the ralstonia solanacearum species.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/114ab91c6c014b6293c638b4bc875aa3
work_keys_str_mv	AT pierrelefeuvre constraintsongenomedynamicsrevealedfromgenedistributionamongtheralstoniasolanacearumspecies AT gillescellier constraintsongenomedynamicsrevealedfromgenedistributionamongtheralstoniasolanacearumspecies AT benoitremenant constraintsongenomedynamicsrevealedfromgenedistributionamongtheralstoniasolanacearumspecies AT fredericchiroleu constraintsongenomedynamicsrevealedfromgenedistributionamongtheralstoniasolanacearumspecies AT philippeprior constraintsongenomedynamicsrevealedfromgenedistributionamongtheralstoniasolanacearumspecies
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Constraints on genome dynamics revealed from gene distribution among the Ralstonia solanacearum species.

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