Pangenome Evolution in theMarine Bacterium Alteromonas

Wehave examined a collection of the free-livingmarine bacterium Alteromonas genomeswith cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., frommicrobes that can be consideredmembers of a natural clone (like in a clinical epidemiological outbreak) to borderline genu...

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Detalles Bibliográficos
Autores: López Pérez, Mario, Rodríguez Valera, Francisco
Tipo de recurso: artículo
Fecha de publicación:2016
País:España
Institución:Universidad Miguel Hernández de Elche
Repositorio:REDIUMH. Depósito Digital de la UMH
OAI Identifier:oai:dspace.umh.es:11000/4840
Acceso en línea:http://hdl.handle.net/11000/4840
Access Level:acceso abierto
Palabra clave:Alteromonas
pangenome
genomic islands
recombination
intraspecies diversity
phages
579 - Microbiología
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spelling Pangenome Evolution in theMarine Bacterium AlteromonasLópez Pérez, MarioRodríguez Valera, FranciscoAlteromonaspangenomegenomic islandsrecombinationintraspecies diversityphages579 - MicrobiologíaWehave examined a collection of the free-livingmarine bacterium Alteromonas genomeswith cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., frommicrobes that can be consideredmembers of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7–83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9–5.1%). Regarding the flexible genome, itsmain expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche andmustflowfast throughout thewholegenus as they are found, withnearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed.This work was supported by projects MEDIMAX BFPU2013-48007-P from the Spanish Ministerio de Economía y CompetitividadMaCuMBA Project 311975 of the European Commission FP7 and PROMETEO II/2014/012 project AQUAMET from the Generalitat ValencianaStrain D7 was kindly provided by Professor A° ke Hagstro¨m (Linnaeus University, SwedenDepartamentos de la UMH::Producción Vegetal y Microbiología2018201820162018info:eu-repo/semantics/articleapplication/pdf15application/pdfhttp://hdl.handle.net/11000/4840reponame:REDIUMH. Depósito Digital de la UMHinstname:Universidad Miguel Hernández de ElcheIngléshttps://doi.org/10.1093/gbe/evw098info:eu-repo/semantics/openAccessoai:dspace.umh.es:11000/48402026-05-27T13:36:21Z
dc.title.none.fl_str_mv Pangenome Evolution in theMarine Bacterium Alteromonas
title Pangenome Evolution in theMarine Bacterium Alteromonas
spellingShingle Pangenome Evolution in theMarine Bacterium Alteromonas
López Pérez, Mario
Alteromonas
pangenome
genomic islands
recombination
intraspecies diversity
phages
579 - Microbiología
title_short Pangenome Evolution in theMarine Bacterium Alteromonas
title_full Pangenome Evolution in theMarine Bacterium Alteromonas
title_fullStr Pangenome Evolution in theMarine Bacterium Alteromonas
title_full_unstemmed Pangenome Evolution in theMarine Bacterium Alteromonas
title_sort Pangenome Evolution in theMarine Bacterium Alteromonas
dc.creator.none.fl_str_mv López Pérez, Mario
Rodríguez Valera, Francisco
author López Pérez, Mario
author_facet López Pérez, Mario
Rodríguez Valera, Francisco
author_role author
author2 Rodríguez Valera, Francisco
author2_role author
dc.contributor.none.fl_str_mv Departamentos de la UMH::Producción Vegetal y Microbiología
dc.subject.none.fl_str_mv Alteromonas
pangenome
genomic islands
recombination
intraspecies diversity
phages
579 - Microbiología
topic Alteromonas
pangenome
genomic islands
recombination
intraspecies diversity
phages
579 - Microbiología
description Wehave examined a collection of the free-livingmarine bacterium Alteromonas genomeswith cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., frommicrobes that can be consideredmembers of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7–83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9–5.1%). Regarding the flexible genome, itsmain expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche andmustflowfast throughout thewholegenus as they are found, withnearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed.
publishDate 2016
dc.date.none.fl_str_mv 2016
2018
2018
2018
dc.type.none.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/11000/4840
url http://hdl.handle.net/11000/4840
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv https://doi.org/10.1093/gbe/evw098
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
15
application/pdf
dc.source.none.fl_str_mv reponame:REDIUMH. Depósito Digital de la UMH
instname:Universidad Miguel Hernández de Elche
instname_str Universidad Miguel Hernández de Elche
reponame_str REDIUMH. Depósito Digital de la UMH
collection REDIUMH. Depósito Digital de la UMH
repository.name.fl_str_mv
repository.mail.fl_str_mv
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