Evolutionary Genomics of <named-content content-type="genus-species">Salmonella enterica</named-content> Subspecies

ABSTRACT Six subspecies are currently recognized in Salmonella enterica. Subspecies I (subspecies enterica) is responsible for nearly all infections in humans and warm-blooded animals, while five other subspecies are isolated principally from cold-blooded animals. We sequenced 21 phylogenetically di...

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Autores principales:	Prerak T. Desai, Steffen Porwollik, Fred Long, Pui Cheng, Aye Wollam, Sandra W. Clifton, George M. Weinstock, Michael McClelland
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Lenguaje:	EN
Publicado:	American Society for Microbiology 2013
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b211aacd26b44a8388bbe120828050f2
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spelling	oai:doaj.org-article:b211aacd26b44a8388bbe120828050f22021-11-15T15:40:26ZEvolutionary Genomics of <named-content content-type="genus-species">Salmonella enterica</named-content> Subspecies10.1128/mBio.00579-122150-7511https://doaj.org/article/b211aacd26b44a8388bbe120828050f22013-05-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.00579-12https://doaj.org/toc/2150-7511ABSTRACT Six subspecies are currently recognized in Salmonella enterica. Subspecies I (subspecies enterica) is responsible for nearly all infections in humans and warm-blooded animals, while five other subspecies are isolated principally from cold-blooded animals. We sequenced 21 phylogenetically diverse strains, including two representatives from each of the previously unsequenced five subspecies and 11 diverse new strains from S. enterica subspecies enterica, to put this species into an evolutionary perspective. The phylogeny of the subspecies was partly obscured by abundant recombination events between lineages and a relatively short period of time within which subspeciation took place. Nevertheless, a variety of different tree-building methods gave congruent evolutionary tree topologies for subspeciation. A total of 285 gene families were identified that were recruited into subspecies enterica, and most of these are of unknown function. At least 2,807 gene families were identified in one or more of the other subspecies that are not found in subspecies I or Salmonella bongori. Among these gene families were 13 new candidate effectors and 7 new candidate fimbrial clusters. A third complete type III secretion system not present in subspecies enterica (I) isolates was found in both strains of subspecies salamae (II). Some gene families had complex taxonomies, such as the type VI secretion systems, which were recruited from four different lineages in five of six subspecies. Analysis of nonsynonymous-to-synonymous substitution rates indicated that the more-recently acquired regions in S. enterica are undergoing faster fixation rates than the rest of the genome. Recently acquired AT-rich regions, which often encode virulence functions, are under ongoing selection to maintain their high AT content. IMPORTANCE We have sequenced 21 new genomes which encompass the phylogenetic diversity of Salmonella, including strains of the previously unsequenced subspecies arizonae, diarizonae, houtenae, salamae, and indica as well as new diverse strains of subspecies enterica. We have deduced possible evolutionary paths traversed by this very important zoonotic pathogen and identified novel putative virulence factors that are not found in subspecies I. Gene families gained at the time of the evolution of subspecies enterica are of particular interest because they include mechanisms by which this subspecies adapted to warm-blooded hosts.Prerak T. DesaiSteffen PorwollikFred LongPui ChengAye WollamSandra W. CliftonGeorge M. WeinstockMichael McClellandAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 4, Iss 2 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Prerak T. Desai Steffen Porwollik Fred Long Pui Cheng Aye Wollam Sandra W. Clifton George M. Weinstock Michael McClelland Evolutionary Genomics of <named-content content-type="genus-species">Salmonella enterica</named-content> Subspecies
description	ABSTRACT Six subspecies are currently recognized in Salmonella enterica. Subspecies I (subspecies enterica) is responsible for nearly all infections in humans and warm-blooded animals, while five other subspecies are isolated principally from cold-blooded animals. We sequenced 21 phylogenetically diverse strains, including two representatives from each of the previously unsequenced five subspecies and 11 diverse new strains from S. enterica subspecies enterica, to put this species into an evolutionary perspective. The phylogeny of the subspecies was partly obscured by abundant recombination events between lineages and a relatively short period of time within which subspeciation took place. Nevertheless, a variety of different tree-building methods gave congruent evolutionary tree topologies for subspeciation. A total of 285 gene families were identified that were recruited into subspecies enterica, and most of these are of unknown function. At least 2,807 gene families were identified in one or more of the other subspecies that are not found in subspecies I or Salmonella bongori. Among these gene families were 13 new candidate effectors and 7 new candidate fimbrial clusters. A third complete type III secretion system not present in subspecies enterica (I) isolates was found in both strains of subspecies salamae (II). Some gene families had complex taxonomies, such as the type VI secretion systems, which were recruited from four different lineages in five of six subspecies. Analysis of nonsynonymous-to-synonymous substitution rates indicated that the more-recently acquired regions in S. enterica are undergoing faster fixation rates than the rest of the genome. Recently acquired AT-rich regions, which often encode virulence functions, are under ongoing selection to maintain their high AT content. IMPORTANCE We have sequenced 21 new genomes which encompass the phylogenetic diversity of Salmonella, including strains of the previously unsequenced subspecies arizonae, diarizonae, houtenae, salamae, and indica as well as new diverse strains of subspecies enterica. We have deduced possible evolutionary paths traversed by this very important zoonotic pathogen and identified novel putative virulence factors that are not found in subspecies I. Gene families gained at the time of the evolution of subspecies enterica are of particular interest because they include mechanisms by which this subspecies adapted to warm-blooded hosts.
format	article
author	Prerak T. Desai Steffen Porwollik Fred Long Pui Cheng Aye Wollam Sandra W. Clifton George M. Weinstock Michael McClelland
author_facet	Prerak T. Desai Steffen Porwollik Fred Long Pui Cheng Aye Wollam Sandra W. Clifton George M. Weinstock Michael McClelland
author_sort	Prerak T. Desai
title	Evolutionary Genomics of <named-content content-type="genus-species">Salmonella enterica</named-content> Subspecies
title_short	Evolutionary Genomics of <named-content content-type="genus-species">Salmonella enterica</named-content> Subspecies
title_full	Evolutionary Genomics of <named-content content-type="genus-species">Salmonella enterica</named-content> Subspecies
title_fullStr	Evolutionary Genomics of <named-content content-type="genus-species">Salmonella enterica</named-content> Subspecies
title_full_unstemmed	Evolutionary Genomics of <named-content content-type="genus-species">Salmonella enterica</named-content> Subspecies
title_sort	evolutionary genomics of <named-content content-type="genus-species">salmonella enterica</named-content> subspecies
publisher	American Society for Microbiology
publishDate	2013
url	https://doaj.org/article/b211aacd26b44a8388bbe120828050f2
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Evolutionary Genomics of <named-content content-type="genus-species">Salmonella enterica</named-content> Subspecies

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