Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.

Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that dete...

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Autores principales:	Jaime Iranzo, Manuel J Gómez, Francisco J López de Saro, Susanna Manrubia
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/54d19b3d592742959c1ebf70b370df79
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spelling	oai:doaj.org-article:54d19b3d592742959c1ebf70b370df792021-11-11T05:52:04ZLarge-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.1553-734X1553-735810.1371/journal.pcbi.1003680https://doaj.org/article/54d19b3d592742959c1ebf70b370df792014-06-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24967627/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that determine IS content in genomes are, though, a matter of debate. In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. We evaluate the roles played by duplication, lateral gene transfer, deletion and purifying selection. We find that the observed IS abundances are compatible with a neutral scenario where IS proliferation is controlled by deletions instead of purifying selection. Even if there may be some cases driven by selection, neutral behavior dominates over large evolutionary scales. According to this view, IS and hosts tend to coexist in a dynamic equilibrium state for most of the time. Our approach also allows for a detection of recent IS expansions, and supports the hypothesis that rapid expansions constitute transient events-punctuations-during which the state of coexistence of IS and host becomes perturbated.Jaime IranzoManuel J GómezFrancisco J López de SaroSusanna ManrubiaPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 10, Iss 6, p e1003680 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Jaime Iranzo Manuel J Gómez Francisco J López de Saro Susanna Manrubia Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.
description	Insertion sequences (IS) are the simplest and most abundant form of transposable DNA found in bacterial genomes. When present in multiple copies, it is thought that they can promote genomic plasticity and genetic exchange, thus being a major force of evolutionary change. The main processes that determine IS content in genomes are, though, a matter of debate. In this work, we take advantage of the large amount of genomic data currently available and study the abundance distributions of 33 IS families in 1811 bacterial chromosomes. This allows us to test simple models of IS dynamics and estimate their key parameters by means of a maximum likelihood approach. We evaluate the roles played by duplication, lateral gene transfer, deletion and purifying selection. We find that the observed IS abundances are compatible with a neutral scenario where IS proliferation is controlled by deletions instead of purifying selection. Even if there may be some cases driven by selection, neutral behavior dominates over large evolutionary scales. According to this view, IS and hosts tend to coexist in a dynamic equilibrium state for most of the time. Our approach also allows for a detection of recent IS expansions, and supports the hypothesis that rapid expansions constitute transient events-punctuations-during which the state of coexistence of IS and host becomes perturbated.
format	article
author	Jaime Iranzo Manuel J Gómez Francisco J López de Saro Susanna Manrubia
author_facet	Jaime Iranzo Manuel J Gómez Francisco J López de Saro Susanna Manrubia
author_sort	Jaime Iranzo
title	Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.
title_short	Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.
title_full	Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.
title_fullStr	Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.
title_full_unstemmed	Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.
title_sort	large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/54d19b3d592742959c1ebf70b370df79
work_keys_str_mv	AT jaimeiranzo largescalegenomicanalysissuggestsaneutralpunctuateddynamicsoftransposableelementsinbacterialgenomes AT manueljgomez largescalegenomicanalysissuggestsaneutralpunctuateddynamicsoftransposableelementsinbacterialgenomes AT franciscojlopezdesaro largescalegenomicanalysissuggestsaneutralpunctuateddynamicsoftransposableelementsinbacterialgenomes AT susannamanrubia largescalegenomicanalysissuggestsaneutralpunctuateddynamicsoftransposableelementsinbacterialgenomes
_version_	1718439487670845440

Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.

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