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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-06-01
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| Series: | PLoS Computational Biology |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24967627/?tool=EBI |
| _version_ | 1819180896172900352 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-22T22:21:37Z |
| format | Article |
| id | doaj.art-54d19b3d592742959c1ebf70b370df79 |
| institution | Directory Open Access Journal |
| issn | 1553-734X 1553-7358 |
| language | English |
| last_indexed | 2024-12-22T22:21:37Z |
| publishDate | 2014-06-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Computational Biology |
| spelling | doaj.art-54d19b3d592742959c1ebf70b370df792022-12-21T18:10:40ZengPublic Library of Science (PLoS)PLoS Computational Biology1553-734X1553-73582014-06-01106e100368010.1371/journal.pcbi.1003680Large-scale genomic analysis suggests a neutral punctuated dynamics of transposable elements in bacterial genomes.Jaime IranzoManuel J GómezFrancisco J López de SaroSusanna ManrubiaInsertion 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.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24967627/?tool=EBI |
| spellingShingle | 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. PLoS Computational Biology |
| title | 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_short | 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 |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24967627/?tool=EBI |
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