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Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu

Recent genome-wide analyses have revealed patterns of positive selection acting on protein-coding genes in humans and mammals. To assess whether the conclusions drawn from these analyses are valid for other vertebrates and to identify mammalian specificities, I have investigated the selective pressu...

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Autor principal: Montoya-Burgos, Juan I.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3172292/
https://www.ncbi.nlm.nih.gov/pubmed/21935469
http://dx.doi.org/10.1371/journal.pone.0024800
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author Montoya-Burgos, Juan I.
author_facet Montoya-Burgos, Juan I.
author_sort Montoya-Burgos, Juan I.
collection PubMed
description Recent genome-wide analyses have revealed patterns of positive selection acting on protein-coding genes in humans and mammals. To assess whether the conclusions drawn from these analyses are valid for other vertebrates and to identify mammalian specificities, I have investigated the selective pressure acting on protein-coding genes of the puffer fishes Tetraodon and Takifugu. My results indicate that the strength of purifying selection in puffer fishes is similar to previous reports for murids but stronger in hominids, which have a smaller population size. Gene ontology analyses show that more than half of the biological processes targeted by positive selection in mammals are also targeted in puffer fishes, highlighting general patterns for vertebrates. Biological processes enriched with positively selected genes that are shared between mammals and fishes include immune and defense responses, signal transduction, regulation of transcription and several of their descendent terms. Mammalian-specific processes displaying an excess of positively selected genes are related to sensory perception and neurological processes. The comparative analyses also revealed that, for both mammals and fishes, genes encoding extracellular proteins are preferentially targeted by positive selection, indicating that adaptive evolution occurs more often in the extra-cellular environment rather than inside the cell. Moreover, I present here the first genome-wide characterization of neutrally-evolving regions of protein-coding genes. This analysis revealed an unexpectedly high proportion of genes containing both positively selected motifs and neutrally-evolving regions, uncovering a strong link between neutral evolution and positive selection. I speculate that neutrally-evolving regions are a major source of novelties screened by natural selection.
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spelling pubmed-31722922011-09-20 Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu Montoya-Burgos, Juan I. PLoS One Research Article Recent genome-wide analyses have revealed patterns of positive selection acting on protein-coding genes in humans and mammals. To assess whether the conclusions drawn from these analyses are valid for other vertebrates and to identify mammalian specificities, I have investigated the selective pressure acting on protein-coding genes of the puffer fishes Tetraodon and Takifugu. My results indicate that the strength of purifying selection in puffer fishes is similar to previous reports for murids but stronger in hominids, which have a smaller population size. Gene ontology analyses show that more than half of the biological processes targeted by positive selection in mammals are also targeted in puffer fishes, highlighting general patterns for vertebrates. Biological processes enriched with positively selected genes that are shared between mammals and fishes include immune and defense responses, signal transduction, regulation of transcription and several of their descendent terms. Mammalian-specific processes displaying an excess of positively selected genes are related to sensory perception and neurological processes. The comparative analyses also revealed that, for both mammals and fishes, genes encoding extracellular proteins are preferentially targeted by positive selection, indicating that adaptive evolution occurs more often in the extra-cellular environment rather than inside the cell. Moreover, I present here the first genome-wide characterization of neutrally-evolving regions of protein-coding genes. This analysis revealed an unexpectedly high proportion of genes containing both positively selected motifs and neutrally-evolving regions, uncovering a strong link between neutral evolution and positive selection. I speculate that neutrally-evolving regions are a major source of novelties screened by natural selection. Public Library of Science 2011-09-13 /pmc/articles/PMC3172292/ /pubmed/21935469 http://dx.doi.org/10.1371/journal.pone.0024800 Text en Juan I. Montoya-Burgos. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Montoya-Burgos, Juan I.
Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu
title Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu
title_full Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu
title_fullStr Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu
title_full_unstemmed Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu
title_short Patterns of Positive Selection and Neutral Evolution in the Protein-Coding Genes of Tetraodon and Takifugu
title_sort patterns of positive selection and neutral evolution in the protein-coding genes of tetraodon and takifugu
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3172292/
https://www.ncbi.nlm.nih.gov/pubmed/21935469
http://dx.doi.org/10.1371/journal.pone.0024800
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