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Differential Selection on Carotenoid Biosynthesis Genes as a Function of Gene Position in the Metabolic Pathway: A Study on the Carrot and Dicots
BACKGROUND: Selection of genes involved in metabolic pathways could target them differently depending on the position of genes in the pathway and on their role in controlling metabolic fluxes. This hypothesis was tested in the carotenoid biosynthesis pathway using population genetics and phylogeneti...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3377682/ https://www.ncbi.nlm.nih.gov/pubmed/22737218 http://dx.doi.org/10.1371/journal.pone.0038724 |
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author | Clotault, Jérémy Peltier, Didier Soufflet-Freslon, Vanessa Briard, Mathilde Geoffriau, Emmanuel |
author_facet | Clotault, Jérémy Peltier, Didier Soufflet-Freslon, Vanessa Briard, Mathilde Geoffriau, Emmanuel |
author_sort | Clotault, Jérémy |
collection | PubMed |
description | BACKGROUND: Selection of genes involved in metabolic pathways could target them differently depending on the position of genes in the pathway and on their role in controlling metabolic fluxes. This hypothesis was tested in the carotenoid biosynthesis pathway using population genetics and phylogenetics. METHODOLOGY/PRINCIPAL FINDINGS: Evolutionary rates of seven genes distributed along the carotenoid biosynthesis pathway, IPI, PDS, CRTISO, LCYB, LCYE, CHXE and ZEP, were compared in seven dicot taxa. A survey of deviations from neutrality expectations at these genes was also undertaken in cultivated carrot (Daucus carota subsp. sativus), a species that has been intensely bred for carotenoid pattern diversification in its root during its cultivation history. Parts of sequences of these genes were obtained from 46 individuals representing a wide diversity of cultivated carrots. Downstream genes exhibited higher deviations from neutral expectations than upstream genes. Comparisons of synonymous and nonsynonymous substitution rates between genes among dicots revealed greater constraints on upstream genes than on downstream genes. An excess of intermediate frequency polymorphisms, high nucleotide diversity and/or high differentiation of CRTISO, LCYB1 and LCYE in cultivated carrot suggest that balancing selection may have targeted genes acting centrally in the pathway. CONCLUSIONS/SIGNIFICANCE: Our results are consistent with relaxed constraints on downstream genes and selection targeting the central enzymes of the carotenoid biosynthesis pathway during carrot breeding history. |
format | Online Article Text |
id | pubmed-3377682 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-33776822012-06-26 Differential Selection on Carotenoid Biosynthesis Genes as a Function of Gene Position in the Metabolic Pathway: A Study on the Carrot and Dicots Clotault, Jérémy Peltier, Didier Soufflet-Freslon, Vanessa Briard, Mathilde Geoffriau, Emmanuel PLoS One Research Article BACKGROUND: Selection of genes involved in metabolic pathways could target them differently depending on the position of genes in the pathway and on their role in controlling metabolic fluxes. This hypothesis was tested in the carotenoid biosynthesis pathway using population genetics and phylogenetics. METHODOLOGY/PRINCIPAL FINDINGS: Evolutionary rates of seven genes distributed along the carotenoid biosynthesis pathway, IPI, PDS, CRTISO, LCYB, LCYE, CHXE and ZEP, were compared in seven dicot taxa. A survey of deviations from neutrality expectations at these genes was also undertaken in cultivated carrot (Daucus carota subsp. sativus), a species that has been intensely bred for carotenoid pattern diversification in its root during its cultivation history. Parts of sequences of these genes were obtained from 46 individuals representing a wide diversity of cultivated carrots. Downstream genes exhibited higher deviations from neutral expectations than upstream genes. Comparisons of synonymous and nonsynonymous substitution rates between genes among dicots revealed greater constraints on upstream genes than on downstream genes. An excess of intermediate frequency polymorphisms, high nucleotide diversity and/or high differentiation of CRTISO, LCYB1 and LCYE in cultivated carrot suggest that balancing selection may have targeted genes acting centrally in the pathway. CONCLUSIONS/SIGNIFICANCE: Our results are consistent with relaxed constraints on downstream genes and selection targeting the central enzymes of the carotenoid biosynthesis pathway during carrot breeding history. Public Library of Science 2012-06-18 /pmc/articles/PMC3377682/ /pubmed/22737218 http://dx.doi.org/10.1371/journal.pone.0038724 Text en Clotault et al. 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 Clotault, Jérémy Peltier, Didier Soufflet-Freslon, Vanessa Briard, Mathilde Geoffriau, Emmanuel Differential Selection on Carotenoid Biosynthesis Genes as a Function of Gene Position in the Metabolic Pathway: A Study on the Carrot and Dicots |
title | Differential Selection on Carotenoid Biosynthesis Genes as a Function of Gene Position in the Metabolic Pathway: A Study on the Carrot and Dicots |
title_full | Differential Selection on Carotenoid Biosynthesis Genes as a Function of Gene Position in the Metabolic Pathway: A Study on the Carrot and Dicots |
title_fullStr | Differential Selection on Carotenoid Biosynthesis Genes as a Function of Gene Position in the Metabolic Pathway: A Study on the Carrot and Dicots |
title_full_unstemmed | Differential Selection on Carotenoid Biosynthesis Genes as a Function of Gene Position in the Metabolic Pathway: A Study on the Carrot and Dicots |
title_short | Differential Selection on Carotenoid Biosynthesis Genes as a Function of Gene Position in the Metabolic Pathway: A Study on the Carrot and Dicots |
title_sort | differential selection on carotenoid biosynthesis genes as a function of gene position in the metabolic pathway: a study on the carrot and dicots |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3377682/ https://www.ncbi.nlm.nih.gov/pubmed/22737218 http://dx.doi.org/10.1371/journal.pone.0038724 |
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