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An efficient method to find potentially universal population genetic markers, applied to metazoans

BACKGROUND: Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerou...

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Autores principales: Chenuil, Anne, Hoareau, Thierry B, Egea, Emilie, Penant, Gwilherm, Rocher, Caroline, Aurelle, Didier, Mokhtar-Jamai, Kenza, Bishop, John DD, Boissin, Emilie, Diaz, Angie, Krakau, Manuela, Luttikhuizen, Pieternella C, Patti, Francesco P, Blavet, Nicolas, Mousset, Sylvain
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2949868/
https://www.ncbi.nlm.nih.gov/pubmed/20836842
http://dx.doi.org/10.1186/1471-2148-10-276
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author Chenuil, Anne
Hoareau, Thierry B
Egea, Emilie
Penant, Gwilherm
Rocher, Caroline
Aurelle, Didier
Mokhtar-Jamai, Kenza
Bishop, John DD
Boissin, Emilie
Diaz, Angie
Krakau, Manuela
Luttikhuizen, Pieternella C
Patti, Francesco P
Blavet, Nicolas
Mousset, Sylvain
author_facet Chenuil, Anne
Hoareau, Thierry B
Egea, Emilie
Penant, Gwilherm
Rocher, Caroline
Aurelle, Didier
Mokhtar-Jamai, Kenza
Bishop, John DD
Boissin, Emilie
Diaz, Angie
Krakau, Manuela
Luttikhuizen, Pieternella C
Patti, Francesco P
Blavet, Nicolas
Mousset, Sylvain
author_sort Chenuil, Anne
collection PubMed
description BACKGROUND: Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families. RESULTS: In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals. CONCLUSIONS: Our new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa.
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spelling pubmed-29498682010-10-06 An efficient method to find potentially universal population genetic markers, applied to metazoans Chenuil, Anne Hoareau, Thierry B Egea, Emilie Penant, Gwilherm Rocher, Caroline Aurelle, Didier Mokhtar-Jamai, Kenza Bishop, John DD Boissin, Emilie Diaz, Angie Krakau, Manuela Luttikhuizen, Pieternella C Patti, Francesco P Blavet, Nicolas Mousset, Sylvain BMC Evol Biol Methodology Article BACKGROUND: Despite the impressive growth of sequence databases, the limited availability of nuclear markers that are sufficiently polymorphic for population genetics and phylogeography and applicable across various phyla restricts many potential studies, particularly in non-model organisms. Numerous introns have invariant positions among kingdoms, providing a potential source for such markers. Unfortunately, most of the few known EPIC (Exon Primed Intron Crossing) loci are restricted to vertebrates or belong to multigenic families. RESULTS: In order to develop markers with broad applicability, we designed a bioinformatic approach aimed at avoiding multigenic families while identifying intron positions conserved across metazoan phyla. We developed a program facilitating the identification of EPIC loci which allowed slight variation in intron position. From the Homolens databases we selected 29 gene families which contained 52 promising introns for which we designed 93 primer pairs. PCR tests were performed on several ascidians, echinoderms, bivalves and cnidarians. On average, 24 different introns per genus were amplified in bilaterians. Remarkably, five of the introns successfully amplified in all of the metazoan genera tested (a dozen genera, including cnidarians). The influence of several factors on amplification success was investigated. Success rate was not related to the phylogenetic relatedness of a taxon to the groups that most influenced primer design, showing that these EPIC markers are extremely conserved in animals. CONCLUSIONS: Our new method now makes it possible to (i) rapidly isolate a set of EPIC markers for any phylum, even outside the animal kingdom, and thus, (ii) compare genetic diversity at potentially homologous polymorphic loci between divergent taxa. BioMed Central 2010-09-13 /pmc/articles/PMC2949868/ /pubmed/20836842 http://dx.doi.org/10.1186/1471-2148-10-276 Text en Copyright ©2010 Chenuil et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Chenuil, Anne
Hoareau, Thierry B
Egea, Emilie
Penant, Gwilherm
Rocher, Caroline
Aurelle, Didier
Mokhtar-Jamai, Kenza
Bishop, John DD
Boissin, Emilie
Diaz, Angie
Krakau, Manuela
Luttikhuizen, Pieternella C
Patti, Francesco P
Blavet, Nicolas
Mousset, Sylvain
An efficient method to find potentially universal population genetic markers, applied to metazoans
title An efficient method to find potentially universal population genetic markers, applied to metazoans
title_full An efficient method to find potentially universal population genetic markers, applied to metazoans
title_fullStr An efficient method to find potentially universal population genetic markers, applied to metazoans
title_full_unstemmed An efficient method to find potentially universal population genetic markers, applied to metazoans
title_short An efficient method to find potentially universal population genetic markers, applied to metazoans
title_sort efficient method to find potentially universal population genetic markers, applied to metazoans
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2949868/
https://www.ncbi.nlm.nih.gov/pubmed/20836842
http://dx.doi.org/10.1186/1471-2148-10-276
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