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

dc.contributor.authorChenuil, Anne
dc.contributor.authorHoareau, Thierry B.
dc.contributor.authorEgea, Emilie
dc.contributor.authorPenant, Gwilherm
dc.contributor.authorAurelle, Didier
dc.contributor.authorMokhtar-Jamai, Kenza
dc.contributor.authorBishop, John D.D.
dc.contributor.authorBoissin, Emilie
dc.contributor.authorDiaz, Angie
dc.contributor.authorKrakau, Manuela
dc.contributor.authorLuttikhuizen, Pieternella C.
dc.contributor.authorPatti, Francesco P.
dc.contributor.authorBlavet, Nicolas
dc.contributor.authorMousset, Sylvain
dc.date.accessioned2011-05-11T07:00:51Z
dc.date.available2011-05-11T07:00:51Z
dc.date.issued2010
dc.description.abstractBACKROUND: 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.en
dc.identifier.citationChenuil et al.: An efficient method to find potentially universal population genetic markers, applied to metazoans. BMC Evolutionary Biology 2010 10:276. [http://www.biomedcentral.com/bmcevolbiol/]en
dc.identifier.issn1471-2148
dc.identifier.other10.1186/1471-2148-10-276
dc.identifier.urihttp://hdl.handle.net/2263/16516
dc.language.isoenen_US
dc.publisherBioMed Centralen_US
dc.rights© 2010 Chenuil et al; licensee BioMed Central Ltd. 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.en_US
dc.subject.lcshGenetic markersen
dc.subject.lcshMetazoaen
dc.subject.lcshPopulation geneticsen
dc.subject.lcshPhylogeographyen
dc.titleAn efficient method to find potentially universal population genetic markers, applied to metazoansen
dc.typeArticleen

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