ArticleBMC evolutionary biology2010
An efficient method to find potentially universal population genetic markers, applied to metazoans.
Article in BMC evolutionary biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed.
- Application of Exon Primed Intron Crossing Markers to Cross-AmplifyEcology and evolution · 2026Article
- Temporal and spatial variation in population structure among brooding sea stars in the genusEcology and evolution · 2021Article
- A workflow of massive identification and application of intron markers using snakes as a model.Ecology and evolution · 2017Article
- Pyrosequencing for accurate imprinted allele expression analysis.Journal of cellular biochemistry · 2015Article
- Efficient Detection of Novel Nuclear Markers for Brassicaceae by Transcriptome Sequencing.PloS one · 2015Article
- Pyrosequencing for the rapid and efficient quantification of allele-specific expression.Epigenetics · 2013Article
- Molecular hyperdiversity and evolution in very large populations.Molecular ecology · 2013Article
- A next-generation sequencing method for overcoming the multiple gene copy problem in polyploid phylogenetics, applied to Poa grasses.BMC biology · 2011Article
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15 authors.
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Abstract
backgroundDespite 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.
resultsIn 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.
conclusionsOur 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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