Abstract:
BACKROUND: 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.
