Abstract
Exon Primed Intron Crossing (EPIC) markers provide molecular tools that are susceptible to be variable within species while remaining amplifiable by PCR using potentially universal primers. In this study we tested the possibility of obtaining PCR products from 50 EPIC markers on 23 species belonging to seven different phyla (Porifera, Cnidaria, Arthropoda, Nematoda, Mollusca, Annelida, Echinodermata) using 70 new primer pairs. A previous study had identified and tested those loci in a dozen species, including another phylum, Urochordata (Chenuil et al., 2010). Results were contrasted among species. The best results were achieved with the oyster (Mollusca) where 28 loci provided amplicons susceptible to contain an intron according to their size. This was however not the case with the other mollusk Crepidula fornicata, which seems to have undergone a reduction in intron number or intron size. In the Porifera, 13 loci appeared susceptible to contain an intron, a surprisingly high number for this phylum considering its phylogenetic distance with genomic data used to design the primers. For two cnidarian species, numerous loci (24) were obtained. Ecdysozoan phyla (arthropods and nematodes) proved less successful than others as expected considering reports of their rapid rate of genome evolution and the worst results were obtained for several arthropods. Some general patterns among phyla arose, and we discuss how the results of this EPIC survey may give new insights into genome evolution of the study species. This work confirms that this set of EPIC loci provides an easy-to-use toolbox to identify genetic markers potentially useful for population genetics, phylogeography or phylogenetic studies for a large panel of metazoan species. We then argue that obtaining diploid sequence genotypes for these loci became simple and affordable owing to Next-Generation Sequencing development. Species surveyed in this study belong to several genera (Acanthaster, Alvinocaris, Aplysina, Aurelia, Crepidula, Eunicella, Hediste, Hemimysis, Litoditis, Lophelia, Mesopodopsis, Mya, Ophiocten, Ophioderma, Ostrea, Pelagia, Platynereis, Rhizostoma, Rimicaris), two of them, belonging to the family Vesicomydae and Eunicidae, could not be determined at the genus level.
Highlights
Population genetics and genomics of non-model species are hampered by the lack of knowledge of their genome and the absence of universal primers (e.g. Chenuil 2006)
The good results obtained for cnidarians are not due to the design of special primers using cnidarian EST information, because, contrary to the ecdysozoans for which most primers were newly designed, few newly-designed primers were used for cnidarians (Table 1 -Table S1)
This, together with the good results obtained for the sponge, confirms that our approach enables finding candidate loci across the genome, for species for which only very few polymorphic markers are available, across a very wide phylogenetic range
Summary
Population genetics and genomics of non-model species (including ecologically relevant model species) are hampered by the lack of knowledge of their genome and the absence of universal primers (e.g. Chenuil 2006). This is a particular problem for phyla of marine invertebrates which encompass a much wider phylogenetic range than terrestrial metazoans. About 50 introns, framed by one or several alternative primer pairs in exons, were tested for PCR amplification and an average of 24 introns per species appeared promising in Bilaterian species Among those promising introns, five were amplified successfully in all 10 species including cnidarians. Some of these loci were sequenced in numerous individuals and proved useful for population genetic and phylogeographic studies
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