PCR survey of 50 introns in animals: Cross-amplification of homologous EPIC loci in eight non-bilaterian, protostome and deuterostome phyla

Type Article
Date 2013-12
Language English
Author(s) Gerard K.1, Guilloton E.2, Arnaud-Haond SophieORCID3, Aurelle D.2, Bastrop R.4, Chevaldonne P.2, Derycke S.5, Hanel R.6, Lapegue Sylvie7, Lejeusne C.8, Mousset Sylvain9, Ramsak A.10, Remerie T.5, Viard Frederique11, Feral Jean-Pierre2, Chenuil A.2
Affiliation(s) 1 : Lab Ecol Mol, Santiago, Chile.
2 : Aix Marseille Univ, Inst Mediterraneen Biodiversite & Ecol Marine & C, CNRS UMR 7263, Stn Marine Endoume, F-13007 Marseille, France.
3 : IFREMER, Ctr Brest, DEEP, LEP, F-29280 Plouzane, France.
4 : Univ Rostock, Inst Biol, D-18059 Rostock, Germany.
5 : Univ Ghent, Dept Biol, Marine Biol Sect, B-9000 Ghent, Belgium.
6 : Thunen Inst Fisheries Ecol, D-22767 Hamburg, Germany.
7 : IFREMER, SG2M LGPMM, Lab Genet & Pathol Mollusques Marins, F-17390 La Tremblade, France.
8 : Wetland Ecol Dept, Donana Biol Stn CSIC, Seville 41092, Spain.
9 : Univ Lyon 1, CNRS, UMR 5558, F-69622 Villeurbanne, France.
10 : Natl Inst Biol, Marine Biol Stn, Piran 6330, Slovenia.
11 : Univ Paris 06, CNRS, UMR Adaptat & Divers 7144, Marine Environm Stn Biol Roscoff, F-29688 Roscoff, France.
Source Marine Genomics (1874-7787) (Elsevier Science Bv), 2013-12 , Vol. 12 , P. 1-8
DOI 10.1016/j.margen.2013.10.001
WOS© Times Cited 4
Keyword(s) Universal primers, Alternative barcoding, Non-model species, Genetic marker, Intron
Abstract Exon Primed Intron Crossing (EPIC) markers providemolecular tools that are susceptible to be variable within specieswhile remaining amplifiable by PCR using potentially universal primers. In this studywe 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 othermollusk 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 distancewith 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. Thiswork 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.
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Gerard K., Guilloton E., Arnaud-Haond Sophie, Aurelle D., Bastrop R., Chevaldonne P., Derycke S., Hanel R., Lapegue Sylvie, Lejeusne C., Mousset Sylvain, Ramsak A., Remerie T., Viard Frederique, Feral Jean-Pierre, Chenuil A. (2013). PCR survey of 50 introns in animals: Cross-amplification of homologous EPIC loci in eight non-bilaterian, protostome and deuterostome phyla. Marine Genomics, 12, 1-8. Publisher's official version : https://doi.org/10.1016/j.margen.2013.10.001 , Open Access version : https://archimer.ifremer.fr/doc/00166/27775/