title: Characterization of genome-wide SNPs for the water flea Daphnia pulicaria generated by genotyping-by-sequencing (GBS).
abstract: The keystone aquatic herbivore Daphnia has been studied for more than 150 years in the context of evolution, ecology and ecotoxicology. Although it is rapidly becoming an emergent model for environmental and population genomics, there have been limited genome-wide level studies in natural populations. We report a unique resource of novel Single Nucleotide Polymorphic (SNP) markers for Daphnia pulicaria using the reduction in genomic complexity with the restriction enzymes approach, genotyping-by-sequencing. Using the genome of D. pulex as a reference, SNPs were scored for 53 clones from five natural populations that varied in lake trophic status. Our analyses resulted in 32,313 highly confident and bi-allelic SNP markers. 1,364 outlier SNPs were mapped on the annotated D. pulex genome, which identified 2,335 genes, including 565 within functional genes. Out of 885 EuKaryotic Orthologous Groups that we found from outlier SNPs, 294 were involved in three metabolic and four regulatory pathways. Bayesian-clustering analyses showed two distinct population clusters representing the possible combined effects of geography and lake trophic status. Our results provide an invaluable tool for future population genomics surveys in Daphnia targeting informative regions related to physiological processes that can be linked to the ecology of this emerging eco-responsive taxon.
authors.affiliation: Doñana Biological Station (CSIC), Isla de La Cartuja, Av. Américo Vespucio S/N, 41092-Seville, Spain.|Department of Biology, Program in Ecology and Evolutionary Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Muñoz
authors.affiliation: Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium.
authors.forename: Anurag
authors.initials: A
authors.lastname: Chaturvedi
authors.affiliation: Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, Leuven 3000, Belgium.
authors.forename: Luc
authors.initials: L
authors.lastname: De Meester
authors.affiliation: Department of Biology, Program in Ecology and Evolutionary Biology, The University of Oklahoma, 730 Van Vleet Oval, Norman, OK 73019, USA.
authors.forename: Lawrence J
authors.initials: LJ
authors.lastname: Weider
mesh_terms: D000483:Alleles; D000818:Animals; D001499:Bayes Theorem; D033361:Cladocera / Q000235:genetics*; D003621:Daphnia / Q000235:genetics*; D023281:Genomics / Q000379:methods; D005838:Genotype; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D052587:Pulicaria / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods