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.
Highlights
High-throughput sequencing methodologies have opened up exciting possibilities in the fields of population genetics, conservation and evolutionary biology by enabling the assessment of genetic variation at genome-wide scales
The D. pulex reference genome is available in scaffolds with different sequence lengths, and the number of Single Nucleotide Polymorphic (SNP) per scaffold depends on scaffold length
We found 93.84% of SNPs (i.e., 30,323) in the first 220 scaffolds, whose individual length is greater than 100 Kb
Summary
High-throughput sequencing methodologies have opened up exciting possibilities in the fields of population genetics, conservation and evolutionary biology by enabling the assessment of genetic variation at genome-wide scales. The genotyping-by-sequencing strategy (GBS)[1] is a generation sequencing (NGS)-based method providing a cost effective approach to reduce genome complexity using restriction enzymes, being currently applied in numerous species[2] In such a way, one can sequence part of the whole genome and generate hundreds or thousands of Single Nucleotide Polymorphisms (SNPs), providing a direct way to characterize bi-allelic molecular markers with a more-or-less uniform distribution throughout the genome. The development and characterization of hundreds of SNPs with a regular distribution across the genome will provide an invaluable genetic resource in this emergent model organism, and should give us the option to screen regions under selection This new methodological approach will allow us to face challenges such as identifying the mechanisms and processes related to the genetic basis of adaptation in natural populations[18]
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