2024-03-28T15:06:23Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/1346522021-12-27T15:59:11Zcom_10261_13com_10261_8col_10261_266
DIGITAL.CSIC
author
Muñoz, Joaquín
author
Chaturvedi, Anurag
author
De Meester, Luc
author
Weider, L.J.
funder
European Commission
funder
National Science Foundation (US)
funder
European Science Foundation
funder
University of Leuven
2016-07-11T09:25:24Z
2016-07-11T09:25:24Z
2016-06
Scientific Reports 6: 28569 (2016)
2045-2322
http://hdl.handle.net/10261/134652
10.1038/srep28569
http://dx.doi.org/10.13039/501100000780http://dx.doi.org/10.13039/100000001http://dx.doi.org/10.13039/501100000782
27346179
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.
eng
openAccess
Characterization of genome-wide SNPs for the water flea Daphnia pulicaria generated by genotyping-by-sequencing (GBS)
artículo
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URL
https://digital.csic.es/bitstream/10261/134652/1/daphnia_pulicaria_Munoz.pdf
File
MD5
7756be39dbcf20676bd6dbde680cc44a
893257
application/pdf
daphnia_pulicaria_Munoz.pdf