Over het archief
Het OWA, het open archief van het Waterbouwkundig Laboratorium heeft tot doel alle vrij toegankelijke onderzoeksresultaten van dit instituut in digitale vorm aan te bieden. Op die manier wil het de zichtbaarheid, verspreiding en gebruik van deze onderzoeksresultaten, alsook de wetenschappelijke communicatie maximaal bevorderen.
Dit archief wordt uitgebouwd en beheerd volgens de principes van de Open Access Movement, en het daaruit ontstane Open Archives Initiative.
Basisinformatie over ‘Open Access to scholarly information'.
A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel
Pujolar, J.M.; Jacobsen, M.W.; Frydenberg, J.; Als, T.D.; Larsen, P.F.; Maes, G.E.; Zane, L.; Jian, J.B.; Cheng, L.; Hansen, M.M. (2013). A resource of genome-wide single-nucleotide polymorphisms generated by RAD tag sequencing in the critically endangered European eel. Mol. Ecol. Resour. 13(4): 706-714. dx.doi.org/10.1111/1755-0998.12117
In: Molecular Ecology Resources. Blackwell Publishing: Oxford. ISSN 1755-098X; e-ISSN 1755-0998, meer
|  |
| Author keywords |
effective population size; population genomics; RAD sequencing; SNPdiscovery |
| Auteurs | | Top |
- Pujolar, J.M.
- Jacobsen, M.W.
- Frydenberg, J.
- Als, T.D.
|
- Larsen, P.F.
- Maes, G.E., meer
- Zane, L.
|
- Jian, J.B.
- Cheng, L.
- Hansen, M.M.
|
| Abstract |
Reduced representation genome sequencing such as restriction-site-associated DNA (RAD) sequencing is finding increased use to identify and genotype large numbers of single-nucleotide polymorphisms (SNPs) in model and nonmodel species. We generated a unique resource of novel SNP markers for the European eel using the RAD sequencing approach that was simultaneously identified and scored in a genome-wide scan of 30 individuals. Whereas genomic resources are increasingly becoming available for this species, including the recent release of a draft genome, no genome-wide set of SNP markers was available until now. The generated SNPs were widely distributed across the eel genome, aligning to 4779 different contigs and 19703 different scaffolds. Significant variation was identified, with an average nucleotide diversity of 0.00529 across individuals. Results varied widely across the genome, ranging from 0.00048 to 0.00737 per locus. Based on the average nucleotide diversity across all loci, long-term effective population size was estimated to range between 132000 and 1320000, which is much higher than previous estimates based on microsatellite loci. The generated SNP resource consisting of 82425 loci and 376918 associated SNPs provides a valuable tool for future population genetics and genomics studies and allows for targeting specific genes and particularly interesting regions of the eel genome. |
IMIS is ontwikkeld en wordt gehost door het VLIZ.
