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Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species

  • Targeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species’ European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out withTargeted capture coupled with high-throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for nonmodel organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a nonmodel organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species’ European range. A large set of biallelic candidate SNPs was then evaluated using a high-throughput SNP genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance and reliability; validation was carried out with 100 additional Eurasian lynx samples not included in the SNP discovery phase. The 96 SNP-panel developed from CDS performed very successfully in the identification of individuals and in population genetic structure inference (including the assignment of individuals to their source population). In keeping with recent studies, our results show that genic SNPs can be valuable for genetic monitoring of wildlife species.zeige mehrzeige weniger

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Metadaten
Verfasserangaben:Daniel W. FörsterORCiD, James K. Bull, Dorina Lenz, Marijke AutenriethORCiDGND, Johanna L. A. PaijmansORCiDGND, Robert H. S. Kraus, Carsten Nowak, Helmut Bayerl, Ralph KühnORCiD, Alexander P. SaveljevORCiD, Magda Sindicic, Michael HofreiterORCiDGND, Krzysztof SchmidtORCiD, Jörns FickelORCiDGND
DOI:https://doi.org/10.1111/1755-0998.12924
ISSN:1755-098X
ISSN:1755-0998
Pubmed ID:https://pubmed.ncbi.nlm.nih.gov/29978939
Titel des übergeordneten Werks (Englisch):Molecular ecology resources
Verlag:Wiley
Verlagsort:Hoboken
Publikationstyp:Wissenschaftlicher Artikel
Sprache:Englisch
Datum der Erstveröffentlichung:06.07.2018
Erscheinungsjahr:2018
Datum der Freischaltung:08.07.2021
Freies Schlagwort / Tag:CDS; Eurasian lynx; conservation genetics; genetic monitoring; hybridization capture; single nucleotide polymorphism
Band:18
Ausgabe:6
Seitenanzahl:18
Erste Seite:1356
Letzte Seite:1373
Fördernde Institution:Leibniz-Gemeinschaft [SAW-2011-SGN-3]; Deutscher Akademischer AustauschdienstDeutscher Akademischer Austausch Dienst (DAAD) [A/11/93927]; Narodowe Centrum Nauki [2014/15/B/NZ8/00212]
Organisationseinheiten:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Biochemie und Biologie
DDC-Klassifikation:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Peer Review:Referiert
Publikationsweg:Open Access / Green Open-Access
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