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

Lade...
Vorschaubild
Dateien
Zu diesem Dokument gibt es keine Dateien.
Datum
2018
Autor:innen
Förster, Daniel W.
Bull, James K.
Lenz, Dorina
Autenrieth, Marijke
Paijmans, Johanna L. A.
Nowak, Carsten
Bayerl, Helmut
Kuehn, Ralph
Saveljev, Alexander P.
et al.
Herausgeber:innen
Kontakt
ISSN der Zeitschrift
Electronic ISSN
ISBN
Bibliografische Daten
Verlag
Schriftenreihe
Auflagebezeichnung
URI (zitierfähiger Link)
ArXiv-ID
Internationale Patentnummer
EU-Projektnummer
DFG-Projektnummer
Projekt
Open Access-Veröffentlichung
Sammlungen
Gesperrt bis
Titel in einer weiteren Sprache
Forschungsvorhaben
Organisationseinheiten
Zeitschriftenheft
Publikationstyp
Zeitschriftenartikel
Publikationsstatus
Published
Erschienen in
Molecular Ecology Resources. 2018, 18(6), pp. 1356-1373. ISSN 1755-098X. eISSN 1755-0998. Available under: doi: 10.1111/1755-0998.12924
Zusammenfassung

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 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.

Zusammenfassung in einer weiteren Sprache
Fachgebiet (DDC)
570 Biowissenschaften, Biologie
Schlagwörter
Konferenz
Rezension
undefined / . - undefined, undefined
Zitieren
ISO 690FÖRSTER, Daniel W., James K. BULL, Dorina LENZ, Marijke AUTENRIETH, Johanna L. A. PAIJMANS, Robert KRAUS, Carsten NOWAK, Helmut BAYERL, Ralph KUEHN, Alexander P. SAVELJEV, 2018. Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species. In: Molecular Ecology Resources. 2018, 18(6), pp. 1356-1373. ISSN 1755-098X. eISSN 1755-0998. Available under: doi: 10.1111/1755-0998.12924
BibTex
@article{Forster2018-11Targe-45124,
  year={2018},
  doi={10.1111/1755-0998.12924},
  title={Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species},
  number={6},
  volume={18},
  issn={1755-098X},
  journal={Molecular Ecology Resources},
  pages={1356--1373},
  author={Förster, Daniel W. and Bull, James K. and Lenz, Dorina and Autenrieth, Marijke and Paijmans, Johanna L. A. and Kraus, Robert and Nowak, Carsten and Bayerl, Helmut and Kuehn, Ralph and Saveljev, Alexander P.}
}
RDF
<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/45124">
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2019-02-20T13:23:55Z</dcterms:available>
    <dc:creator>Autenrieth, Marijke</dc:creator>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dc:contributor>Förster, Daniel W.</dc:contributor>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dc:contributor>Bull, James K.</dc:contributor>
    <dc:contributor>Lenz, Dorina</dc:contributor>
    <dc:creator>Nowak, Carsten</dc:creator>
    <bibo:uri rdf:resource="https://kops.uni-konstanz.de/handle/123456789/45124"/>
    <dc:contributor>Kuehn, Ralph</dc:contributor>
    <dc:creator>Kraus, Robert</dc:creator>
    <dcterms:issued>2018-11</dcterms:issued>
    <dc:creator>Bayerl, Helmut</dc:creator>
    <dc:contributor>Kraus, Robert</dc:contributor>
    <dc:creator>Saveljev, Alexander P.</dc:creator>
    <dc:language>eng</dc:language>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dc:creator>Bull, James K.</dc:creator>
    <dc:contributor>Nowak, Carsten</dc:contributor>
    <dc:creator>Kuehn, Ralph</dc:creator>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2019-02-20T13:23:55Z</dc:date>
    <dcterms:abstract xml:lang="eng">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 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.</dcterms:abstract>
    <dc:creator>Paijmans, Johanna L. A.</dc:creator>
    <dc:contributor>Saveljev, Alexander P.</dc:contributor>
    <dc:creator>Lenz, Dorina</dc:creator>
    <dc:contributor>Autenrieth, Marijke</dc:contributor>
    <dc:contributor>Bayerl, Helmut</dc:contributor>
    <dc:creator>Förster, Daniel W.</dc:creator>
    <dcterms:title>Targeted resequencing of coding DNA sequences for SNP discovery in nonmodel species</dcterms:title>
    <dc:contributor>Paijmans, Johanna L. A.</dc:contributor>
  </rdf:Description>
</rdf:RDF>
Interner Vermerk
xmlui.Submission.submit.DescribeStep.inputForms.label.kops_note_fromSubmitter
Kontakt
URL der Originalveröffentl.
Prüfdatum der URL
Prüfungsdatum der Dissertation
Finanzierungsart
Kommentar zur Publikation
Allianzlizenz
Corresponding Authors der Uni Konstanz vorhanden
Internationale Co-Autor:innen
Universitätsbibliographie
Nein
Begutachtet
Ja