Datensatz:

Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

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September 16, 2016

Autor:innen

Smitz, Nathalie
Van Hooft, Pim
Heller, Rasmus
Cornélis, Daniel
Chardonnet, Philippe
Greyling, Ben J.
Crooijmans, Richard
Groenen, Martien
Michaux, Johan
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https://doi.org/10.5061/dryad.q8q11
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Zusammenfassung

This study aimed to develop a set of SNP markers with high resolution and accuracy within the African buffalo. Such a set can be used, among others, to depict subtle population genetic structure for a better understanding of buffalo population dynamics. In total, 18.5 million DNA sequences of 76 bp were generated by next generation sequencing on an Illumina Genome Analyzer II from a reduced representation library using DNA from a panel of 13 African buffalo representative of the four subspecies. We identified 2534 SNPs with high confidence within the panel by aligning the short sequences to the cattle genome (Bos taurus). The average sequencing depth of the complete aligned set of reads was estimated at 5x, and at 13x when only considering the final set of putative SNPs that passed the filtering criterion. Our set of SNPs was validated by PCR amplification and Sanger sequencing of 15 SNPs. Of these 15 SNPs, 14 amplified successfully and 13 were shown to be polymorphic (success rate: 87%). The fidelity of the identified set of SNPs and potential future applications are finally discussed.

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570 Biowissenschaften, Biologie

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molecular markers, Disease ecology, Syncerus caffer

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Item type: Publikation , Zeitschriftenartikel
Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
(2016) Smitz, Nathalie; Van Hooft, Pim; Heller, Rasmus; Cornélis, Daniel; Chardonnet, Philippe; Kraus, Robert; Greyling, Ben; Crooijmans, Richard; Groenen, Martien; Michaux, Johan
Erschienen in: Mammalian Biology - Zeitschrift für Säugetierkunde. 2016, 81(6), S. 595-603. ISSN 1616-5047. eISSN 1618-1476. Verfügbar unter: doi: 10.1016/j.mambio.2016.07.047
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https://doi.org/10.1016/j.mambio.2016.07.047
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ISO 690SMITZ, Nathalie, Pim VAN HOOFT, Rasmus HELLER, Daniel CORNÉLIS, Philippe CHARDONNET, Robert KRAUS, Ben J. GREYLING, Richard CROOIJMANS, Martien GROENEN, Johan MICHAUX, Ben GREYLING, 2016. Data from: Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing
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