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Isolation, characterization and genotyping of single nucleotide polymorphisms in the non-model tree species Frangula alnus (Rhamnaceae)

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Abstract

The genomic content of the non-model plant Frangula alnus remains largely unexplored. However, because of its occurrence over a wide latitudinal range and its invasive nature in the US and Canada, F. alnus may serve as an excellent study species in tree conservation genomic research. We used pooled paired-end sequencing of Restriction-site Associated DNA to discover SNPs in the insect pollinated shrub F. alnus. We identified 7,383 SNPs from which the corresponding contig sequences were annotated to the available plant genomes. An enrichment analysis showed an excess of putatively adaptive and plastic gene ontology terms.

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Acknowledgments

We would like to thank K Van Acker, S Maccherini, G Decocq and BG Jonsson for assisting with sample collection. We also appreciate the contributions from Thomas Lee for providing additional information regarding the invasion of Frangula alnus in Northern America. HDK holds a doctoral funding from the agency for Innovation by Science and Technology (IWT). The genetic analyses were funded by a grant of the Agentschap voor Natuur en Bos (ANB) to JM.

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Authors and Affiliations

  1. Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, 3001, Heverlee, Belgium

    Hanne De Kort, Katrien Vandepitte & Olivier Honnay

  2. Research Institute for Nature and Forest, Gaverstraat 4, 9500, Geraardsbergen, Belgium

    Joachim Mergeay

Authors
  1. Hanne De Kort
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  2. Katrien Vandepitte
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  3. Joachim Mergeay
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  4. Olivier Honnay
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Corresponding author

Correspondence to Hanne De Kort.

Electronic supplementary material

Data Archiving Statement

Data Archiving Statement

We have provided GenBank accession numbers for our contig sequences. The records will be released to the public database once they are processed by GenBank (http://www.ncbi.nlm.nih.gov/genbank/).

As soon as the sequences are released, they can be found in Genbank using one of the following project details:

Submission ID:

: SUB200632

BioProject ID:

: PRJNA203129

Organism name/label:

: Frangula alnus

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De Kort, H., Vandepitte, K., Mergeay, J. et al. Isolation, characterization and genotyping of single nucleotide polymorphisms in the non-model tree species Frangula alnus (Rhamnaceae). Conservation Genet Resour 6, 267–269 (2014). https://doi.org/10.1007/s12686-013-0083-6

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  • DOI: https://doi.org/10.1007/s12686-013-0083-6

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