Isolation, characterization and genotyping of single nucleotide polymorphisms in the non-model tree species Frangula aln
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TECHNICAL NOTE
Isolation, characterization and genotyping of single nucleotide polymorphisms in the non-model tree species Frangula alnus (Rhamnaceae) Hanne De Kort • Katrien Vandepitte Joachim Mergeay • Olivier Honnay
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Received: 17 October 2013 / Accepted: 23 October 2013 Ó Springer Science+Business Media Dordrecht 2013
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. Keywords RAD paired-end sequencing SNP discovery Frangula alnus Conservation genomics Adaptation Plasticity
The alder buckthorn (Frangula alnus), an insect pollinated small tree, has a wide geographical distribution, covering large parts of Eurasia (Hampe et al. 2003). The exploration of the F. alnus genome may therefore yield interesting insights into its adaptive potential in the face of global Electronic supplementary material The online version of this article (doi:10.1007/s12686-013-0083-6) contains supplementary material, which is available to authorized users. H. De Kort (&) K. Vandepitte O. Honnay Plant Conservation and Population Biology, Biology Department, University of Leuven, Kasteelpark Arenberg 31, 3001 Heverlee, Belgium e-mail: [email protected] J. Mergeay Research Institute for Nature and Forest, Gaverstraat 4, 9500 Geraardsbergen, Belgium
change (De Kort et al. 2012). Furthermore, the species is invasive in Northern America, where it has probably been introduced before the nineteenth century (Wyman 1971). After numerous introductions into private and public gardens, the species became widespread and naturalized from the early twentieth century and has started to invade natural ecosystems from the mid-twentieth century (Lee and Thompson 2012). Except for the 16 polymorphic nuclear microsatellite markers that have been developed for the species (Rigueiro et al. 2009), the Frangula alnus genome remains unexplored. We applied a next-generation sequencing approach to increase genomic resources available for population genomics, functional genomics and conservation genomics. More specifically, Paired-End Restriction-site Associated DNA sequencing (RAD-PE) was performed on a HiSeq2000 (Illumina) at Floragenex Inc. (USA) as described by Etter et al. (2011). To reduce the cost of RAD library preparation and sequencing, we screened a pooled set of eight individuals, which were sampled across the species’ latitudinal distribution range to reduce ascertainment bias. The samples originated from Tuscany (Italy), Picardy (France), Walloni
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