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Open Access Research article

Genomic analysis of the native European Solanum species, S. dulcamara

Nunzio D’Agostino12, Tomek Golas16, Henri van de Geest36, Aureliano Bombarely4, Thikra Dawood1, Jan Zethof1, Nicky Driedonks1, Erik Wijnker5, Joachim Bargsten3, Jan-Peter Nap36, Celestina Mariani16 and Ivo Rieu1*

Author Affiliations

1 IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands

2 Consiglio per la ricerca e la sperimentazione in agricoltura, Centro di ricerca per l’orticoltura, via Cavalleggeri 25, Pontecagnano, SA, 84098, Italy

3 Applied Bioinformatics, Bioscience, Plant Research International, Wageningen University & Research Centre, PO Box 619, Wageningen, 6700 AP, The Netherlands

4 Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, New York, 14853-1801, USA

5 Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands

6 Centre for BioSystems Genomics 2012 (CBSG2012), PO Box 98, Wageningen, 6700 AB, The Netherlands

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BMC Genomics 2013, 14:356  doi:10.1186/1471-2164-14-356

Published: 28 May 2013

Abstract

Background

Solanum dulcamara (bittersweet, climbing nightshade) is one of the few species of the Solanaceae family native to Europe. As a common weed it is adapted to a wide range of ecological niches and it has long been recognized as one of the alternative hosts for pathogens and pests responsible for many important diseases in potato, such as Phytophthora. At the same time, it may represent an alternative source of resistance genes against these diseases. Despite its unique ecology and potential as a genetic resource, genomic research tools are lacking for S. dulcamara. We have taken advantage of next-generation sequencing to speed up research on and use of this non-model species.

Results

In this work, we present the first large-scale characterization of the S. dulcamara transcriptome. Through comparison of RNAseq reads from two different accessions, we were able to predict transcript-based SNP and SSR markers. Using the SNP markers in combination with genomic AFLP and CAPS markers, the first genome-wide genetic linkage map of bittersweet was generated. Based on gene orthology, the markers were anchored to the genome of related Solanum species (tomato, potato and eggplant), revealing both conserved and novel chromosomal rearrangements. This allowed a better estimation of the evolutionary moment of rearrangements in a number of cases and showed that chromosomal breakpoints are regularly re-used.

Conclusion

Knowledge and tools developed as part of this study pave the way for future genomic research and exploitation of this wild Solanum species. The transcriptome assembly represents a resource for functional analysis of genes underlying interesting biological and agronomical traits and, in the absence of the full genome, provides a reference for RNAseq gene expression profiling aimed at understanding the unique biology of S. dulcamara. Cross-species orthology-based marker selection is shown to be a powerful tool to quickly generate a comparative genetic map, which may speed up gene mapping and contribute to the understanding of genome evolution within the Solanaceae family.

Keywords:
Solanum dulcamara; Bittersweet; de novo transcriptome assembly; Genetic map; Comparative genomics