title: Genomic analysis of the native European Solanum species, S. dulcamara.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: IWWR, Department of Molecular Plant Physiology, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, The Netherlands.
authors.forename: Nunzio
authors.initials: N
authors.lastname: D'Agostino
authors.forename: Tomek
authors.initials: T
authors.lastname: Golas
authors.forename: Henri
authors.initials: H
authors.lastname: van de Geest
authors.forename: Aureliano
authors.initials: A
authors.lastname: Bombarely
authors.forename: Thikra
authors.initials: T
authors.lastname: Dawood
authors.forename: Jan
authors.initials: J
authors.lastname: Zethof
authors.forename: Nicky
authors.initials: N
authors.lastname: Driedonks
authors.forename: Erik
authors.initials: E
authors.lastname: Wijnker
authors.forename: Joachim
authors.initials: J
authors.lastname: Bargsten
authors.forename: Jan-Peter
authors.initials: JP
authors.lastname: Nap
authors.forename: Celestina
authors.initials: C
authors.lastname: Mariani
authors.forename: Ivo
authors.initials: I
authors.lastname: Rieu
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics; D016000:Cluster Analysis; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005819:Genetic Markers / Q000235:genetics; D023281:Genomics; D018895:Microsatellite Repeats / Q000235:genetics; D008957:Models, Genetic; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D032322:Solanum / Q000235:genetics*; D013045:Species Specificity
chemical_list: D005819:Genetic Markers