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

Nunzio D’Agostino,Joachim Bargsten,Celestina Mariani,Nicky Driedonks,Erik Wijnker,Thikra Dawood,Tomek Golas,Henri Van De Geest,Aureliano Bombarely,Jan-Peter Nap,Jan Zethof,Ivo Rieu

doi:10.1186/1471-2164-14-356

Abstract

BackgroundSolanum 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.ResultsIn 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.ConclusionKnowledge 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.

Highlights

Solanum dulcamara is one of the few species of the Solanaceae family native to Europe
De novo transcriptome assembly Short reads from seventeen different S. dulcamara cDNA libraries that were sequenced using either Roche GS-FLX or Illumina HiSeq2000 sequencing technologies (Table 1; Additional file 1: Table S1) were combined to build de novo a consensus transcriptome using the Trinity package [14]
We present a variety of genomics resources for the nonmodel species S. dulcamara and demonstrate their use for functional, genetic and comparative analyses

Summary

Introduction

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. Solanum dulcamara (bittersweet, climbing nightshade) is an allogamous diploid (2n = 2x = 24) species with a genome size of ~ 780 Mb [1]. It is one of the few Solanaceae species native to Europe, it has been widely naturalised around the world (e.g. North America, Asia). We have recently reported on the identification of two resistance loci to Phytophthora infestans, Rpi-dlc and Rpi-dlc, which are located on chromosome 9 and 10, respectively [9,10]

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