De novo transcriptome characterization and development of genomic tools for Scabiosa columbaria L. using next-generation sequencing techniques

Next-generation sequencing (NGS) technologies are increasingly applied in many organisms, including nonmodel organisms that are important for ecological and conservation purposes. Illumina and 454 sequencing are among the most used NGS technologies and have been shown to produce optimal results at reasonable costs when used together. Here, we describe the combined application of these two NGS technologies to characterize the transcriptome of a plant species of ecological and conservation relevance for which no genomic resource is available, Scabiosa columbaria. We obtained 528557 reads from a 454 GS-FLX run and a total of 28993627 reads from two lanes of an Illumina GAII single run. After read trimming, the de novo assembly of both types of reads produced 109630 contigs. Both the contigs and the >75bp remaining singletons were blasted against the Uniprot/Swissprot database, resulting in 29676 and 10515 significant hits, respectively. Based on sequence similarity with known gene products, these sequences represent at least 12516 unique genes, most of which are well covered by contig sequences. In addition, we identified 4320 microsatellite loci, of which 856 had flanking sequences suitable for PCR primer design. We also identified 75054 putative SNPs. This annotated sequence collection and the relative molecular markers represent a main genomic resource for S. columbaria which should contribute to future research in conservation and population biology studies. Our results demonstrate the utility of NGS technologies as starting point for the development of genomic tools in nonmodel but ecologically important species.