Supporting Data for: Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae)

Background: Plant volatiles play an important role in both plant-pollinator and plant-herbivore interactions. Intraspecific polymorphisms in volatile production are ubiquitous, but studies that explore underlying differential gene expression are rare. Oenothera harringtonii populations are polymorphic in floral emission of the monoterpene (R)-(-)-linalool; some plants emit (R)-(-)-linalool (linalool+ plants) while others do not (linalool- plants). However, the genes associated with differential production of this floral volatile in Oenothera are unknown. We used RNA-Seq to broadly characterize differential gene expression involved in (R)-(-)-linalool biosynthesis. To identify genes that may be associated with the polymorphism for this trait, we used RNA-Seq to compare gene expression in six different Oenothera harringtonii tissues from each of three linalool+ and linalool- plants. Results: Three clusters of differentially expressed genes were enriched for terpene synthase activity: two were characterized by tissue-specific upregulation and one by upregulation only in plants with flowers that produce (R)-(-)-linalool. A molecular phylogeny of all terpene synthases identified two putative (R)-(-)-linalool synthase transcripts in Oenothera harringtonii, a single allele of which is found exclusively in linalool+ plants. Conclusions: By using a naturally occurring polymorphism and comparing different tissues, we were able to identify genes putatively involved in the biosynthesis of (R)-(-)-linalool. Expression of these genes in linalool- plants suggests a regulatory polymorphism, rather than a population-specific loss-of-function allele. Additional terpene biosynthesis-related genes that are up-regulated in plants that emit (R)-(-)-linalool may be associated with herbivore defense, suggesting a potential economy of scale between plant reproduction and defense.,transcriptome_and_mapping.tar.gz RNA-Seq was carried out on an Illumina HiSeq 2500 system. Reads were trimmed with Trimmomatic and filtered for rRNA and plastid RNA. Reads from all libraries were pooled and normalized in silico, and subsequently assembled using Trinity with default settings, resulting in the O.harringtonii.ref_transcriptome.fasta reference assembly. For each of the 32 libraries, the reads were mapped to the reference assembly to determine expression levels using RSEM. The reference assembly and individual results for each library are provided. SNP_analysis.tar.gz These files contain the haplotype analysis for Oenothera harringtonii R-linalool-synthase (OhRLS) to identify whether heterozygosity in some individuals reflects alleles or paralogs and to determine the number of reads that map to OhRLS for each individual library. terpene_synthase.hmm Profile Hidden Markov Model (pHMM) used to identify terpene synthase transcripts from the reference assembly. terpene_synthase_alignment.fasta Multiple sequence alignment of all terpene synthase transcripts identified from the Oenothera harringtonii reference transcriptome assembly, and all sequences included in van Schie et al. (2007; Plant Mol Biol 64:251-71).,