DOI: 10.5061/dryad.np5hqbzrz
title: Supporting Data for: Differential gene expression associated with a floral scent polymorphism in the evening primrose Oenothera harringtonii (Onagraceae)

description: 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.
description: <strong>transcriptome_and_mapping.tar.gz</strong><br> 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. <strong>SNP_analysis.tar.gz</strong><br> 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. <strong>terpene_synthase.hmm</strong><br> Profile Hidden Markov Model (pHMM) used to identify terpene synthase transcripts from the reference assembly. <strong>terpene_synthase_alignment.fasta</strong><br> 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).