Hinesetal_BMCGenomics_fulldatainfoThis file includes accessory information on each transcript contig used from the associated microarray study, including annotation results from various analyses, mean values across probes for that gene across the tested conditions, and significance across the variety of statistical analyses performed. By column this dataset includes: | Transcript ID – The identifications assigned to each transcript on the array. These IDs are referenced in the text and sequences for each contig are available at . | Blast2Go Annotation – Annotation term assigned during the Blast2Go analysis of these transcripts. | Flybase Gene ID and Flybase Annotation Abbr. – The gene ID the contig blasted to in Flybase and the name assigned to that gene. | Manual Anno Flybase Gene ID and Manual Anno Flybase Anno Abbr. – Flybase gene identifications and terms for genes that did not hit to Flybase with the contig sequence but were whose identity were determined manually using various parameters outlined in the manuscript. | Significant for Hindwing, Significant for Forewing – If an ID is listed, that gene was significant in either the hindwing or forewing analyses. | Lsmean columns – These provide the mean expression across probes across each array condition, including in the title Race, Stage, and (for forewings) Wing Section. | -log10(p-value) columns– These provide the p-values from ANOVAs for the two listed pairwise comparisons of those Lsmeans | Significant Index columns – Indicate whether p-values of various pairwise comparisons were significant (1) or not (0). | Columns FR – GT- IDs are listed where significant differences were found with various analyses, described in the manuscript. | Columns GU – HM – These refer to the genes that are differentially expressed in an ANOVA along the proximal-distal forewing axis and the significance columns refer to whether there was significance for each of the wing section comparisons. F1 is the basal section, F2 is the medial section, and F3 is the apical section.

BACKGROUND: Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Positional cloning and candidate gene studies have identified a handful of regulatory and pigmentation genes implicated in Heliconius wing pattern variation, but little is known about the greater developmental networks within which these genes interact to pattern a wing. Here we took a large-scale transcriptomic approach to identify the network of genes involved in Heliconius wing pattern development and variation. This included applying over 140 transcriptome microarrays to assay gene expression in dissected wing pattern elements across a range of developmental stages and wing pattern morphs of Heliconius erato. RESULTS: We identified a number of putative early prepattern genes with color-pattern related expression domains. We also identified 51 genes differentially expressed in association with natural color pattern variation. Of these, the previously identified color pattern “switch gene” optix was recovered as the first transcript to show color-specific differential expression. Most differentially expressed genes were transcribed late in pupal development and have roles in cuticle formation or pigment synthesis. These include previously undescribed transporter genes associated with ommochrome pigmentation. Furthermore, we observed upregulation of melanin-repressing genes such as ebony and Dat1 in non-melanic patterns. CONCLUSIONS: This study identifies many new genes implicated in butterfly wing pattern development and provides a glimpse into the number and types of genes affected by variation in genes that drive color pattern evolution.