Table S1. Sequence Summary Statistics. Table S2. Differentially expressed genes between Sue 1 and Sue 16. Homoeologs are indicated in matching color pairs. Table S3. Enriched Gene Ontology Categories in 148 Differentially Expressed Genes. Analysis was performed using topGO in R (Alexa and Rahnenfuhrer [36]). P-values are from Fisher’s Exact Test under a weighted model (Alexa et al. [37]). We further categorized the GO categories into either biotic stress response, abiotic stress response, general stress response (both biotic and abiotic), or not stress related categories. Table S4. Observed SNP distribution in DEGs and non-differentially expressed genes. Total basepairs (bps) in coding sequence (CDS) in the bottom right cell came from the A. thaliana CDS FASTA file. Of those, 155,619 bps fall in differentially expressed genes (DEGs). Our analysis found 71,636 SNPs between Sue 1 and Sue 16,203 of which fall in DEGs. We performed a chi-square analysis and got a p-value of .32 indicating there is no difference from the expected distribution if SNPs fell randomly in all genes. Table S5. SNPs in Sue 1, Sue 16, and the 1001 genomes database. Table S6. Comparison of Sue 1 and Sue 16 SNPs to ecotypes in the 1001 genomes database using SNPmatch. (XLSX 36 kb
