SNP dataset for M. truncatula HapMap collection

SNP database files generated using SNPmatch for Medicago truncatula HapMap collection

SNP dataset for A. thaliana RegMap panel

Biallelic SNP database files used in SNPmatch for RegMap panel of Arabidopsis thalian

SNP dataset for A. thaliana 1001 Genomes project

SNP database files generated using SNPmatch from published 1001 genomes SNP

Additional file 1 of Diversity and evolution of the repetitive genomic content in Cannabis sativa

Table S1. Raw data information and repeat content for different varieties of Cannabis sativa, Humulus lupulus, Morus notabilis and Arabidopsis thaliana. Table S2. Repetitive content (percentage of the genome) in the genomes of C. sativa PK, Finola (FIN), USO31 (USO), H. lupulus (HUM) and, M. notabilis (MOR). Table S3. Repeat sequence conservation, as measured by percent sequence similarity among consensus sequences from each repeat class in each genotype, compared to the consensus repeats from the C. sativa PK genome. The missing entries are due to the absence of specific families in either of the genomes’ repeat libraries. (PDF 163 kb

Additional file 2: of Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

Figure S1. Members of the xyloglucan transglycosylase/hydrolase (XTH) family are significantly differentially upregulated in Sue 16 relative to Sue 1. Shown are FPKM expression values with confidence intervals from Cuffdiff analysis for both homoeologs of XTH4 and XTH22. (PDF 471 kb

Additional file 1: of Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

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

Additional file 4: of Natural variation in stress response gene activity in the allopolyploid Arabidopsis suecica

Table S7. Complete RNA seq data. (TXT 9489 kb