Dataset for "Population-level transposable element expression dynamics influence trait evolution in a fungal crop pathogen"

<strong>Supplementary Tables</strong> <strong>Supplementary Table S1: </strong>SRA accession list of RNAseq reads. <strong>Supplementary Table S2:</strong> Genomic localization of TEs in gene elements and 10 kb windows upstream and downstream of the transcription start site (TSS) in the reference genome IPO323. <strong>Supplementary Table S3:</strong> Genome-wide TE insertion polymorphism (TIPs) in the pathogen population. 0 represents TE absence and 1 represents TE presence. <strong>Supplementary Table S4:</strong> Gene expression (log-transformed RPKM) values across the population. <strong>Supplementary Table S5:</strong> Locus-specific transcript abundance at individual TE loci (FPKM) across individuals. <strong>Supplementary Table S6:</strong> Percent of expressed copies within each TE family in the reference genome IPO323 and percent expressed TE copies in each TE family across the population. <strong>Supplementary Table S7:</strong> Linkage disequilibrium of TIP in the genome and neighboring SNPs within the 600bp distance from the TE loci. <strong>Supplementary Table S8:</strong> Genome-wide association mapping of the virulence-associated trait (PLACP: percent leaf area covered by pycnidia) and TE insertion polymorphisms in the genome. <strong>Supplementary Table S9:</strong> TIPs in the genome significantly associated with metabolite peak intensity variation in the pathogen population (filtered by Bonferroni threshold).