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Stage-specific expression of C. higginsianum transposable elements (TEs). (A) Heatmap showing the expression profiles of TEs. (B) K-means clustering of 441 TE copies considered to be expressed in at least one fungal stage (VA = in vitro appressoria, PA = in planta appressoria, BP = biotrophic phase). For each of the five clusters, the average profile is shown in red. (C) Localization of in planta-expressed LTR transposon fragments in the 3’ UTR regions of C. higginsianum effector genes. IGV screenshots showing the genomic locations of TE copies RXX_R113 and RLX_P25.13 (red) in relation to effector genes ChEC35 and ChEC117 (green), respectively. RNA-Seq reads are displayed for appressoria in vitro (VA) and the biotrophic phase (BP). The RLX_P25.13 copy comprises a ‘solo’-LTR, likely produced by homologous recombination between two LTRs, leading to deletion of the internal retrotransposon sequence. (PDF 2850 kb)

Text S1. Supplementary methods. (DOCX 16 kb)

Text S1. Supplementary methods. (DOCX 16 kb)

(A) Dinucleotide mutation bias among TE copies belonging to different TE orders. Mutation rates were calculated using RIPCAL by comparing each TE copy with a Ti/Tv > 1.5 to the TE consensus sequence. Y-axis: percentage relative to the total number of copies used in RIPCAL analysis. Coloured bars indicate the percentage of copies with expected RIP (Ti/Tv > 1.5) and dinucleotide preferentially used (>1/3) in CN- > TN and (cNG - > cNA) mutations. Black bar: percentage of copies without expected RIP (Ti/Tv > 1.5). Gray bar: percentage of copies with expected RIP (Ti/Tv > 1.5) but no evidence of dinucleotide bias. (B) Plot showing the sequence divergence of TE copies belonging to different TE orders relative to their respective consensus sequences. (PDF 466 kb)