Fig. 2
TE families exhibit infection stage-specific expression patterns. A and B We mapped the reads from the time-course RNA-seq experiment to our repetitive elements database containing 344 individual non-redundant TE families (Table 1). The violin plots show the Log2 of the average normalized expression (y-axis) of each family expressed as transcripts per million (TPM); the types of repetitive elements (blue, DNA transposons; light green, LINE; dark green, LTR; red, NonLTR retrotransposons; magenta, SINE; grey, low complexity regions, satellites, simple repeats, and unknown repeats) are indicated on the x-axis. C We used TCseq [37] to cluster time-course expression patterns of the 344 consensus TEs. The lines represent single consensus TEs; the color shade denotes the cluster membership by Spearman correlation (the darker the shade of green, the higher the correlation R with the respective expression cluster according to the color scheme). The x-axis denotes the time points of infection (Fig. 1A), i.e., 0 hpi (conidiospore germination), 6 hpi (appressorium formation), 18 hpi (host cell penetration), 24 hpi (haustorium formation), 72 hpi (epiphytic colonization), and 120 hpi (conidiogenesis). The y-axis indicates the relative z-score based on reads per kb of transcript per million mapped reads (RPKM). D We conducted qRT-PCR analysis of selected TE families (for the whole set of tested TE families, see Supplementary Fig. 2). The dot plots display the relative transcript abundance (according to ΔΔCT analysis; y-axis) of the respective TE family indicated on the top-left in B. hordei isolate K1AC at seven time points of host infection (x-axis; see also Fig. 1A). TE transcript levels were normalized to B. hordei GAPDH (BLGH_00691); three independent replicates (n = 3), consisting of three technical replicates each, were performed. The shades of green indicate the replicate each data point belongs to; the black bar shows the median