Fig. 6

Co-expression patterns of TEs and lncRNAs in B. hordei. A We used TCseq [37] to cluster time-resolved coding gene (mRNA), lncRNA, and consensus TE expression patterns. Each line represents a single transcript; the color shade indicates the cluster membership according to Spearman correlation (the darker the color, the higher the correlation R with the respective expression cluster; see color scheme in the bottom right corner). Shades of purple (upper panel), mRNAs; shades of orange (middle panel), lncRNAs; shades of green (bottom panel), consensus TEs. The x-axis indicates the time points of infection: 0 hpi (spore germination), 6 hpi (appressorium formation), 18 hpi (early primary haustorium), 24 hpi (mature primary haustorium), 72 hpi (host colonization), and 120 hpi (conidia formation). The y-axis displays the relative z-score based on reads per kb of transcript per million mapped reads (RPKM). B Co-regulation networks were discovered using WGCNA [55]. The colored circles indicate transcripts (purple, mRNA; orange, lncRNA; green, consensus TE) and lines significant correlation between two transcripts. The WGCNA-assigned cluster colors are indicated on the top-left of each corresponding cluster of transcripts; the number of genes encoding putative secreted proteins in the respective co-expression cluster is indicated. The clusters were arranged to correspond to the time-resolved expression patterns shown above in (A). C-E The dot plots show examples of expression patterns of TE antisense lncRNA and the corresponding TE, as indicated on top of each plot. Expression values are shown as TPM (y-axis) during six time points of host infection (x-axis; Fig. 1A). The black bar indicates the median of three independent replicates (n = 3)