Fig. 3: Comparison of the nuclear transcriptomic change following illumination in Chroomonas sp. cells before and after ingestion by the dinoflagellate N. aeruginosum.

The RNA-seq data were obtained from the process described in Fig. 2a. a PCA of the transcriptomic changes of the free and ingested Chroomonas sp. following illumination. The raw count data were normalized with TCC using R and then plotted (low count contigs were omitted before normalization). The square and circle correspond to free-living and ingested Chroomonas sp. at the indicated time point, respectively. The color represents the presence (orange) or absence (gray) of light illumination. b Heatmap showing the expression patterns of DEGs (log2-fold-change at any time point from hour 0 > 2; FDR < 0.01; three independent cultures) in the free-living Chroomonas sp. and a comparison with those in the ingested Chroomonas sp. The levels in the free-living Chroomonas sp. at hour 0 were defined as “0.” Yellow and blue indicate upregulation and downregulation of the gene, respectively, compared with the level at hour 0 in the free-living Chroomonas sp. The clustering was performed by the k-means method. c Comparison of the number of contigs whose functions were assigned to respective KEGG functional categories of second level terms in respective clusters. Colors correspond to clusters 1–7 in (b).