Fig. 2: Comparison of the nuclear transcriptome between Chroomonas sp. cells before and after ingestion by the dinoflagellate N. aeruginosum.

a Schematic diagrams showing the culture of free-living Chroomonas sp. Dc01 and that of Chroomonas sp. Dc01 ingested by N. aeruginosum used for comparison of the nuclear transcriptomes of Chroomonas sp. Dc01 in each state. Both cultures were pre-incubated in the dark for 24 h. Then, from hour 0, the cultures were subjected to 12-h-light and subsequently dark. Nuclear transcriptomes of Chroomonas sp. Dc01 were examined at hours 0 (just before illumination), 1, 6 (during the light period), 12 (just before the dark), and 13 (during the dark period). To inhibit N. aeruginosum from ingesting any new Chroomonas sp. Dc01, free-living Chroomonas sp. were removed from the coculture 4 days prior to the dark preincubation. b M-A plot showing 2505 upregulated and 1874 downregulated contigs from Chroomonas sp. ingested by N. aeruginosum cells and free-living Chroomonas sp. cells. The averages of respective mRNA levels at five time points (hours 0, 1, 6, 12, and 13) were compared. Upregulated and downregulated contigs were defined as those that had FDR < 0.01 and logFC > 2 (indicated in red) and FDR < 0.01 and logFC < −2 (indicated in blue), respectively (three independent cultures). The x-axis represents averaged logCPM, and the y-axis represents the base 2 logarithm of the fold change to the free-living condition. c Comparison of the number of upregulated and downregulated contigs whose functions were assigned to respective KEGG functional categories.