Fig 1.
The experimental workflow for RNA-seq analysis of H. pseudoburtonii co-cultured with B. cinerea showing the sampling plan, RNA extraction and processing, as well as the data analysis steps.
Fig 2.
Principal Component Analysis (PCA) plot of the biological replicates of transcripts from H. pseudoburtonii (Hp) monocultures and H. pseudoburtonii and B. cinerea mixed cultures (Hp+B).
Fig 3.
Representation of differentially expressed genes (DEGs) in H. pseudoburtonii at different time points (24, 48, and 120 h) in the presence of B. cinerea FF1.
(A) Total number of up-regulated and down-regulated genes in H. pseudoburtonii in the co-culture. (B) Venn diagram showing the number of unique and shared DEGs between the different time points.
Fig 4.
Subsystems associated with differentially expressed genes detected at 24, 48 and 120 h, in H. pseudoburtonii co-cultured with B. cinerea compared to H. pseudoburtonii monoculture.
Each dot displayed on the vertical line represents the expression value for the genes. Whiskers, associated with box-and-whisker plots, indicate data range and variability. Bars represent averages or central tendencies. The Y-axis scales between the panels are different, impacting the comparability of values across the graph.
Table 1.
Log2 fold change of the top 15 up-regulated genes in H. pseudoburtonii co-cultured with B. cinerea at 24, 48 and 120 h compared to the monoculture.
Fig 5.
Energy metabolism-associated differentially expressed genes detected at 24, 48 and 120 h, in H. pseudoburtonii co-cultured with B. cinerea compared to H. pseudoburtonii monoculture.
Fig 6.
Gene ontology classification of up-regulated (A) and down-regulated (B) genes (Log2FC ≥1, p- value < 0.05) in H. pseudoburtonii co- cultured with B. cinerea compared to the monoculture at 24 h, showing enriched biological process (BP), cellular component (CC) and molecular function (MF).
Fig 7.
Gene ontology classification of up-regulated DEGs in H. pseudoburtonii grown for (A) 48 h and (B) 120 h in the presence of B. cinerea, showing enriched biological process (BP), cellular component (CC) and molecular function (MF).
Fig 8.
Up-regulated and down-regulated genes associated with the enrichment of the cellular component GO term: Cell periphery, extracellular region and plasma membrane of H. pseudoburtonii co-cultured with B. cinerea at 120 h.
Fig 9.
KEGG pathways of down and up- regulated genes in H. pseudoburtonii grown for (A) 24 and (B) 120 h in the presence of B. cinerea.
Table 2.
Unique and differentially abundant proteins identified in H. pseudoburtonii + B. cinerea (Hp+B) co-cultures.