Fig 1.
In silico analysis pipeline used in this study.
Squares represent analysis steps, while bold text denotes the software or tools used. Arrows indicate both the data/material type and the direction of workflow.
Fig 2.
Principal component analysis (PCA) of isoform-level transcript expression.
Left, PCA plot based on isoform-level transcript counts, showing the distribution of biological replicates from the diatom-fed and reed leaf–fed groups. Each point represents one biological replicate. Samples from the diatom-fed group cluster closely together, whereas those from the reed leaf–fed group are more widely dispersed, indicating greater variability in transcriptomic responses under the reed leaf feeding condition. Right, Scree plot showing the proportion of variance explained by each principal component. The first two principal components (PC1 and PC2) together explained 42.3% of the total variance.
Table 1.
Summary of the extracted enzymes of interest. Total counts of both genes and isoforms are presented. For each of the four enzyme types, the numbers of genes and transcripts aligned with the M. gigas genome and those unaligned (presumed contaminants) are shown.
Fig 3.
Metabolic pathways of interest in this study, including glycolysis, the pentose phosphate pathway, and lipid catabolism.
Thin arrows indicate the detection of corresponding enzymes in M. gigas, while bold arrows represent upregulated enzymes under either the cellulose-fed or diatom-fed conditions.
Fig 4.
Volcano plots of the four enzyme groups of interest.
The horizontal axis represents the log₂ fold change in expression. Transcripts to the left of the “no effect” line are upregulated in the cellulose-fed group, whereas those to the right are upregulated in the diatom-fed group. The vertical axis represents p values, with a reference line at p = 0.05 for visualization.