Transcriptome reallocation during infection reshapes synonymous codon demand in Botrytis cinerea

Abstract

While genomic codon usage is fixed within an individual isolate, the synonymous codons represented in its RNA pool can change when transcription shifts among genes. We tested whether this transcript-level phenotype accompanies infection by reanalyzing 39 libraries from three public Botrytis cinerea RNA-sequencing (RNA-seq) time series in S. lycopersicum, Arabidopsis thaliana, and Physcomitrium patens. Gene counts were corrected for coding length, combined with fixed gene-specific codon inventories, and analyzed as centered log ratios within synonymous amino-acid families. Sampling time accounted for 95-98% of fungal codon-demand variation in each series. The association persisted after effective-length correction, unique-only competitive mapping, host-homology exclusion, depth equalization, protein-family weighting, and removal of translation-associated genes. Change vectors over the interpolated, time-aligned 16-24-h interval were positively aligned among studies, whereas later trajectories diverged. Matched reassignments of complete expression trajectories showed more full-series organization than expected in S. lycopersicum and Arabidopsis, but not in P. patens. Codon-preference-weighted abundance and expression breadth also changed through infection, although their directions were not universal. Across systems, large non-translation contributors repeatedly carried ATP-synthase/respiratory and extracellular annotations, although their timing and companion functions differed. Infection-associated transcriptional reallocation therefore repeatedly restructures the synonymous composition of the inferred fungal transcript pool. This establishes a dynamic allocation phenotype and a basis for testing consequences for RNA stability and translation during host-pathogen interactions.