Transcriptome reallocation during infection reshapes synonymous codon demand in Botrytis cinerea

Infection-associated transcriptome reallocation in Botrytis cinerea reshapes synonymous codon demand, with sampling time explaining 95–98% of fungal codon-demand variation across three host time series.

• Why it matters: Genomic codon usage is fixed, but the RNA codon pool can shift when transcription reallocates among genes; infection may therefore create a dynamic codon-demand phenotype.
• What they did: The authors reanalyzed 39 Botrytis cinerea RNA-seq libraries from time series in S. lycopersicum, Arabidopsis thaliana, and Physcomitrium patens, correcting gene counts for coding length and analyzing centered log ratios within synonymous amino-acid families.
• The result: Codon-demand changes aligned across studies over the interpolated 16–24-h interval and persisted after multiple mapping and correction controls, enabling tests of how this dynamic allocation may affect RNA stability and translation during host-pathogen interactions.

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