Transcriptome reallocation during infection reshapes synonymous codon demand in Botrytis cinerea
Year: 2026
Type: preprint
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.
Authors: Jordan Dowell, Lori Pradhan, Melanie Madrigal
Institution: Louisiana State University
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7225399174