{
  "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.",
  "abstract_shown": true,
  "affiliations": [
    "Louisiana State University"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 3,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "J. Dowell"
    },
    {
      "name": "L. Pradhan"
    },
    {
      "name": "M. Madrigal"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/9zre7628ckg2g.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.11.04.764316",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.11.04.764316v1.full",
  "id": "9zre7628ckg2g",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.11.04.764316v1",
  "language": null,
  "licence": "CC-BY-NC",
  "licence_label": "CC BY-NC",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "genomics"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.11.04.764316v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-11-04",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/9zre7628ckg2g.ris",
  "sources": [
    {
      "first_seen": "2026-11-07T00:21:14Z",
      "native_id": "10.64898/2026.11.04.764316",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.11.04.764316v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:genomics",
      "subfield": "genetics-genomics"
    }
  ],
  "title": "Transcriptome reallocation during infection reshapes synonymous codon demand in Botrytis cinerea",
  "title_text": "Transcriptome reallocation during infection reshapes synonymous codon demand in Botrytis cinerea",
  "type": "preprint",
  "updated_at": "2026-11-08T00:21:05Z",
  "url": "https://research.draconitic.com/paper/9zre7628ckg2g",
  "venue": "bioRxiv",
  "versions": []
}