A claim-centred atlas distinguishes biological corroboration from analytical depth in plant stress transcriptomes

Abstract

Plant stress transcriptomes are reanalysed far more often than independently replicated, obscuring whether apparent consensus reflects biological corroboration or repeated analysis of the same experiments. Here we present PLEASE (PLant Evidence Atlas for StrEss), a claim-centred atlas that treats the independent experiment, rather than the analysis, as the unit of evidence. PLEASE resolves 88,789 analytical records into 62 dependency-resolved study families. A calibrated core of abiotic and biotic stress programmes persists after dependency collapse. Yet support erodes sharply as claims become more specific. Across stress, organ and cell-lineage contexts, independent-match coverage falls from 1.00 to 0.26 while directional agreement remains near 0.68. Three quarters of sampled contexts contain only one study family. Thus, missing comparable experiments, not pervasive disagreement, is the main barrier to context-specific corroboration. PLEASE separates analytical depth from biological corroboration and pinpoints where independent experiments are most needed.