Biology subjects

Madrigal, M.

Publications and source records attributed to Madrigal, M..

4 recordsLinked to original sources

bioRxiv2026

Transcriptome reallocation during infection reshapes synonymous codon demand in Botrytis cinerea

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.

genomics↗

bioRxiv2026

Strategy Sets the Scene: Genetic architecture of linalool resistance in Botrytis cinerea

Botrytis cinerea is a necrotrophic fungal pathogen that infects thousands of plant species. During infection, these diverse plant hosts produce different specialized metabolites that can inhibit pathogen growth and shape pathogen fitness. However, the genetic architecture of pathogen resistance toward individual host defense metabolites remains poorly understood. To address this question, we exposed 83 B. cinerea isolates to the metabolite linalool and quantified metabolic and structural responses. Exposure revealed extensive phenotypic diversity across isolates. Population structure analysis using genome-wide SNP data showed little genetic subdivision despite diverse hosts and geographic location. Genome-wide association identified 98 genes of interest associated with membrane transport and stress response regulation. Genetic associations were stronger for morphological traits than for metabolic traits, suggesting that hyphal architecture may have a complex genetic architecture contributing to linalool resistance. Together, these results establish natural variation in linalool response and provide candidate loci for understanding how generalist pathogens respond to host-derived chemical defenses. Article SummaryTo understand how a generalist pathogen responds to host defenses, we asked how Botrytis cinerea responds to linalool, a widespread monoterpene involved in plant defense. We exposed 83 B. cinerea isolates to 1000 {micro}M of linalool for 72 hours and quantified metabolic traits (growth curves and growth dynamics over time) and morphological traits (hyphal network features). Using GWA, we linked phenotypic variation to genetic variants. Results indicate substantial natural variation in linalool resistance and distinct genetic architectures across trait classes: metabolic responses are driven by a relatively small number of loci with larger effects, whereas structural/morphological responses appear more polygenic.

genomics↗

bioRxiv2025

HyPhy: A Skeletonization-Based Approach For Fungal Network Analysis

PremiseTraditional methods to quantify mycelial growth rely on destructive sampling to quantify biomass. However, these approaches limit continuous observation and require a large enough mass to measure. Recent work examines hyphal network traits by reconstructing the hyphal network from spatial coordinates via images, providing information about branching patterns and spatial growth over time. Methods and ResultsWe developed HyPhy, a Python-based graphical user interface that skeletonizes images of hyphal networks and extracts biologically relevant structural parameters such as fractal dimension, a proxy for the complexity and branching structure of the hyphal network. Using a high-throughput pipeline method, we imaged three isolates of Botrytis cinerea grown under liquid culture for 72 hours, generating a dataset of 180 time series images. ConclusionsHyPhy enables efficient, non-destructive, and scalable quantification of hyphal growth and complexity from time-resolved image datasets, providing a powerful and user-friendly tool for studying fungal network dynamics.

microbiology↗

bioRxiv2023

Evolutionary dynamics of proteinaceous MAMPs reveals intrabacterial antagonism of plant immune perception

Plants and animals detect biomolecules termed Microbe-Associated Molecular Patterns (MAMPs) and induce immunity. Agricultural production is severely impacted by pathogens which can be controlled by transferring immune receptors. However, most studies use a single MAMP epitope and the impact of diverse multi-copy MAMPs on immune induction is unknown. Here we characterized the epitope landscape from five proteinaceous MAMPs across 4,228 plant-associated bacterial genomes. Despite the diversity sampled, natural variation was constrained and experimentally testable. Immune perception in both Arabidopsis and tomato depended on both epitope sequence and copy number variation. For example, Elongation Factor Tu is predominantly single copy and 92% of its epitopes are immunogenic. Conversely, 99.9% of bacterial genomes contain multiple Cold Shock Proteins and 46% carry a non-immunogenic form. We uncovered a new mechanism for immune evasion, intrabacterial antagonism, where a non-immunogenic Cold Shock Protein blocks perception of immunogenic forms encoded in the same genome. These data will lay the foundation for immune receptor deployment and engineering based on natural variation. Significance StatementPlants recognize pathogens as non-self using innate immune receptors. Receptors on the cell surface can recognize amino acid epitopes present in pathogen proteins. Despite many papers investigating receptor signaling, the vast majority use a single epitope. Here, we analyzed the natural variation across five different epitopes and experimentally characterized their perception in plants. We highlight the importance of analyzing all epitope copies within a pathogen genome. Through genetic and biochemical analyses, we revealed a mechanism for immune evasion, intrabacterial antagonism, where a non-immunogenic epitope blocks perception of immunogenic forms encoded in a single genome. These data can directly inform disease control strategies by enabling prediction of receptor utility and deployment for current and emerging pathogens.

microbiology↗