Phenotypic, metabolomic and phylogenetic datasets with R workflows for the analysis of tomato resistance to Phthorimaea (=Tuta) absoluta

Résumé fourni par la source

Tomato (Solanum lycopersicum) production is severely threatened worldwide by the invasive tomato leaf miner (Phthorimaea absoluta), one of the most destructive pests affecting cultivated tomato. Although cultivated germplasm generally exhibits limited resistance, wild tomato relatives represent a valuable reservoir of natural defensive traits that can be exploited for sustainable crop protection and breeding. This repository contains the complete datasets and reproducible R scripts associated with the study investigating the natural diversity of resistance to P. absoluta across cultivated and wild tomato germplasm, together with the constitutive foliar metabolomic diversity underlying these resistance patterns. The study combines complementary experimental approaches conducted under controlled and semi-field conditions. A greenhouse no-choice bioassay was first performed on twenty-four cultivated and wild tomato accessions to quantify antibiosis-related resistance using leaflet lesion type, percentage of attacked leaflets, and mining intensity. These data were analysed using analysis of variance, least significant difference (LSD) tests, principal component analysis (PCA), and Ward hierarchical clustering to characterize inter- and intra-specific variation in resistance. A choice bioassay, conducted under tunnel conditions, subsequently compared the most resistant accession (S. habrochaites PI248707) with the susceptible cultivar Rose de Berne (RdB). Oviposition, larval development and feeding damage were quantified to validate resistance under conditions allowing insect preference. To investigate the biochemical basis of constitutive resistance, untargeted LC–MS metabolomic profiling was performed on leaf extracts from all twenty-four accessions, generating 3,764 metabolic features. Metabolites were annotated according to the NPClassifier ontology and organized into major metabolic classes. These data were used to reconstruct the constitutive metabolic landscape of tomato diversity through chemosystematic analyses. Multivariate analyses, including Bray–Curtis PERMANOVA, multivariate dispersion (betadisper), and SIMPER analyses, were performed to quantify metabolic differentiation among species and identify the metabolic classes contributing most strongly to clade-wide chemical divergence. Additional enrichment analyses were conducted to identify metabolic pathways significantly enriched or depleted between resistant and susceptible accessions within phylogenetically related groups. The repository includes: raw phenotypic datasets from greenhouse no-choice and tunnel choice bioassays; untargeted LC–MS metabolomic abundance matrices; metabolite annotation tables; sample metadata; phylogenetic tree used for chemosystematic visualization; fully reproducible R scripts reproducing all statistical analyses, figures and supplementary tables presented in the associated manuscript. The analytical workflow was reorganized into modular scripts to facilitate reproducibility and long-term reuse. All analyses can be reproduced directly from the deposited raw datasets using the accompanying R scripts. This repository accompanies the manuscript submitted to Peer Community in Plant Biology (PCI Plant) and provides the complete computational workflow supporting the reported results.

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