README.md

Scripts from Mesny et al., 2021

Mesny, F., Miyauchi, S., Thiergart, T. et al. Genetic determinants of endophytism in the Arabidopsis root mycobiome. Nat Commun 12, 7227 (2021). https://doi.org/10.1038/s41467-021-27479-y

Below are linked the different scripts that were used in each paragraph of the study

Cultured isolates are representative of wild A. thaliana root mycobiomes

• Re-analysing data from Thiergart et al. 2020 and assembling figure 1: https://github.com/ththi/Mesny-et-al-2021

Root mycobiota members evolved from ancestors with diverse lifestyles

• Results of OrthoFinder orthology prediction (orthogroups tables and species tree): https://github.com/fantin-mesny/Scripts-from-Mesny-et-al.-2021/tree/main/orthology_prediction_results
• Ancestral lifestyles prediction: https://github.com/fantin-mesny/Scripts-from-Mesny-et-al.-2021/tree/main/predicting_ancestral_lifestyles

Functional overlap in genomes of root mycobiota members and endophytes

• Genome functional annotation with PRINGO: https://github.com/ShingoMiyauchi/PRINGO
• PERMANOVA-based comparison of gene repertoires: https://github.com/fantin-mesny/Effect-Of-Biological-Categories-On-Genomes-Composition Statistical testing of this specific study can be found with count data here: https://github.com/fantin-mesny/Scripts-from-Mesny-et-al.-2021/tree/main/gene_repertoires_counts_data

Genomic traits of the endophytic lifestyle

• SVM-RFE mining genomes for orthogroups best segregating endophytes and mycobiota members from other fungi: https://github.com/fantin-mesny/Scripts-from-Mesny-et-al.-2021/tree/main/finding_gene_families_determinant_for_endophytism

Root colonization capabilities explain fungal outcome on plant growth

• Analysis of shoot fresh weight data from plant recolonization experiments: https://github.com/fantin-mesny/Scripts-from-Mesny-et-al.-2021/tree/main/plant_fungi_interaction_experiments
• Analysis of qPCR-measured fungal colonization: https://github.com/fantin-mesny/Scripts-from-Mesny-et-al.-2021/tree/main/analysis_of_qPCR_colonization_data

A conserved set of CAZyme-encoding genes is induced in planta by diverse root mycobiota members

• Analysis of the transcriptomes of fungi and Arabidopsis thaliana: https://github.com/fantin-mesny/Scripts-from-Mesny-et-al.-2021/tree/main/transcriptomics

Polysaccharide lyase family PL1_7 as a key component linking colonization aggressiveness to plant health

• ANOVA multiple testing linking PPI to secreted CAZyme counts: https://github.com/fantin-mesny/Scripts-from-Mesny-et-al.-2021/tree/main/anova_testing_for_association_between_cazymes_and_ppi
• SVM-RFE identifying orthogroups best segregating pathogens from others: https://github.com/fantin-mesny/Scripts-from-Mesny-et-al.-2021/tree/main/linking_effects_on_plants_to_genome_content
• Plant recolonization experiments with T. reseii heterologous expression lines of PL1_7: https://github.com/fantin-mesny/Scripts-from-Mesny-et-al.-2021/tree/main/analysis_of_exp_with_knock_in_lines