This repository contains R scripts and supporting data for the study "Genomic signatures in Variovorax enabling colonization of the Populus endosphere." The provided code demonstrates read alignment, feature counting, orthogroup and KEGG Ortholog annotation, normalization, and statistical aggregation workflows, with each script (01–07) corresponding to specific analyses and figure panels in the manuscript. The uncompressed files represent the finalized, formatted datasets used to generate all figures and tables in the published study, including the supplemental .csv files referenced in the manuscript. The accompanying .zip archive contains the full codebase and example data folders (data_input/, data_output/) used to illustrate the analytical workflow; these example files reproduce the pipeline structure but may not exactly replicate the finalized data products used in the paper. Raw sequencing reads are available separately through the NCBI Sequence Read Archive under BioProject accession number PRJNA1322484.