Immunity and the secondary metabolome of Streptomyces: analysis code and data

This repository contains the analysis code and processed data for the study "The secondary metabolome of Streptomyces is decoupled from its immune repertoire: horizontally acquired biosynthetic gene clusters show no association with CRISPR-Cas or restriction–modification systems". The study tests whether the native immune repertoire of Streptomyces (CRISPR-Cas, restriction–modification systems and the wider anti-phage defensome) is associated with the horizontally acquired fraction of the secondary metabolome, across 190 dereplicated genomes. Starting from 400 RefSeq assemblies, dereplication at 96% average nucleotide identity yielded 266 representatives; the analysis was restricted to the 190 genomes carrying both biosynthetic and CRISPR-Cas annotation. The repository provides: (i) the full pipeline of shell, Python and R scripts, from genome download and dereplication through biosynthetic gene cluster detection (antiSMASH), CRISPR-Cas typing (CRISPRCasTyper), defence-system annotation (DefenseFinder) and phylogenetically controlled statistical analysis (PGLS); and (ii) the processed intermediate tables sufficient to reproduce all figures, tables and statistics without re-running the external annotation tools. Raw genome assemblies are publicly available from NCBI RefSeq (accession numbers in Supplementary Table S1 of the article). Code is released under the MIT License; processed data under CC BY 4.0.