Comparative Phylogenomics and Restriction–Modification Systems in 196 Lactic Acid Bacterial Genomes: Data and Reproducibility Materials

This dataset provides genomic, phylogenetic, and restriction–modification (R–M) system annotation data for a curated panel of 196 RefSeq assemblies representing ten operational genera of lactic acid bacteria (LAB). The repository includes accession-level genome metadata, source sequence and annotation checksums, conserved host-marker sequences and search evidence, individual marker alignments, and the accepted 100-marker concatenated amino-acid alignment (17,456 positions). Phylogenetic materials comprise the inferred 196-genome host tree, partition definitions, model information, and 1,000 ultrafast bootstrap trees. R–M system annotations were obtained using PADLOC and DefenseFinder and reconciled at the physical-locus level. The curated inventory contains 436 candidate loci, comprising 417 complete predicted systems, 17 partial candidates, and two unresolved candidates. Native detector outputs, protein-to-locus mappings, gene-level evidence, curated classifications, and genome-level occurrence matrices for R–M Types I–IV are provided. The dataset also includes phylogenetic character-randomization analyses, genus-constrained null-model tests, species-balanced sensitivity analyses, statistical output tables, figure-generation resources, and computational scripts for data verification and reproduction. Original complete genome assemblies and their full annotation packages are not redistributed. Versioned NCBI RefSeq assembly accessions, source-file checksums, and retrieval instructions are included. Predicted R–M classifications represent computationally inferred genomic architectures and do not, by themselves, establish biochemical activity. The accompanying README and reproduction guide describe the directory structure, software requirements, data definitions, and procedures for reproducing the reported analyses.