Data and code for multi-layer comparative genomics of Lautropia mirabilis

This record contains organized genomic resources, annotations, metadata, scripts, intermediate outputs, quality-control reports, final workbooks, publication figures, supplementary tables and multi-layer comparative genomics analyses supporting research on Lautropia mirabilis. The deposited material includes genome FASTA, GFF, protein FASTA and GenBank files; assembly reports; QUAST, GTDB-Tk, FastANI and Gubbins outputs; pangenome, Microbializer and AAI analyses; phylogenomics; genomic-island and viral-like sequence analyses; PHI-base, HPIDB, DIAMOND, IntAct and DeepHPI host-context analyses; Cytoscape networks; eggNOG-mapper and KEGG module-completeness analyses; PRIMARY23-versus-60-genome denominator validation; reviewer-justification material; and the SAHIEI evidence-integration and robustness framework. Project-specific derived IntAct outputs are included. Three large public raw IntAct source-database files are excluded to avoid redistributing redundant upstream database material.