Plasmid pUO1 Reveals Mercury-Driven Co-Selection of a Fluoroacetate Dehalogenase Gene: A Model for HGT-Mediated Spread of Organofluorine Degradation Potential

This dataset contains the raw data, analysis results, and analysis scripts supporting the manuscript "Plasmid pUO1 Reveals Mercury-Driven Co-Selection of a Fluoroacetate Dehalogenase Gene: A Model for HGT-Mediated Spread of Organofluorine Degradation Potential." The study systematically characterizes the horizontal gene transfer (HGT) signature of the fluoroacetate dehalogenase gene *dehH1* and its functional implications for PFAS binding through five integrated approaches: (1) plasmid pUO1 annotation, (2) GC content profiling of 289 *dehH1* homologs, (3) phylogenetic reconstruction, (4) molecular docking of PFAS compounds to the DehH1 catalytic pocket, and (5) molecular clock dating of the *dehH1* gene family.The dataset is organized into six directories:1. **01_Plasmid_Annotation/** — Complete nucleotide sequence of plasmid pUO1 (GenBank accession AB063332.1, 67,066 bp) in GenBank format, along with functional annotation tables categorizing all ORFs into five groups: dehalogenase genes, mercury resistance operon, conjugative transfer system, replication/maintenance module, and transposable elements.2. **02_GC_Content_Analysis/** — Protein sequences (FASTA) and metadata (CSV) for 289 *dehH1* homologs retrieved from NCBI via E-utilities API.

GC content was calculated at four codon positions (GC_total, GC1, GC2, GC3) and HGT signature quantified as ΔGC = |GC_gene − GC_genome|. Results include per-gene GC analysis, HGT candidate classification (Strong/Moderate/Unlikely), and host genome GC data. Analysis scripts for sequence fetching and the GC analysis pipeline are included in the `scripts/` subdirectory.3. **03_Phylogenetic_Analysis/** — 21 representative *dehH1* sequences (FASTA), multiple sequence alignment, and the phylogenetic tree constructed using pairwise k-mer (k=4) Jaccard dissimilarity with UPGMA clustering (SciPy v1.12).