Lactococcus_paper_data

Supplementary data and figure code for:

Phenotypic and Phylogenomic Characterization of Lactococcus garvieae Isolates from Rainbow Trout (Oncorhynchus mykiss) in Türkiye

Everything here is derived data — summary tables, annotation output and the R scripts that draw the figures. Raw reads and assemblies live at NCBI, not in this repository; see Data availability.

Contents

Supplementary tables

File	Contents
Sup_Table_1-LG2_Genome_Statistics.xlsx	Assembly statistics for the focal genome LG2
Sup_Table_2_Annotation.xlsx	Full Bakta annotation of LG2
Sup_Table_3-SuppTable_species_verification_ANItoType.xlsx	Species verification — ANI of each genome against type strains
Sup_Table_4_Genome_metadata_237_species_verified.xlsx	Metadata and assembly statistics for all 237 Lactococcus genomes in the study
removed_genomes.tsv	Genomes excluded during QC, with the reason (BUSCO / CheckM2 completeness and contamination)

Focal genome (LG2)

File	Contents
LG2.txt	Assembly summary: 1 contig, 2,214,687 bp, 2,212 CDS, 16 rRNA, 66 tRNA
LG2_bakta.txt	Bakta annotation summary — GC 38.5%, N50 2,214,687, coding density 88.6%
LG2_bakta_v6.xlsx	Bakta annotation as a spreadsheet
genome_assembly.cmt	NCBI structured comment: Flye v2.9.2 + Racon + Medaka v2.2.1, 130× Oxford Nanopore

Figure code

All scripts are standalone Rscript files.

Script	Produces
make_figures_lg.R	Fig 1–2: L. garvieae phylogeny rooted on an L. petauri outgroup with country and host; AMR gene content
make_fig1_v3.R	Fig 1, final version — subclades moved into the legend, 300 dpi PNG
make_fig4_cgmlst.R	Fig 4–5: cgMLST allelic-distance NJ tree, Turkish vs other-country isolates, and concordance with the ML core-genome phylogeny
make_fig6_mst.R	Fig 6: minimum spanning tree of 42 isolates on cgMLST allelic distances, edges labelled with allele differences
make_figS_ani.R	Supplementary: fastANI heatmap of the 44-genome working set
make_supp_table_genomes.R	Builds Supplementary Table 4 by joining source metadata to QUAST statistics and quality metrics

Reproducing the figures

install.packages(c("ggplot2", "dplyr", "readxl", "igraph"))
if (!require("BiocManager")) install.packages("BiocManager")
BiocManager::install(c("ggtree", "treeio"))

Rscript make_fig1_v3.R

The scripts expect the trees, alignments and cgMLST profiles produced during the analysis. Those inputs are not in this repository — regenerate them from the archived assemblies, or request them from the corresponding author.

Data availability

Assemblies and raw reads are deposited at NCBI. Accessions are listed in the paper; the cgMLST scheme used here is published separately as Lgarvieae-cgMLST (chewBBACA-compatible, 1100 loci, built from 247 QC'd genomes).

NCBI submission intermediates (*.sqn) are deliberately excluded — they contain unreleased sequence and submitter contact details.

Citation

See CITATION.cff, or use GitHub's "Cite this repository" button. Please cite the paper itself as the primary reference.