Comparative Genomics Analysis of Enterocloster spp. Genomes for the Presence of ucd and uxd Operons

Dataset for the analysis of Enterocloster spp. genomes for the presence/absence of ucd and uxd operons. Entry includes R code, RData, tables, FASTA queries (operon sequences), and Enterocloster spp. genomes from the NCBI genomes database. The results from the analysis are summarized in the operon_prevalence_by_accession_GTDB_sorted.csv file. General Methods: The analysis of ucd and uxd operon presence in Enterocloster spp. genomes was done by first downloading all available (n = 452) Enterocloster spp. genome sequences (FASTA format) from the NCBI genomes database (excluding atypical genomes) [https://www.ncbi.nlm.nih.gov/datasets/genome/?taxon=2719313&typical_only=true] (Accessed 01-08-2025). All FASTA files with GenBank GCA accessions were retained for further analysis (n = 452). The Genome Taxonomy Database (GTDB) table for Enterocloster spp. (release 10-RS226 (16-04-2025)) was downloaded from [https://gtdb.ecogenomic.org/searches?s=al&q=Enterocloster] (Accessed 02-08-2025). Each genome was queried using rBLAST (v1.2.0, DOI: 10.18129/B9.bioc.rBLAST) for matches to the E. bolteae ucd operon and E. asparagiformis uxd operon nucleotide sequences with criteria: -perc_identity 60 -max_target_seqs 5 -subject_besthit. Matches were further filtered for length > 300 bases to exclude small fragments. NCBI GenBank accessions for all queries without GTDB taxonomy or the "Undefined (Failed Quality Check)" flag were removed from further analyses, yielding a total of n = 329 genomes. Presence/absence of each operon was plotted in ggplot2 (v.3.5.2).