DOI: 10.6084/m9.figshare.22181983
title: Preprint of the Supplementary Material of the manuscript entitled "Comparative genomics of Stutzerimonas balearica (Pseudomonas balearica): diversity, habitats and biodegradation of aromatic compounds"

description: This dataset contains the Supplementary Material of the manuscript entitled "Comparative genomics of <em>Stutzerimonas balearica</em> (<em>Pseudomonas balearica</em>): diversity, habitats and biodegradation of aromatic compounds", which has not been certified by peer review and which is part of the PhD thesis of Francisco Salvà Serra, entitled "Bacterial whole-genome sequencing for establishment of reference sequences, comparative genomics, biomarker discovery and characterization of novel taxa". The PhD thesis is part of the PhD programme in Environmental and Biomedical Microbiology of the University of the Balearic Islands (Spain). <br> Description of the files: <br> <strong>Supplementary Figure 1.</strong> Phylogenetic tree based on partial <em>rpoD </em>sequences (549 bp). The tree includes 111 of the 113 genome sequences included in the study; the other two did not contain any <em>rpoD </em>sequence in the assembly. The phylogenetic analysis also includes the reference <em>rpoD </em>sequences of most of the described species and phylogenomic species of <em>Stutzerimonas</em>. The GenBank accession numbers of the genome sequences are listed in Supplementary Table 1 and those of the reference sequences obtained from the PseudoMLSA database are indicated in parenthesis. For each strain, the final taxonomic assignment is indicated. The final phylogenomic species assignment of each strain is indicated in parenthesis. The distances were calculated, using the Jukes-Cantor method, and the tree was constructed, using the neighbor-joining method. Bootstrap values of 50% or greater (from 1,000 replicates) are shown at the nodes. <em>P. aeruginosa </em>CCM 1960<sup>T </sup>was used as an outgroup. Pgs: phylogenomic species; gv.: genomovar; ref.: reference. <br> <strong>Supplementary Figure 2.</strong> Core genome-based phylogenomic tree of the 11 isolate-derived genome sequences of <em>S. balearica</em>, 81 strains listed as <em>S. stutzeri </em>in NCBI and the type strains of 11 additional species of the genus <em>Stutzerimonas</em>. The tree was generated, based on 210,488 homologous amino acid positions, derived from 699 single copy core proteins. Pgs: phylogenomic species; ref.: reference. <br> <strong>Supplementary Table 1. </strong>List of the 113 genome sequences used in this study and their associated metadata. <br> <strong>Supplementary Table 2.</strong> ANIb values between the 113 genome sequences (all vs. all) included in this study. Each pairwise comparison was performed bidirectionally; the average value is displayed. <br> <strong>Supplementary Table 3.</strong> List of the 176 confirmed <em>S. balearica</em> strains and their associated metadata. <br> <strong>Supplementary File 1.</strong> Metagenome assembled genome (MAG) sequence of <em>S. balearica</em> UBA3230, annotated using DFAST, in GBK format. <br> <strong>Supplementary File 2. </strong>Metagenome assembled genome (MAG) sequence of <em>S. balearica</em> UBA6635, annotated using DFAST, in GBK format. <br> <strong>Supplementary File 3.</strong> Metagenome assembled genome (MAG) sequence of <em>S. balearica </em>3300027365_7, annotated using DFAST, in GBK format. <br> <strong>Supplementary File 4.</strong> Genomic features of the genome sequences of <em>S. balearica</em>. Sheet 1: Pan-genes of <em>S. balearica</em>. Sheet 2: Genes encoding enzymes for catabolism of aromatic compounds detected in one or more genome sequences of <em>S. balearica</em>. Sheet 3: Genes for catabolism of aromatic compounds not detected in the genome sequences of <em>S. balearica</em>. Sheet 4: Antibiotic resistance genes detected, using Resistance Gene Identifier (RGI) and the Comprehensive Antibiotic Resistance Database (CARD). Sheet 5: Biocide and metal resistance genes predicted by BacMet. Sheet 6: Virulence determinants detected, using VFanalyzer. Sheet 7: CRISPR-Cas systems predicted by CRISPRone. Sheet 8: Prophages predicted by PHASTER. Sheet 9: Integrative and conjugative elements (ICEs) and integrative and mobilizable elements (IMEs) predicted by ICEfinder. Sheet 10: genes associated with natural transformation capacity. Sheet 11: Regulatory genes predicted, using P2RP.