DOI: 10.6084/m9.figshare.14826086
title: Additional file 1 of Genome analysis of Pseudomonas sp. OF001 and Rubrivivax sp. A210 suggests multicopper oxidases catalyze manganese oxidation required for cylindrospermopsin transformation

description: Additional file 1: Fig. S1. Phylogenetic tree based on 16S rDNA sequences and whole genome sequences including strain OF001 sequence. Tree inferred with FastME 2.1.6.1 [129] from GBDP distances calculated from a) 16S rDNA gene sequences and b) genome sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values &gt; 60% from 100 replications, with an average branch support of a) 68.8% and b) 92.5%. Tree was rooted at the midpoint [163]. Bold text represent the sequences generated in the present work. Scale bar represent sequence divergence. Fig. S2. Phylogenetic tree based on 16S rDNA sequences and whole genome sequences including strain A210 sequence. Tree inferred with FastME 2.1.6.1 [129] from GBDP distances calculated from a) 16S rDNA gene sequences and b) genome sequences. The branch lengths are scaled in terms of GBDP distance formula d5. The numbers above branches are GBDP pseudo-bootstrap support values &gt; 60% from 100 replications, with an average branch support of a) 76.8% and b) 83.4%. Tree was rooted at the midpoint [163]. Bold text represent the sequences generated in the present work. Scale bar represent sequence divergence. Fig. S3. Pan- and core genome overview. Venn diagram shows the number of shared and specific Microscope gene families (MICFAM) a) among Pseudomonas sp. OF001 and the members of the Pseudomonas_K group, and b) among Rubrivivax sp. A210 and the members of the Rubrivivax genus. MICFAM grouping was based on 50% amino acid identity cut-off and at least 80% amino-acid alignment coverage. Fig. S4. Pan- and core- genome sizes estimated evolution. a, c) Number of MICFAM families in the pan-genome size by the number of genomes, and b, d) number of MICFAM families in the core-genome by the number of genomes. a, b) Including Pseudomonas sp. OF001, and c, d) including Rubrivivax sp. A210. Fig. S5. Maximum Likelihood phylogenetic tree based on multicopper oxidases sequences with and without reported Mn2+ oxidation activity. Sequences of the studied strains in the present study are not included. Numbers in the branches represent bootstrap value. Scale bar represent sequence divergence. Fig. S6. Putative genomic islands harbored by the studied MOB. a) Pseudomonas sp. OF001, and b) Rubrivivax sp. A210. Outer circle represents the genome size in Mbps. Genomic islands obtained by different prediction methods are highlighted in color. Integrated represent those islands detected by at least one method. Fig. S7. Distribution and genetic features of prophages detected in Pseudomonas sp. OF001 and Rubrivivax sp. A210. a) Circular genome map of strain OF001, b) genetic features of the complete prophages in strain OF001, and b) circular genome map of strain A210. In the genome maps location of prophages are highlighted in colors depending on the completeness of the prophages (Table S9). Number assigned to each prophage region is based on the genome location retrieved by PHASTER [147]. Fig. S8. Whole proteomic tree of Pseudomonas sp. OF001 prophages based on genome-wide similarities computed by tBLASTx. The tree was constructed using the VIPTree web server v.1.9 [154]. Numbers in brackets in the figure legend represent the number of virus genomes. Red stars represent the three complete prophages of strain OF001. Scale bar represent sequence divergence. Fig. S9. Coverage-GC plots of contig properties for strain OF001 and A210. a, c) Coverage vs GC content, and b, d) coverage vs length. Both samples has a primary, high abundance cluster of contigs, with GC centered around 0.6 with arise form the primary culture populations. For strain OF001 a second contig cluster with GC centered around 0.35 at a much lower abundance was detected, which might represent a slight DNA contamination. Table S1. List of genes in strains OF001 and A210 with homology to putative Mn2+ oxidases from other MOB. Table S2. Functional domains and ontology classification of MO-mco and MO-hpox from MOB. Table S3. List of sequences of MO-mco and non- Mn2+ oxidases. Table S4. List of genes related to the metabolic potential of Pseudomonas sp. OF001 and Rubrivivax sp. A210. Table S5. List of cytochrome genes within Pseudomonas sp. OF001 and Rubrivivax sp. A210. Table S6. List of genes related to cell motility and biofilm formation within Pseudomonas sp. OF001 and Rubrivivax sp. A210. Table S7. List of genes related to degradation of organic compounds in Pseudomonas sp. OF001 and Rubrivivax sp. A210. Table S8. Genomic islands identified within Pseudomonas sp. OF001 and Rubrivivax sp. A210 genome sequences. Table S9. Characteristics of prophage regions identified in Pseudomonas sp. OF001 and Rubrivivax sp. A210 genome. Table S10. CRISPR-Cas systems detected within Pseudomonas sp. OF001 and Rubrivivax sp. A210 genome. Table S11. Characteristics of the cas genes detected within Pseudomonas sp. OF001 and Rubrivivax sp. A210 genome. Table S12. Comparison of repeats in the CRISPR of confidence level 4 found in strain OF001 to CRISPRCasdb. Table S13. Comparison of spacers in the CRISPR of confidence level 4 found in strain OF001 to CRISPRCasdb. Table S14. Comparison of repeats in the CRISPR of confidence level 4 found in strain A210 to CRISPRCasdb. Table S15. Comparison of spacers in the CRISPR of confidence level 4 found in strain A210 to CRISPRCasdb.