Additional file 1 of Comparative genome analysis of Vagococcus fluvialis reveals abundance of mobile genetic elements in sponge-isolated strains
Creators: name: Rodriguez Jimenez, Ana
name: Guiglielmoni, Nadège
name: Goetghebuer, Lise
name: Dechamps, Etienne
name: George, Isabelle F.
name: Flot, Jean-François
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Supplementary Table S1. Characteristics of the thirteen Vagococcus fluvialis genomes available online and of the representative genomes of other Vagococcus genera. Supplementary Figure S1. Average amino acid identity matrix of the V. fluvialis genomes and the representative genomes of other Vagococcus species. Supplementary Figure S2. KEGG functional category enrichment heatmap of chromosomal genes in Enterococcaceae genomes. The genomes are ordered according to the dendrogram, constructed using hierarchical clustering based on the enrichment matrix. Supplementary Figure S3. Gene presence/absence matrix of all orthologous gene clusters in the V. fluvialis pan genome. The genomes are ordered according to the dendrogram constructed using hierarchical clustering based on the gene presence/absence matrix. Genes shown in blue represent the core genome (present in all V. fluvialis genomes), those in green represent the shell genomes (present in more than 2 genomes), and those in yellow are unique genes (present in only one genome). Supplementary Table S3. Characteristics of all extrachromosomal circular sequences identified in the genomes of the five sponge-isolated V. fluvialis strains. Sequence length, Rep genes (number), relaxase gene presence, origin of transfer (oriT) presence, mobility, MOB group and MPF type. Supplementary Figure S4. Prophage-encoding circular sequence c1 map. The 3 outer rings represent prophage related elements. From outer to inner (1) phage attachment sites, (2) phage function annotation, and (3) predicted prophage regions. The inner rings (4) and (5) represent GC content and GC skew. Supplementary Figure S5. KAT plot of the genome assembly of strain 12B2. Left: assembly without extrachromosomal contig 12B2_c1. Right, assembly including 12B2_c1. Supplementary Figure S6. KAT plot of the genome assembly of strain 35B2. Left: assembly without extrachromosomal contig 35B2_c1. Right, assembly including 35B2_c1. Supplementary Figure S7. KAT plot of the genome assembly of strain 110B2. Left: assembly without extrachromosomal contig 110B2_c1. Right, assembly including 110B2_c1. Supplementary Table S4. Best blast hits of all extrachromosomal circular sequences. Sequences not reported in the table did not have any hit (12B2_c1, 35B2_c1, 36B2_p1, and 110B2_c1). Supplementary Table S5. Rep genes encoded in the plasmids: Rep group, position, closest hit, plasmid host of closest Rep protein hit and identity percentage. Results retrieved from PlasmidFinder. Supplementary Table S6. Relaxase protein genes encoded in the plasmids: protein length, gene coordinates and homolog BLASTp identity percentage. Supplementary Table S7. Origin of transfer and relaxase protein of the plasmid 36B2_p1: oriT coordinates, size and sequence and relaxase protein length, gene coordinates and BLASTp identity percentage. Supplementary Figure S8. Circular map of the conjugative plasmid 36B2_p1. From outer to inner ring, these represent (1) conjugation-related genes, (2 and 3) COG functional categories, (4) GC content and (5) GC skew. Supplementary Table S8. Prophage annotation results. Results for each genome sequence of prophage detection using Phaster, ProphageHunter, Phigaro, PhiSpy and Prophinder. Supplementary Figure S9. Maximum likelihood phylogenetic tree of all chromosomal prophage sequences identified in all V. fluvialis genomes, with bootstrap support values indicated by the nodes. Supplementary Table S9. Detailed list of the reference genomes of the Enterococcaceae family and all Vagococcus spp. genomes, used for functional comparison. Supplementary Figure S10. KoT species delimitation of the V. fluvialis genomes and the representative genomes of other Vagococcus species. Supplementary Figure S11. Gene presence/absence matrix of all orthologous gene clusters in the V. fluvialis pan-genome, using the short-read assemblies of the sponge-isolated V. fluvialis strains genomes (sr). The genomes are ordered according to the dendrogram constructed using hierarchical clustering based on the gene presence/absence matrix. Genes shown in blue represent the core genome (present in all V. fluvialis genomes), those in green represent the shell genomes (present in more than 2 genomes), and those in yellow are unique genes (present in only one genome).