Additional file 1: Figure S1. of Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe
Creators: name: Chandirasegaran Massilamany
name: Mohammed, Akram
name: Loy, John
name: Purvis, Tanya
name: Bharathi Krishnan
name: Basavalingappa, Rakesh
name: Kelley, Christy
name: Chittibabu Guda
name: Barletta, Raúl
name: Moriyama, Etsuko
name: Smith, Timothy
name: Reddy, Jay
Publisher: name: Figshare
Year: 2016
Subjects: subject: Medicine
subject: Microbiology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Genetics
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Identification of Bacillus sp. NRRL B-14911 spores. Bacterial smear was stained with malachite green and safranin as described in the Methods section and examined under oil immersion microscope. Arrows indicate round and symmetrical endospores present both within and outside the bacteria. Original magnification: 100x. Figure S2. The genes encoded by the plasmid of Bacillus sp. NRRL B-14911. The plasmid sequence was generated from the sequence data obtained by sequencing of the genomic DNA from Bacillus sp. NRRL B-14911 in long-reads. The genes encoded by the plasmid were annotated as described for the bacterial chromosome (see methods).Figure S3. Alignment of contigs previously reported for Bacillus sp. NRRL B-14911 to the new long-read-based finished assembly. The inner ring (blue) represents contigs assembled from short-reads without any scaffolding (middle panel in Figure 1) as aligned to our de novo assembly based on long-reads. The outer ring (pink and black) represents alignment of contigs after scaffolding (top and bottom panels in Fig. 1). Note, white lines and blocks show large areas without any coverage in the prior assembly. Designations for each scaffold and contig are derived from GenBank accession numbers, which are abbreviated for convenience in display. Scaffolds are shown in pink and have full accessions with the format CH6723XX, where XX is the number shown on the figure following “CH”. Black- and blue-shaded regions represent un-scaffolded contigs, which have full accessions with the format AAOX01000XYY, where X is either 0 (for YY between 23 and 99) or 1 (for YY between 00 and 09). Only contigs with ≥ 99.900 % identity are shown. The scale in the middle of the circle is based on the finished de novo assembly, made using long-read sequencing. Figure S4. Circular genome map of Bacillus sp. NRRL B-14911 showing the location of genes for virulence factors that are unique to this bacterium in relation to other Bacillus. The circular map of Bacillus sp. NRRL B-14911 shows the locations of 18 virulence factor genes that are unique to this bacterium as determined by comparing the genomes of three pathogenic, and three non-pathogenic bacteria as described in the ‘Methods’ section. The two outer blue circles represent the genes for virulence factors present in forward and reverse directions. The innermost circle represents the GC skewness, and the second innermost circle represents the GC content of the Bacillus sp. NRRL B-14911 genome. The coordinates of each gene are listed in Additional file 1: Table S3. The start and end positions in Additional file 1: Table S3 match with the location of genes in Additional file 1: Figure S4. Figure S5. Circular genome map showing the location of virulence factor genes common to both Bacillus sp. NRRL B-14911 and other pathogenic bacilli. The circular map shows the locations of 225 virulence factor genes that are common to both Bacillus sp. NRRL B-14911 and three other pathogenic bacilli. Their genome comparisons were made as described in the ‘Methods’ section. The two outer blue circles represent the genes for virulence factors shown in forward and reverse directions. The innermost circle represents the GC skewness, and the second innermost circle represents the GC content of the Bacillus sp. NRRL B-14911 genome. The coordinates of each gene are listed in Additional file 1: Table S4. The start and end positions in Additional file 1: Table S4 match with the location of genes in Additional file 1: Figure S5. Table S1. Comparison of the issues with sequencing by scaffolds in the bioproject in relation to our method of sequencing by long-reads. Table S2. List of genes for virulence factor encoded in the genome of Bacillus sp. NRRL B-14911. Table S3. List of unique genes for virulence factor encoded in the genome of Bacillus sp. NRRL B-14911. Table S4. List of genes for virulence factor encoded in the genome of Bacillus sp. NRRL B-14911 that are in common with pathogenic Bacilli. Table S5. Comparative analysis of the presence or absence of common methyltransferases between Bacillussp. NRRL B-14911 and other Bacillus species. Table S6. Comparative analysis of the presence or absence of transporters between Bacillus sp. NRRL B-14911 and other Bacillus species. Table S7. Comparison of the nucleotide sequences and amino acid sequences corresponding to the epitope BAC 25-40 from Bacillus sp. NRRL B-14911and B. infantis JCM 13438 T. Table S8. Comparative analysis of the presence or absence of enzymes and biochemical pathways of Bacillus sp. NRRL B-14911 in relation to other Bacillus species. Table S9. Comparison of insertion sequence elements between Bacillus sp. NRRL B-14911 and other Bacillus species. (PDF 2089 kb)