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International Journal of Genomics
Volume 2017 (2017), Article ID 8724304, 14 pages
https://doi.org/10.1155/2017/8724304
Research Article

Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome

1Los Alamos National Laboratory, Biosciences Division, Genome Science, Los Alamos, NM 87545, USA
2School of Computer, Mathematical and Natural Sciences, Morgan State University, Baltimore, MD 21251, USA
3LOEWE Centre for Synthetic Microbiology-SYNMIKRO, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, 35032 Marburg, Germany
4Tauri Group, LLC, Alexandria, VA 22310, USA
5Defense Biological Product Assurance Office, 110 Thomas Johnson Drive, Frederick, MD 21702, USA

Correspondence should be addressed to Shanmuga Sozhamannan; lim.liam@rtc.nannamahzos.agumnahs

Received 21 February 2017; Revised 15 June 2017; Accepted 22 June 2017; Published 29 August 2017

Academic Editor: Graziano Pesole

Copyright © 2017 Gary Xie et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Supplementary Material

Figure S1. Mauve alignment of NSCV1 (S1a) and NSCV2 (S1b) with other genomes. NSCV1 and NSCV2 whole genome sequences were aligned to the genome sequences of V. cholerae strains MS6, N16961, MO10 and TSY216. The various collinear regions are indicated by different colored blocks. The Chr2 sections of NSCV1 and NSCV2 are indicated by a red line below the scale (bps). The large chromosomal inversion in NSCV2 (Figure S1b) can be seen as the blocks that are indicated on the opposite strand in MS6. Figure S2. BRIG view of genomic comparisons of NSCV1, NSCV2, N16961, TSY216 and MS6. For genome comparisons, default blastn parameters were used. Unique regions (Uni_region) ˜ 10 kb or more (along with annotation of the region if known) including prophages are indicated around the circle. In Figure 2c, using N16961 as the reference genome, Chr1 and Chr2 sequences are concatenated end to end and the various known virulence markers are indicated. N16961 is a prototypical V. cholerae with two chromosomes and the sequences are concatenated here for illustrative purpose only. Figure S3. Circular maps of NSCV1 (S3a) and NSCV2 (S3b) showing various features. Circular map of the NSCV1 (S3a) and NSCV2 (S3b) genomes, showing the distribution of coding sequences, mobile elements, GC content and GC skew. For this analyses the sequences with large tandem repeats were included. From outside to the center: Circles 1 and 2: forward and reverse strand genes; Circle 3: unique genes in NSCV1 or NSCV2 in comparison with V. cholerae MS6, serogroup O1 biovar El Tor str. N16961, and serogroup O139 MO10; Circle 4: Chr2 in grey color and large tandem repeat in pink; Circle 5: OriC for Chr1 and 2; Circle 6: Prophage predicted by Phast; Circle 7: Genomic island Predicted by multiple methods: IslandPick, SIGI-HMM and IslandPath-DIMOB; Circle 8: GC content; Circle 9: GC skew. Figure S4. WGM maps compared to in silico generated restriction maps of WGS. Whole genome optical maps (AflII) of NSCV1 (top panel) NSCV 2 (bottom panel) aligned to in silico restriction maps (AflII) using genome assemblies. The region of the sequence that appear as tandem repeats in the optical map are highlighted by the yellow arrows. Figure S5. Genome coverage at tandem repeats of NSCV1 and NSCV2. Sequence reads of NSCV1 and NSCV 2 generated from Illumina and 454 sequencers were mapped against the respective final assemblies and displayed as function of fold coverage vs genome position in the assembly. Note that increased coverage indicated by the star is readily apparent except in the case of 454 SE read data for NSCV1. This anomaly could not be resolved at this time. Figure S6. Genome maps of NSCV1 and NSCV2 with the large tandem repeats. Circular genome maps of NSCV1 and NSCV2 similar to Figure 1 with the tandem repeats included (red features). Fusion of Chr1 (dark grey) to Chr2 (blue) is shown in the circle at the respective locations. Various unique features such as tandem repeats, prophages and the origins of replication and replication associated genes are indicated around the circles. Figure S7. Overlap of repeat regions between NSCV1 and NSCV2. The identity plot indicates the first 40,398 bps of NSCV1 tandem repeat region (total length of the repeat: 196,770 bps) which is 97% identical to the terminal 40,285 bps of NSCV2 tandem repeat region (total length of the repeat: 79,821 bps). Figure S8. Artemis Comparison Tool (ACT) view of NSCV1 Chr1 and Chr2 fusion junction. ACT was used to compare the MS6 Chr1 and Chr2 sequences against NSCV1 sequence. Genome sequences were aligned from the predicted ori1 and visualized in ACT with a cut-off set to blast scores >500. Red and blue bars indicate regions of similarity in the same orientation (blue) and inverted (red). B) Zoom-in region of MS6-like Chr2 inserted in ChrI. All homologous genes at the insertion boundaries are the same color coded and the 2 prophages are indicated by the green bar. Figure S9. Artemis Comparison Tool (ACT) view of NSCV2 Chr1 and Chr2 fusion junction. ACT was used to compare the MS6 Chr1 and Chr2 sequences against NSCV2. Genome sequences were aligned from the predicted OriC and visualized in ACT with a cut-off set to blast scores >500. Red and blue bars indicate regions of similarity in the same orientation (blue) and inverted (red) respectively. B) Zoom-in region of MS6 like Chr2 inserted in ChrI. All homologous genes at insertion boundaries are the same color coded. The green bars indicate the two prophages. The 12 bps and 245 bps repeats are labeled in yellow and blue line, respectively. Table S1. Whole Genome Sequence Statistics of NSCV1 and NSCV2. Table S2. Nucmer based pairwise comparison of genome sequences. Table S3. Unique Regions ˜10 Kb and over in NSCV1, NSCV2 and N16961 in comparison to others genomes. Table S4. List of potential dif sites in NSCV1 and NSCV2. Table S5. Summary of nucleotide and amino acid changes in origins of replication genes and corresponding proteins. Table S6. Summary of nucleotide and amino acid changes in replication associated and mismatch repair genes and corresponding proteins.

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