Table 1.
Features of 11 sequenced strains of Mannheimia haemolytica.
Fig 1.
UPGMA phylogenetic tree based on whole genome sequence alignment of 11 Mannheimia haemolytica strains.
The tree was generated from full genome alignment produced using Mauve in Geneious version 6.1.8 using Tamura-Nei distance correction with no specified outgroup. The scale length is equal to 0.001 nucleotide substitutions per site.
Fig 2.
Size of the core genome and dispensable genome and number of strain unique CDS in 21 Mannheimia haemolytica genomes.
Petals contain number of unique CDS per strain. Petals a-h represent the serotype 1 strains M. haemolytica L024A, M. haemolytica 157-4-1, M. haemolytica L044A, M. haemolytica 535A, M. haemolytica D153, M. haemolytica MhBrain2012, M. haemolytica D193, and M. haemolytica USDA-ARS-USMARC-183 respectively. Petals i-o represent the serotype 6 strains M. haemolytica T14, M. haemolytica H23, M. haemolytica 3927A, M. haemolytica L038A, M. haemolytica D174, D38, and M. haemolytica USDA-ARS-USMARC-185 respectively. Petals p-u represent the serotype 2 strains M. haemolytica 587A, M. haemolytica L033A, M. haemolytica T2, M. haemolytica D171, M. haemolytica D35 and M. haemolytica Bovine A2, respectively. Analysis based on 85% sequence identity across 90% length.
Fig 3.
Pan-genome and core genome of 21 M. haemolytica isolates.
For both the pan-genome and the core genome, the number of genes is plotted as a function of the number n of strains sequential added. The curve for the pan-genome represents the least-squares fit for the function y = AxB + C with the best fit obtained with a correlation r2 = 0.999 for A = 613.27 ± 1.08, B = 0.81, C = 2050.92 ± 10.41. The curve for the core genome represents the least-squares fit for the function y = AeBx + C with the best fit obtained with a correlation r2 = 0.948 for A = 1444.89 ± 118.98, B = -0.32, C = 1409.54 ± 1.2.
Fig 4.
New gene discovery plot for pan-genome analysis of 21 Mannheimia haemolytica genomes.
Bars represent the number of new genes as the function of the number n or strains sequentially added. The curve represents the least-squares fit for the function y = AxB with the best fit obtained with a correlation r2 = 0.875 for A = 566.17 ± 3.16, B = -0.22. The extrapolated number of new genes expected after the number of genomes increases to 100 is 123 new genes.
Fig 5.
Pan-genome and core genome of 21 M. haemolytica isolates.
For both the pan-genome (grey) and the core genome (black), the number of genes is plotted as a function of the number n of strains sequentially added. Panel A: serotype 1 strains, n = 8. Panel B: serotype 6 strains, n = 7. Panel C: serotype 2 strains, n = 6. The curve for the S1 pan-genome represents the least-squares fit for the function y = AxB + C with the best fit obtained with a correlation r2 = 0.999 for A = 572.81 ± 4.45, B = 0.79, C = 2104.32 ± 19.12. The curve for the S1 core genome represents the least-squares fit for the function y = AeBx + C with the best fit obtained with a correlation r2 = 0.976 for A = 1549.09 ± 90.55, B = -0.81, C = 1964.34 ± 14.87. The curve for the S6 pan-genome represents the least-squares fit for the function y = AxB + C with the best fit obtained with a correlation r2 = 0.999 for A = 652.62 ± 8.5, B = 0.73, C = 1942.33 ± 25.16. The curve for the S6 core genome represents the least-squares fit for the function y = AeBx + C with the best fit obtained with a correlation r2 = 0.983 for A = 1601.51 ± 92.41, B = -0.74, C = 1806.86 ± 19.97. The curve for the S2 pan-genome represents the least-squares fit for the function y = AxB + C with the best fit obtained with a correlation r2 = 0.999 for A = 944.93 ± 10.83, B = 0.65, C = 1527.44 ± 23.12. The curve for the S2 core genome represents the least-squares fit for the function y = AeBx + C with the best fit obtained with a correlation r2 = 0.988 for A = 2123.13 ± 68.56, B = -0.88, C = 1579.86 ± 5.88.
Fig 6.
Phylogenetic analysis of prophage found in M. haemolytica.
The tree was constructed by neighbour-joining method with the MAFFT program. Bootstrap values (>50) representing 100 sampling replicates are in grey located below branches with the phage cluster numbers adjacent to corresponding nodes above the branches. The scale length is equal to 0.1 nucleotide substitutions per site.
Table 2.
Metadata for prophage identified within the genomes of 11 strains of Mannheimia haemolytica.
Fig 7.
Schematic of CRISPR-Cas systems identified in whole genome sequence analysis of 11 Mannheimia haemolytica genomes.
Panel A: Cas loci present in serotype 1, 6 and 2 genomes. Panel B: consensus sequence for leader and trailer regions of CRISPR arrays. Underlined regions are complementary to psi-tag. Panel C: Sequences of the 6 unique direct repeats detected in CRISPR arrays. Panel D: CRISPR array spacer and direct repeat organization. Diamonds represent direct repeat sequences while numbered tiles represent spacer sequences. Panel E: 3D structure of direct repeats found in CRISPR arrays. Psi-tag indicated by grey shaded regions. Panel F: sequence alignment of protospacers with suspected protospacer adjacent motif (PAM) highlighted in grey (TTC).
Table 3.
Spacer sequences identified in CRISPR arrays from 11 Mannheimia haemolytica genomes.
Fig 8.
Schematic of putative integrative conjugative elements identified in whole genome sequences of Mannheimia haemolytica.
Genes are represented as arrows. Grey background indicated regions >94.5% sequence identity. Panel A: proposed ICE genes arrangement. Panel B: resistance gene regions with alignments against cassettes found in other bacterial species.