Table 1.
Haemorrhagic septicaemia-associated strains of Pasteurella multocida used in this study.
Table 2.
Sequencing and assembly statistics for the genomes of the 12 Asian HS-associated strains.
Table 3.
Genomic features of the 12 Asian strains.
Table 4.
Single-nucleotide polymorphisms (SNPs) and insertion/deletion polymorphisms (indels) in the twelve Asian genomes.
Fig 1.
Unrooted neighbour-joining trees showing the phylogenetic relationship between various strains.
A. Relationship between Gallibacterium anatis, Mannheimia haemolytica, Pasteurella dagmatis, Pasteurella bettyae and the P. multocida strains Pm70, 36950, HN06, P3480, X73, VP161, Anand1C, Anand1B, Anand1P, Anand1G, P1059, P52VAC, VTCCBAA264, M1404 and the twelve Pakistani and Thai isolates. B. Relationship between the P. multocida strains. C. Relationship between the HS-associated P. multocida B:2 strain M1404 and the twelve Pakistani and Thai isolates. Phylogenetic relatedness for all comparisons was determined by analysis of only the single nucleotide polymorphisms found at conserved positions in all genomes of the comparison set (CG-SNPs); 789 shared positions for the tree in panel A, 7,829 shared positions for the tree in panel B and 722 shared positions for the tree in panel C. Trees were rendered with SplitsTree v4.11.3 [34]. The line segments above the trees with the number '0.01' indicate the branch length representing a genetic change of 0.01.
Fig 2.
Flower plot diagram showing core and unique genes across all strains.
The central circle shows the number of genes common to all strains while the petals show the number of genes in addition to the core set, as well as the number of genes unique to each strain (in brackets). Abbreviated strain names are given outside each petal, strain details are given in Table 1. The B:2 HS-related strains are shaded as follows; M1404 is orange, Thai strains are blue and the Pakistani strains are green. Non-B:2 strains are shaded in grey.
Table 5.
Genomic location of each of the four putative temperate phages identified by PHAST.
Fig 3.
Comparison of the genomes of 3480, 36950, HN06, Pm70, M1404, BUKK, TX1, THA, THD, THF, ATTK, Faisal, Islm, Pesh, PVAcc, V1 and Karachi with the genome of the PVAcc strain.
The three inner rings show the DNA size, GC content and GC skew of the reference genome (PVAcc strain). The 17 outer rings show regions of the comparison genomes that match the reference genome PVAcc and in the order (inside to outside) 3480, 36950, HN06, Pm70, M1404, BUKK, Tx1, THA, THD, THF, ATTK, Faisal, Islm, Pesh, PVAcc, V1 and Karachi. Regions 1–4 on the outside identify particular regions of difference between the strains that are potential prophage elements. The position of the type B capsule locus is also noted between regions 2 and 3. This figure was drawn using BLAST ring image generator (BRIG) [39].
Fig 4.
Comparison of the integrative conjugative element, ICEPmu1, present in 36950 strain [33] with the genomes of 36950, Pm70, combined HN06 and 3480, combined M1404 (B:2), ATTK, BUKK, Faisal, Karachi, Islm, Pesh, PVAcc, THA, THD and THF strains and combined BUKK and TX1 strains, displayed as the outer rings inside to outside respectively.
The three inner rings show the DNA size, GC content and GC skew of the reference element (ICEPmu1). The five outer rings show regions of the comparison genomes that match the reference ICEPmu1. Figure was drawn using BRIG [39].