Color code stands for maximal length of those regions with highly homologous sequences between genomes: red, >10 kb; blue, 5–10 kb; cyan, 1–5 kb. The boxes in green represent phage-associated CDSs of L20. Besides the strain L20-specific prophage region illustrated below the linear genomic diagram as an enlarged drawing, four special genomic regions highlighted (B, C, D, E) were magnified in the corresponding panels. The genetic organizations of the cys operons (B), the CPS biosynthesis and export gene clusters (D), and the LPS O-antigen biosynthesis gene clusters (E) were compared among three isolates of A. pleuropneumoniae: JL03 (serotype 3), L20 (serotype 5b) and 4074 (serotype 1). Comparative genetic organization of the flp operons between JL03 and L20 is illustrated in panel C. Regions presented in gray represent highly homologous sequences. Blue arrows represent putative CDSs with either forward or reverse transcription directions.

All the amino acid sequences are from the genomes of A. pleuropneumoniae JL03 and E. coli K12 MG1655. CDSs designated with numbers and corresponding annotations are listed below: A. wzy (APJL1490) (wbbH), encoding oligosaccharide repeat unit polymerase; B. wzx (APJL1491) (rfbX), encoding O-antigen flippase; C. wcaJ (APJL1493), encoding glycosyltransferase; D. wzz (APJL1485) (cld), encoding an O-antigen chain length determining protein.

(A) Circular genome representation of JL03. Circles are numbered from 1 (outer circle) to 10 (inner circle). The circles 1/2 shows predicted CDSs on the plus and minus strand in JL03 color-coded by COG categories. All genes are colored according to biological functions: gold for translation, ribosomal structure and biogenesis; orange for RNA processing and modification; light orange for transcription; dark orange for DNA replication, recombination and repair; antique white for cell division and chromosome partitioning; pink for defense mechanisms; tomato for signal transduction mechanisms; peach for cell envelope biogenesis and outer membrane; deep pink for intracellular trafficking, secretion and vesicular transport; pale green for posttranslational modification, protein turnover and chaperones; royal blue energy production and conversion; blue for carbohydrate transport and metabolism; dodger blue for amino acid transport and metabolism; sky blue for nucleotide transport and metabolism; light blue for coenzyme metabolism; cyan for lipid metabolism; medium purple for inorganic ion transport and metabolism; aquamarine for secondary metabolites biosynthesis, transport and catabolism; gray for function unknown. Circle 3/4, the putative horizontal transferred genes in deep pink identified by SIGI-HMM on the forward and reverse strand. Circle 5, repetitive elements in yellow, above 200nt and cutoff value 1e-10. Circle 6, transposases in green and potential prophage genes in dark orange. Circle 7, mean centered GC content of JL03 genes (red: above mean, blue-below mean). Circle 8, tRNA genes in orange. Circle 9, rRNA genes in red. Circle 10, GC Skew plot (windowsize: 1000, windowoverlap: 500). (B) Genetic organization of the oriC regions in three representative organisms within the family of Pasteurellaceae: JL03, A. pleuropneumoniae; 35000HP, H. ducreyi; and Pm70, P. multocida.

Diagrammatic representation of carbon flow, electron flow, and biosynthesis of major metabolic intermediates and fatty acid are showed. Midpoint potentials (E^'₀) of some electron donors and acceptors of respiration chains are marked. Genes encoding crucial enzymes and functional proteins involved in the metabolic pathways are illustrated while the corresponding CDSs designated with APJL numbers are listed in Table S2.

CDSs corresponding to the illustrated proteins with designated APJL numbers are listed in Table 5 (adherence and secretion relevant genes), Table 6 (capsule polysaccharide relevant genes), Table 7 (lipopolysaccharide relevant genes), Table S3 (iron relevant genes) and S4 (the rest portion relevant genes). Proteins involved in iron uptake, transport and regulation are colored in yellow.