Figure 1

Location of housekeeping genes used for MLST on the closed chromosome of Y. ruckeri strain YRB and phylogenetic relatedness amongst representative isolates. (a) The positions of the nineteen housekeeping enzymes used to construct phylogeny of Y. ruckeri within the closed genome of strain YRB (GenBank: CP009539.1) are shown. The circular genome map was generated using CGView Server software (V 1.0)⁶⁰ and annotated using Microsoft PowerPoint. (b) A Neighbour joining phylogenetic tree shows the relationship of 16 isolates (Table 1) based on the concatenated sequence of the 19 housekeeping genes (Table 2). This concatenated sequence was 27,363 nucleotides in length and encoded 9121 amino acids. Isolates were recovered from Atlantic salmon (AS; red); rainbow trout (RT; green); and European eel (EE; yellow). Parameters were assessed with a bootstrap method (1000 tests). The tree was constructed using the Jukes–Cantor correction for synonymous changes. Distribution of polymorphic nucleotide sites among concatenated housekeeping gene sequences in reference isolates (c). The numbers above the sequences represent the positions of polymorphic nucleotide sites from the 5′ end of the gene. The dots represent sites where the nucleotides match those of the first sequence (RD6). The boxes highlight regions of sequence identity that represent proposed recombinant segments. Genes within the concatenated sequence are separated by dashed lines. Roman numerals correlate with positions on the phylogenetic tree in (b).