Fig. 1

Nucleotide and amino acid diversity across 10 identified Pst HD locus alleles. A The CDS for each allele of Pst-bW-HD1 and Pst-bE-HD2 were aligned using MUSCLE and visualized in Geneious. Along the top of the alignments is a frequency plot indicating the percentage agreement with the most common nucleotide at that position. At the bottom of each alignment is the domain structure of the sequences in the alignment, and the average pairwise similarity within that domain across each allele. Each large rectangle represents the nucleotide sequence of a particular allele. Grey stretches indicate agreement with the most common nucleotide at that position. Coloured bars indicate a disagreement, shaded according to the base at that position (Red = A, Green = T, Yellow = G, Blue = C). Alignment gaps due to In/Del polymorphisms between alleles are represented as black horizontal bars, and a scale is provided above the sequences. B The amino acid alignments of each translated Pst-bW-HD1 and Pst-bE-HD2 allele were similarly aligned and cross-compared for agreement at each position. Along the top of the alignments is a frequency plot indicating the percentage agreement with the most common amino acid at that position. Each large rectangle represents the primary sequence encoded by that allele. Amino acids are coloured according to their polarity (Red = D,E; Green = C,N,Q,S,T,Y,U; Orange = A,F,G,I,L,M,P,V,W; Blue = H,K,R.) and gaps in the alignment are indicated by a black horizontal bar. A scale is provided above the sequences