Fig. 9

Mean nucleotide diversity (purple line) and pairwise divergence for each haplotype pair (grey lines) across portions of four contigs in LG16 (contig 499 300-850 kb, contig 550 0–250 kb, scaffold 3064 2300–3000 kb) and LG5 (contig 676 150–850 kb) showing high diversity and clusters of transmembrane genes. All plotted genes (shown in red, blue and black) encode single-pass transmembrane proteins (TM1); other genes in these regions are not shown. Key functional domains potentially involved in pathogen recognition include C-type lectin (CTL), fibronectin type III (FN3) and immunoglobulin (Ig), and TMEM154, which is a membrane-spanning domain also found in several polymorphic transmembrane cluster 1 (PTC1) genes [41]. Genes shown in red, including BSUD.12903 (Fig. 10) all have at least three of these four functional domains, while genes shown in blue have only Ig and genes shown in black represent other genes encoding TM1 and various other protein domains