SNPs segregated with transmission status through whole genome comparison and targeted sequencing. A. Genome wide comparison of the non-transmissible Florida strain (red) with the efficiently transmitted St. Maries (green) strain produced 9609 SNPs. From this list we subtracted SNPs that encode for synonymous changes, leaving two types of SNPs that were further characterized: those that resulted in non-synonymous (NS) amino acid changes within ORFs and SNPs located in putative promoter regions. Comparison of these SNPs with genome sequences of three tick transmissible strains was then performed. SNPs that consistently segregated with phenotype were retained. The remaining differences were then targeted sequenced in two additional efficiently transmissible strains. B. A total of 9609 SNPs were found between the transmissible St. Maries and the non-transmissible Florida strain (SNPs). This comparison found 4498 non-synonymous SNPs (represented in black), 1630 SNPs found within putative promoter regions (shown in dark grey) and synonymous SNPs (shown in light gray). Whole genome comparison with three transmissible strains allowed removal of 4127 non-synonymous SNPs and 1568 promoter SNPs from further consideration. Finally, Targeted sequencing in additional transmissible strains of 241 non-synonymous and 62 promoter SNPs allowed retention of 35 NS and 14 promoter SNPs as candidate SNPs involved in tick transmission.