High SNP density in the blacklegged tick, Ixodes scapularis, the principal vector of Lyme disease spirochetes

Single-nucleotide polymorphisms (SNPs) are the most widespread type of sequence variation in genomes. SNP density and distribution varies among different organisms and genes. Here, we report the first estimates of SNP distribution and density in the genome of the blacklegged tick (Ixodes scapularis), an important vector of the pathogens causing Lyme disease, human granulocytic anaplasmosis and human babesiosis in North America. We sampled 10 individuals from each of 4 collections from New Jersey, Virginia, Georgia, and Mississippi and analyzed the sequences of 9 nuclear genes and the mitochondrial 16S gene. SNPs are extremely abundant (one SNP per every 14 bases). This is the second highest density so far reported in any eukaryotic organism. Population genetic analyses based either on haplotype frequencies or the 372 SNPs in these 9 genes showed that the 40 ticks formed 3 genetic groups. In agreement with earlier population genetic studies, northern ticks from New Jersey and Virginia formed a homogeneous group with low genetic diversity, whereas southern ticks from Georgia and Mississippi consisted of 2 separate groups, each with high genetic diversity.