An assessment of genetic differences among ixodid ticks in a locus within the nuclear large subunit ribosomal RNA gene.

We examined the usefulness of the D3 domain and flanking core regions (=D3(+)) of the nuclear large subunit (LSU) ribosomal DNA as a genetic marker for species-level identification and the inference of evolutionary relationships of ixodid ticks. Genetic variation was also examined in relation to the secondary structure of the LSU rDNA. The results revealed a lack of sequence difference in the D3(+) among species of Dermacentor and among some species of Ixodes, demonstrating that this gene region is not suitable as a species marker for all species of ixodid ticks. Of the 45 variable nucleotide positions in the sequence alignment of the D3(+), 23 did not alter the secondary structure of the LSU rDNA, because they occurred in unpaired positions, whereas 16 represented partial or full compensatory changes which maintained the secondary structure. Six deletions in the D3(+) sequence of all Ixodes species examined resulted in a shorter d4_1 helix compared with that of other tick species. The results of the phylogenetic analyses also showed that the D3(+) is of limited value in resolving evolutionary relationships among ixodid ticks. In addition, we also demonstrated that the D3(+) of ascomycete fungi could also be amplified along with, or instead of, the D3(+) of some tick species, depending upon the primers used in PCR. Nonetheless, the D3(+) of the fungal contaminants are readily distinguished from the D3(+) of ixodid ticks because of a shorter length and the absence of helix d4_1 in the secondary structure of the LSU rDNA.