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In spite of the global medical and veterinary importance of Ixodid ticks, relatively little is known about their genome organization. To address this, we developed the first fluorescence in situ hybridization (FISH)-based chromosome markers in the
Lyme disease vector, Ixodes scapularis. Shotgun genomic DNA (gDNA) sequences were used to identify three major tandem repeat families which were localized to specific heterochromatic regions of I. scapularis chromosomes prepared from the mitotic cell line ISE18. Together, these repeats were estimated to contribute approximately 159 Mb (8%) of the 2.1 Gb (haploid) I. scapularis genome. The relative arrangement of each tandem repeat family and the nucleolar organizing regions was determined by rehybridization to individual chromosome spreads, which was useful to distinguish different chromosomes in the ISE18 karyotype. Long stretches (>20 kb) of tandem repeat-containing gDNA were resistant to digestion by the methylation-sensitive restriction enzyme HpaII and localized to the presumed peri-centromeric regions of the chromosomes. A telomeric probe based on the arthropod-conserved (TTAGG)(n) tandemly repetitive motif was localized to the termini of each I. scapularis chromosome. Localization of these markers produced the first link between DNA sequences and major structural features of I. scapularis chromosomes and thereby provided the framework for a FISH-based physical map.