Genome organization of major tandem repeats in Ixodes scapularis, the lyme disease tick

Progress in tick genome research lags behind that in other arthropod vectors such as mosquitoes, however the anticipated publication of the Lyme disease tick (Ixodes scapularis: subphylum Chelicerata; class Arachnida; family Ixodidae) genome sequence will provide significant advancement in this regard. Physical mapping studies to localize DNA sequences to I. scapularis chromosomes (2n=28) have not been reported; however, this research is warranted to improve genome assembly and to address questions about tick genome evolution. Ixodid genomes are relatively large compared to those reported in other arthropods and host large amounts of repetitive DNA. Here, we developed the first fluorescence in situ hybridization (FISH)-based chromosome markers in I. scapularis that target prevalent tandem repeats in the genome. Using shotgun sequencing, six tandem repeat families (TRFs) were identified and estimated to contribute ~159 Mbp of the 2.1 Gbp I. scapularis genome (8%), exceeding the entire genome sizes reported for two other chelicerates. TRFs were localized to significant heterochromatic blocks in I. scapularis chromosomes prepared from mitotic cell line ISE18. Probes for the nucleolar organizing regions, telomere, and centromere were used with TRF probes to characterize chromosome architecture. FISH experiments using bacterial artificial chromosome (BAC) clone probes typically resulted in non-specific hybridizations, illustrating that repetitive DNA is prevalent and widely-distributed throughout the genome. Our identification and localization of TRFs spawns new questions about their role in chromosome structure and influence on cellular processes. This research lays the foundation for developing a FISH-based physical map in I. scapularis useful for the international vector biology community.