Frederick, J. C. | bioRxiv Science

bioRxiv2025

Tick Genome Assemblies: Overcoming biological limitations through advances in sequencing and assembly

Ticks are blood-feeding arthropods with approximately 1,000 species, however, only 24 species currently have a genome assembly. These genome assemblies are important resources to advance tick biology and control of tick-associated diseases. Generating tick genome assemblies is challenging due to their small body size (low DNA input), DNA contamination (from microbiota and host bloodmeals), large genome size (on average 2.4 Gbp for hard ticks), and abundant transposable elements (at least 68% of the assembly for Ixodes species). Advances in sequencing technologies have driven an increasing number of tick assemblies from 2011 to 2025. We characterize and assess the 54 tick genome assemblies within public genome databases using QUAST-LG and BUSCO compleasm. Then we evaluate the impact of biological source material and sequencing platforms on these tick genome assemblies. From the 54 tick assemblies, we identify 34 high-quality assemblies from 21 species that are suitable for downstream analyses. We recommend future tick genome assemblies use long-read sequencing platforms and Hi-C scaffolding to improve genomic resources for these unique blood-feeding parasites.

genomics↗

bioRxiv2024

Duplex PCR assay to determine sex and mating status of Ixodes scapularis (Acari: Ixodidae), vector of the Lyme disease pathogen

Ticks are a major health threat to humans and other animals, through direct damage, toxicoses, and transmission of pathogens. An estimated half a million people are treated annually in the United States of America for Lyme disease, a disease caused by the bite of a black-legged tick (Ixodes scapularis Say) infected with the bacterial pathogen Borrelia burgdorferi. This tick species also transmits another six human-disease causing pathogens, for which vaccines are currently unavailable. While I. scapularis are sexually dimorphic at the adult life stage, the DNA sequence differences between male and female I. scapularis that could be used as a sex-specific marker have not yet been established. We determine the sex-specific DNA sequences for I. scapularis (male heterogametic system with XY), using whole-genome resequencing and restriction site-associated DNA sequencing. Then we identify a male-specific marker that we use as the foundation of a molecular sex identification method (duplex PCR) to differentiate the sex of an I. scapularis tick. In addition, we provide evidence that this molecular sexing method can establish the mating status of adult females that have been mated and inseminated with male-determining sperm. Our molecular tool allows the characterization of mating and sex-specific biology across development for I. scapularis, a major pathogen vector, which is crucial for a better understanding of their biology and controlling tick populations.

genomics↗