A team of scientists led by the University of Maryland has decoded the first comprehensive, continuous genome for a parasite responsible for transmitting Lyme disease and other serious infections to hundreds of thousands of Americans each year. Using their newly described genome for the black-legged tick, or deer tick, the researchers identified thousands of new genes and new protein functions, including proteins associated with tick immunity, disease transmission and developmental stages.
This work provides valuable information for the development of interventions for various tick-borne diseases and far surpasses previous efforts to sequence the tick genome, which resulted in partial genomes or genome fragments with gaps and uncertainties.
The study was published in the journal on January 19, 2023 natural genetics and was made possible through close collaboration between several academic institutions, industry and federal institutions.
“We are very excited to now have this reference genome because there are so many unanswered questions about how these parasites evolved and transmit disease,” said Utpal Pal, senior author of the study and a professor at the Virginia-Maryland College of Veterinary Medicine in college park. “We think there are genetic factors that contribute to why these ticks are such good disease vectors, but we can’t really understand it without a very good genome like this.”
Black-legged ticks (Ixodes scapularis) or closely related species are widespread in North America, Europe, North Africa and Asia. They are the main carriers of a number of diseases, including Lyme disease, which infects nearly half a million Americans annually. However, many aspects of their biology remain unknown.
With a complete genome, scientists can begin to unravel the molecular mechanisms behind many aspects of the parasite’s biology and its interactions with both hosts and the diseases it transmits.
The genome of a black-legged tick consists of more than 2 billion discrete DNA codes (expressed as combinations of four nucleotides represented by the letters ATCG). Like letters bundled together into words in a sentence, the DNA codes are bundled together into genes that make up the genome.
Previous work to decipher the tick genome used many immature ticks or tick cells grown in laboratories over several generations, leading to errors, or combined samples from multiple individual ticks, resulting in fragmented code bundles with many redundant snippets. The researchers had to piece the snippets back together, determining where each gene begins and ends and how they should be arranged.
To overcome these challenges, Pal and his colleagues combined two methods to sequence the genome of a single tick. One method decoded the entire genome at once, producing a sequence that was complete but somewhat “fuzzy,” meaning the code wasn’t clear in many places. In the second method, the researchers used a common technique called polymerase chain reaction, or PCR, to “amplify” small segments of the genome so it could be read more clearly. The team then combined the two results, which was a bit like using a blurry, large image as a reference for piecing together high-resolution jigsaw pieces. Finally, the researchers used a technique called “Hi-C” to bridge small pieces of DNA into longer, connected strands.
The result is a high-quality, contiguous genome that is 98% complete. The new genome showed that 40% of the black-legged tick annotations previously described were based on older technology and needed to be updated.
Next, the researchers compared their whole genome to slices of genomes sequenced from 51 wild-caught ticks, showing that the new work could be used as a reference for identifying segments of genetic material from other individuals. An unrecognized genetic diversity between tick groups from different regions in the USA was also identified
Finally, the team analyzed their tick genome to identify thousands of new genes and proteins and to describe new critical functions of these genes. For example, in one experiment, they found that some proteins were only present during certain phases of a tick’s life cycle, or at certain stages during a tick’s blood meal and digestion. By turning off a gene that tells tick cells to make one of these proteins, they were able to disrupt the tick’s feeding and digestive processes.
Future work like this could help target gene-based therapies and vaccines that disrupt part of the disease transmission cycle between ticks and humans.
Another outcome of the study was that the researchers identified and described a more comprehensive genome for Rickettsia buchnerithe pathogenic bacterium that causes rickettsiosis.
The genomic resources described in the publication are publicly available through large databases and will be helpful in advancing tick research and preventive measures.