Complete genome sequencing of four Ixodes tick species (Ixodes ricinus, Ixodes persulcatus, Ixodes pacificus and Ixodes hexagonus) reveals hallmarks of duplications and gene content evolution in ticks.

Ticks are haematophagous parasites that can transmit pathogens to their vertebrate hosts. Although tick genomics has developed in recent years, until recently there was a lack of high-quality genomes, particularly in the genus Ixodes, which includes the main vectors of Lyme disease. For this study, we sequenced the complete genomes of four tick species, using a single female. This includes the European species Ixodes ricinus, for which a special effort was made in terms of sequencing and manual curation. We obtained an assembly at the chromosome level for I. ricinus and the assemblies for three other species, I. persulcatus, I. pacificus and I. hexagonus, were less contiguous. The high quality of the four genomes, combined with a very complete annotation of several important gene families, has made it possible to study the evolution of gene repertoires at the level of the genus Ixodes and the tick group as a whole. We have determined which gene families and functions have been associated with major duplications during the evolution of this group, while an expression atlas obtained for I. ricinus reveals striking patterns of specialization both between and within gene families. Some of the most significant gene amplifications are clearly associated with a proliferation of single-exon genes (e.g. cytosolic sulfotransferases). Overall, our work, which combines new and published genomes (e.g. I. scapularis and species from other tick genera), provides a comprehensive framework for studying the evolution of this group, and provides the basis for more applied studies and the development of new methods for controlling these organisms.