Chromosome-Scale Atlas of Ixodes scapularis Serine Protease Inhibitors

Background/Objectives: Ticks evade host hemostasis and immunity in part by injecting serine protease inhibitors (serpins) into the host during feeding, yet the genomic organization of tick serpins has remained unresolved. To understand how ticks deploy these proteins, there is a need to elucidate their gene structure, arrangement and copy number in the genome. Methods: We annotated the recent Ixodes scapularis chromosome-level assembly and identified all the serpin genes to build a genome-wide atlas of serpin loci identifying the gene structure and duplication patterns. The gene expression of serpins during blood meal was also analyzed. Results: We identified 74 serpin genes across eight chromosomes and one unplaced scaffold, with a strongly non-random distribution dominated by chromosome 10, which harbored 67.6% of serpin genes in dense tandem clusters. Most genes were intronless and encoded secreted, N-glycosylated proteins, whereas a minority were conserved two-exon loci sharing a common splice junction. Pairwise amino acid comparisons revealed exact duplicates as well as very recent and divergent paralogs, indicating continued local duplication and diversification. Expression analysis across tissues and feeding time showed that serpin expression is structured primarily by organ and feeding stage, including a late feeding increase in midgut serpins that are predicted to inhibit trypsin-like proteases. Conclusions: This atlas provides a comprehensive description of I. scapularis serpins, provides a framework for understanding tick gene structure and function, prioritizes serpins as target candidates for tick control, and functions as a library for other serpin uses in medicine and industry.