Gene duplication and genome evolution in the Ixodidae
Abstract
Hard ticks (Ixodidae) are obligatory hematophagous ectoparasites of worldwide medical and veterinary importance. Ixodid ticks have large genomes (1 to >7 Gbp) compared to those of other arthropods, but little is known about their genome structure and organization. We hypothesize that the evolution of genome size and chromosome number in ixodid ticks is associated with an extensive accumulation of DNA through major duplication events and proliferation of repetitive sequences. To investigate the role of duplication events on genome size, bioinformatics was used to identify putatively duplicated genes (paralogs) from expressed sequence tag sequences (ESTs) from four species of hard ticks, including the prostriate tick Ixodes scapularis (Lyme disease tick) and the metastriate ticks Amblyomma variegatum (tropical bont tick), Rhipicephalus microplus (southern cattle tick) and R. appendiculatus (brown ear tick). Among these ticks, 2–10% of EST sequences represent putatively duplicated genes, and ∼25% of duplicated genes are under positive selection pressure based on ratios of non-synonymous to synonymous nucleotide substitution rates. Many genes under positive selection are associated with tick immunity, blood feeding and detoxification that may include important targets for vaccines or acaricides. Analysis of synonymous substitution rates suggests that two and three large gene duplication events occurred <10–15 MYA within the prostriate and metastriate tick lineages, respectively. Putative functions were assigned to paralogous ESTs using Gene Ontology (GO) searches and Blast2GO software. And functions associated with genes under positive or negative selection, as well as genes duplicated at different evolutionary times were compared. These comparison showed that, among others, genes involved with blood feeding capability and homeostasis were present within the positive selection subset, possibly indicating that these genes are responding to the species need to adapt and evolve. While functions associated with cell death, DNA damage, transcription and translation regulation are present in the negative selection group, probably due to their essential house-keeping functions. Differences in the function associated with the genes duplicated as part of the first or second duplication event were also identified in our analysis. In addition, a more detailed study of a single gene family implicated in gene duplication and having importance for tick control—acetylcholinesterase—was conducted. The identification of the repertoire of ace loci in I. scapularis and implication of specific genes associated with organophosphate insecticide resistance will assist with the design of better diagnostics and in strategies to delay, manage or prevent organophosphate resistance in these pests. This research marks the first genome-wide analysis of gene duplication in ticks and provides insight towards an understanding of genome evolution within the Ixodidae.
Degree
Ph.D.
Advisors
Hill, Purdue University.
Subject Area
Entomology|Public health|Bioinformatics
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