Transposable elements as dual agents in livestock-parasite interactions: From parasite adaptation to host genetic innovation.

Transposable elements (TEs), which were previously seen as genomic parasites, are currently viewed as major contributors to evolutionary innovation in host-parasite interactions. This review provides an overview of the current knowledge of TEs in veterinary parasitology, divided into three interlinked levels. Firstly, in terms of parasite genome biology, TEs are highly diverse and actively transposing, from the extremely active mobilomes of strongylid nematodes and liver flukes to the TE-rich but genomically reduced microsporidian parasites. Secondly, at the host-parasite interface, direct physical contacts help in the horizontal exchange of TEs between the parasites and their hosts. Thirdly, TE activity leads to important functional innovations, including expansions of virulence-related gene families in schistosomes, formation of species-specific stage-regulated non-coding RNAs in liver flukes, and even TE-derived small interfering RNAs secreted by parasitic nematodes as cross-species immune modulators. On the host side, polymorphic TEs, especially SINEs and endogenous retroviruses, provide abundant opportunities to generate phenotypic diversity in livestock by affecting features such as muscle formation, fat accumulation, fur coloration, and immune response. Throughout this review, we clearly separate the established facts from the associations and hypotheses, and highlight the areas of knowledge deficit. In conclusion, we will outline the model of utilizing TE biomarkers in selective breeding, and note that the association between particular polymorphisms of TEs and resistance to parasites is mostly hypothetical and needs further verification.