Genomics and genetic manipulation of protozoan parasites affecting farm animals

In this chapter we present a brief but state-of-the-art account of the genomics and current gene manipulation methods that can be used to improve our understanding of the genetics and the biology of an arbitrary group of 17 protozoan parasites responsible for diseases that affect animals worldwide, including babesiosis, toxoplasmosis, theileriosis, cryptosporidiosis, eimeriosis, trypanosomiasis, and trichomoniasis. Complete genomes are available for all parasites discussed, except for Besnoitia, an apicomplexan parasite responsible for dermatitis and other disorders with high infection rates, but low mortality. Dramatic differences in genome sizes are evident among the group of parasites under study, consistent with the distinct dependency of parasitic lifestyle for each organism. In addition, linear regression analysis correlating the ratios of the number of genes per genome and genome size among all the selected protozoan parasites suggests a strong association between these two parameters, in alignment with the notion that smaller protozoan genomes are generally more compact than larger genomes. A brief description of the methods for genome manipulations, including transient and stable transfections and gene editing methods, is provided. These methods, required to understand gene function and for improving control measures, have been successfully developed so far in most parasites selected. Rapid progress of genomic and gene manipulation techniques will likely result in the constant emergence of novel integrated methods for the interrogation and modification of genomes, leading to our better understanding of parasite lifestyle and, ultimately, to the rational design of improved methods for the control of animal infectious diseases.