Genetic and genomic diversity of crocodylians: applications in evolution and immunogenetics

There are ~27 recognised extant species of crocodylians (Crocodylia), which inhabit a large range of tropical, fresh- or saltwater ecosystems around the world. Crocodylians appear to have an effective immune system that allows them to cope with a variety of pathogenic challenges. Crocodylians have been shown to live with a range of opportunistic infections, and yet wild animals seldom display disease symptoms. Also, reptile immune systems are less well studied than their mammalian and avian counterparts, and yet reptiles hold a unique evolutionary position as cold-blooded amniotes. Studying the evolutionary rates and diversity of immune system components in crocodylians could contribute to our overall understanding of the development of the immune system. Genetic and peptidome studies of the crocodylian immune system have improved our understanding of the organisation, evolution and diversity of some components of the adaptive immune system, however, there is much yet undiscovered when it comes to components that modulate the functions of the adaptive and innate immune systems in crocodylians. The availability of genomic resources would be beneficial to further investigations into disease susceptibility and resistance in industry and endangered wild populations. At present, only four crocodylian draft genomes have been sequenced and are publicly available. The projects undertaken in this thesis were initiated due to the limited genomic and immunogenetic resources available for crocodylian species. This research was to provide foundations in a key immune modulatory system in crocodylians, as well as to investigate applications of crocodylian genomic data in answering current evolutionary and immunogenetic questions