Retracing the evolutionary history of the Trypanosomatidae: the use of kinetoplast DNA in molecular systematics, species identification and diagnostics

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The Trypanosomatidae (class Kinetoplastida) are a diverse and widespread group of protists characterised by their possession of a unique and highly specialised mitochondrial homologue known as the kinetoplast. All trypanosomatid parasites are exclusively parasitic, with the majority of genera being restricted to a single invertebrate host (i.e. monoxenous lifecycle). However, they are primarily known for their pathogenic dixenous members (i.e. having a two-host life cycle), that serve as the aetiologic agents of several important neglected tropical diseases (NTDs) including leishmaniasis, Chagas disease and human African Trypanosomiasis. Recent advancements in molecular biology have improved our knowledge of evolutionary relationships between trypanosomatid species by revolutionising the genetic approach to trypanosomatid systematics. The kinetoplast DNA, and more specifically, the maxicircle genome represents a valuable taxonomic marker given its unique presence across all Kinetoplastids. The research described in this thesis was performed to explore the suitability of the kinetoplast DNA as a much-needed standardised framework for the taxonomic classification and species identification of protozoans falling within the Trypanosomatidae family. The main research outcome provides the most in-depth analysis of the trypanosomatid family to date, demonstrating extensive evidence for the superiority of the maxicircle for the taxonomic resolution of the Trypanosomatidae. Chapter 1 presents a comprehensive review outlining the important developments that have been made in the field of trypanosomatid taxonomy, advancing our current knowledge over the relationships between members of the trypanosomatid family. Chapter 2 demonstrates the superiority of the maxicircle genome for the phylogenetic inference of the Leishmaniinae. Phylogenetic analyses provided support imperative towards the Supercontinents hypothesis of dixenous parasitism within the Trypanosomatidae. The comprehensive analysis of the entire family of trypanosomatid parasites in Chapter 3 revealed strong support for the multiple origin and independent evolution of dixenous parasitism within the trypanosomatid family. Kinetoplast DNA is an organelle exclusive to the Kinetoplastids, unique in its structure, function and mode of replication and thus represents a unique diagnostic target, with the potential to differentiate different species and strains of 𝘓𝘦𝘪𝘴𝘩𝘮𝘢𝘯𝘪𝘢. The implementation of novel diagnostic procedures for leishmaniasis such as the one reported in Chapter 4 is intended to establish a gold standard practice for the diagnosis and treatment of leishmaniasis. Ultimately, Chapter 5 reviews the completion of this thesis, demonstrating that use of the maxicircle genomes provide an excellent benchmark for future studies involving the phylogenetic analyses, taxonomic classification and species identification of the Trypanosomatidae.
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