开题报告内容Content：（包括拟研究或解决的问题、采用的研究手段及文献综述，不少于2000字）Including objectives, methods adopted and literature review, no less than 2000 words
- Introduction
Trypanosomes are single-celled parasites that can infect humans and their livestock. Nearly all trypanosomes possess a unique mitochondrial DNA (mtDNA) (also called kinetoplast DNA or kDNA) network within the kinetoplast, consisting of two types of interlocked DNA molecules — maxicircles and minicircles (1). Some trypanosomes exhibit partial (dyskinetoplastidy (Dk)) or total (akinetoplastidy (Ak)) loss of kDNA in the genome, which leads to a change of their life cycle and host preference (2). Given the fact that classical systematics (Fig. 1) was defined by the life cycle and host (3) but trypanosomes have experienced limited morphological change throughout their evolutionary history despite significant sequence divergence (4), flaws of the classical systematics remain, as classical morphologically based criteria for taxonomic classification is not sufficient enough for the classification within the genus Trypanosoma, especially the classification of those dyskinetoplastic (T. equiperdum andT. evansi) groups that evolved recently. It has been debated for long about whether T. equiperdum and T. evansi are species or subgroups of T. brucei (2). Therefore, to achieve the consensus for delineating species based on molecular divergence, robust phylogenetic approaches should be applied (4, 5).
The mtDNA is a potentially valuable phylogenetic marker as it is shared among most trypanosomes and is relatively conserved in structure and sequence (6). Recent studies favored maxicircle sequences as a phylogenetic marker to reach the consensus for defining species in trypanosomatids (6, 7, 8). If the kDNA can separate isolates of the same species (T. brucei) robustly with good resolution, kDNA is likely to serve as a robust marker in further phylogeny inference and help to identify more precisely the origin and evolutionary history of those Dk/Ak groups. Therefore, the aim of the project is to study the feasibility of using kDNA genome as a robust marker, by comparing and analysing the genome of different isolates included in and closely related to the species T. brucei.
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Figure 1. Classical systematics of the genus Trypanosoma. Based on morphology, geographical distribution, clinical presentation of the disease, and affected host species (3).
- KDNA structure and function in trypanosomes
2.1 The kDNA network
The kDNA of trypanosomes exists as a unique and complex network organized into a disk-shaped structure known as the kinetoplast within a single, large mitochondrion (9). There are approximately 10, 000 heterogenous minicircles and 20–50 homogenous maxicircles in each trypanosome genome. For instance, a T. brucei kDNA network has about 1-kb minicircles and about 23-kb maxicircles (1).
2.2 Maxicircles
Maxicircles are circular DNA molecules conserved in trypanosomes and they are equivalent to mtDNA of other eukaryotes (1). Maxicircles contain a conserved gene coding region of 16–17 kb (10), which encodes many mitochondrial gene homologues involved in energy production and ribosome constitution (Table 1). These genes made maxicircles essential for the survival and transmission of African trypanosomes. For instance, T. brucei requires these mitochondrial genes for oxidative phosphorylation during ATP production, which helped them to undergo their procyclic stage (PS) and survive in tsetse flies after a bloodstream stage (BS) in vertebrates (2).
