Genomic analysis of the impact of sexual recombination on the segregation of virulence genes in African trypanosomes

布氏锥虫是被忽视的热带病、非洲人类锥虫病（昏睡病）和非洲动物锥虫病（那迦纳病）的病原体。这种病媒传播的原生动物寄生虫对撒哈拉以南非洲地区造成了毁灭性的影响。寄生虫可引起慢性、使人衰弱的感染，造成毁灭性的健康和经济影响。锥虫是细胞外寄生虫，这意味着它们的整个生命周期都暴露在宿主的免疫系统中。为了逃避宿主的防御，锥虫有一个高度建立的抗原变异系统，其变异表面糖蛋白（VSGs）。在任何时候只有1个VSG被表达，但是锥虫有大量的VSG基因——超过2000个基因拷贝。这种变异是通过频繁切换VSG表达来逃避宿主免疫系统来实现的。以前的研究表明，锥虫可以在采采蝇载体的唾液腺内进行性重组，最终将混合后代的VSG库。在基因组中，VSG基因存在于大的亚端粒阵列中，众所周知，使用当前的基因组技术很难组装这些区域，因为这些区域高度重复。由于基因组技术的准确性在过去几年中有所提高，特别是在重复区域，现在已经有可能对这些锥虫基因组进行测序。这些技术的进步意味着众所周知的难以组装的区域（即亚端粒，高度重复的阵列）现在可以比以往任何时候都更自信地解决。因此，我的项目目的是利用各种基因组测序策略来分析性重组对非洲锥虫VSG基因的影响。我的目标是结合使用长读技术和短读技术来分析亲本勃氏体菌株的基因组，并将F1后代的基因组映射到亲本上，以确定性重组如何影响后代中VSG基因的分离。

Trypanosoma brucei (T. brucei) is the causative agent of the neglected tropical disease, Human African trypanosomiasis (sleeping sickness), and Animal African trypanosomiasis (Nagana). This vector-borne protozoan parasite has a devastating impact across sub-Saharan Africa. The parasites can cause chronic, debilitating infections resulting in devastating health and economic implications. Trypanosomes are extracellular parasites, meaning they spend their entire lifecycle continually exposed to the host's immune system. To evade host defences, trypanosomes have a highly established system of antigenic variation of their variant surface glycoproteins (VSGs). Only 1 VSG is ever expressed at any one time, but trypanosomes have a huge repertoire of VSG genes - over 2,000 gene copies. The variation is achieved by frequently switching VSG expression to evading the host immune system. It has been shown previously that trypanosomes can undergo sexual recombination within the salivary gland of the tsetse fly vector, which will ultimately mix the VSG repertoire of the progeny. Within the genome, the VSG genes are present in large subtelomeric arrays which are notoriously difficult to assemble using current genome technologies as these regions are highly repetitive. As the accuracy of genome technologies has improved over the last few years, particularly across repetitive regions, it has now been possible to sequence these trypanosomes genomes. The advancement of these technologies means that notoriously difficult regions to assemble (i.e. subtelomeric, highly repetitive arrays) can now be resolved more confidently than ever before. The aim of my project is therefore to utilise various genome sequencing strategies to analyse the impact of sexual recombination on VSG genes in African trypanosomes. I aim to use a combination of long-read technologies and short read technologies to analyse the genomes of the parental T. brucei strains and map the genomes of the F1 progeny onto the parents to identify how sexual recombination has influenced the segregation of the VSG genes within the progeny.