Comparative genomics of leeches: anticoagulants, bacterial symbionts and evolutionary relationships

我的研究计划的总体目标是了解行为、生态学和形态的进化转变，并阐明生物和遗传多样性的起源和分布，这些主题是生物和生物体自然历史的基础。为了实现这一目标，需要了解这些特征变化背后的基因组基础。这一基础将明确事件的方向和时间，并增加我们对导致潜在变化的基因组单位的理解。水蚤(水蚤、小龙虾和棘叶虫)提供了一个很好的系统，用来测试由于生态、行为和形态上的相似而导致的基因组构成中的共性假说。这是由于该目表现出不同的取食行为、栖息地选择、形态可塑性和世界性分布。很少有其他类群能够拥有如此广泛的栖息地和行为范围，同时在物种数量方面也是可接近的(水蚤n=~700)。尽管如此，我们对不同分布、生态和行为的水蚤物种之间的共同和不同特征知之甚少。这项拟议的研究将通过四个广泛的目标来研究水蚤的进化：(目标1)产生新的基因组水平的测序数据，以证明支持不同特征集的基因组骨架(目标2)通过利用约100个末端的靶捕获序列来推断水蚤的全目系统学假说；(目标3)确定水蚤种类繁多的唾液腺分泌抗凝剂的所有主要家族，以便(I)更好地了解水蚤分泌的蛋白质，(Ii)能够比较吸血和非吸血物种之间的抗凝多样性，(Iii)揭示蛋白质家族扩张的驱动因素，以及(Iv)发现新的抗凝剂；(目的4)对舌管吸虫同系物的大量细菌基因组进行测序，以断言(I)它们的主要功能是否是提供水蚤严格的血液饮食所缺乏的B族维生素，以及(Ii)揭示细菌的进化史。我们将寻找额外的功能，并调查B维生素的产生是否在不同的细菌共生体家族中普遍存在。重要的是，我的研究计划是针对HQP的培训，并且是模块化的，以允许项目的独立性。学生将接受在四大洲(澳大利亚、北美、南美和亚洲)进行的实地工作以及尖端测序技术与下游生物信息学相结合的培训。通过这项研究，HQP将在多种基于实验室和现场工作的技能方面接受全面的生物培训，这将使他们在申请未来职位时处于领先地位。

The overall goal of my research program is to understand evolutionary transitions in behaviour, ecology and morphology, as well as to shed light on the origin and distribution of biological and genetic diversity, topics that are fundamental to the biology and natural history of organisms. To achieve this goal, an understanding of the genomic basis that underlies changes to any of these characteristics is required. This foundation will evince the direction and timing of events and increase our understanding of the genomic units that are responsible for the potential change. Hirudinea (leeches, crayfish worms and acanthobdellids) presents an excellent system in which to test hypotheses of commonalities in genomic makeup due to similarities in ecology, behaviour and morphology. This is due to the diverse set of feeding behaviours, habitat choices, morphological plasticity, and the cosmopolitan distribution that the order exhibits. Few other taxa can boast such wide habitat and behavioural ranges while also being approachable in terms of species numbers (n=~700 for leeches). Despite this, we know very little about the common and divergent features between leech species with separate distributions, ecology and behaviour. The proposed research will investigate the evolution of leeches through four broad objectives: (OBJECTIVE 1) generate new genome-level sequencing data to evince the genomic backbone that supports the diverse set of features (OBJECTIVE 2) infer an order-wide phylogenomic hypothesis for leeches by leveraging target-capture sequences for ~100 terminals; (OBJECTIVE 3) identify all major families of salivary gland-secreted anticoagulants across a broad range of leech diversity, in order to (i) allow for a better understanding of the proteins secreted by leeches, (ii) enable comparisons of anticoagulant diversity between bloodfeeding and non-bloodfeeding species, (iii) expose the drivers of protein family expansions and (iv) uncover new anticoagulants; (OBJECTIVE 4) to sequence numerous bacterial genomes of associates of glossiphoniid leeches to assert (i) whether or not their main function is to provide B vitamins that are otherwise lacking from the leeches' strict diet of blood and (ii) to evince the evolutionary histories of the bacteria. We will search for additional functions and investigate if the production of B vitamins is common throughout the different families of bacterial symbionts. Importantly, my research program is geared towards the training of HQP and is modular to allow for independence in projects. Students will be trained in fieldwork conducted on four continents (Australia, North America, South America and Asia), and in cutting-edge sequencing technologies coupled with downstream bioinformatics. Through this research, HQP will receive a well-rounded state of the art biological training in multiple lab-based and fieldwork skills that will place them at the front of the curve when applying for future positions.