A systems biology based approach to functionally annotate and analyse the genome of the fish pathogenic oomycete Saprolegnia parasitica

水霉菌，或卵菌，含有一些最具破坏性的动物和植物病原体，在自然和养殖生态系统中造成巨大的经济和环境破坏。对鱼类最具破坏性的卵菌病原体是寄生水霉（Saprolegnia parasitica）和双枝水霉（Saprolegnia diclina）。这些物种存在于所有淡水栖息地，并代表了水产养殖业的严重问题，据估计，仅这些卵菌就杀死了所有孵化的鲑鱼和卵的10%以上。水霉菌有几个类似真菌的特征，但不是真正的真菌。它们属于一组被称为Strageliles或Heterokonts的生物体，其中还包括金棕色藻类，海带和硅藻。在卵菌的生命周期中发现了几个明确定义的发育阶段，这些阶段在真菌病原体中没有发现，这使得它们独特，现在越来越清楚的是，与其他寄生虫，真菌和细菌病原体相比，它们已经进化出不同的感染策略。菌丝细胞末端形成无性孢子或孢子囊，可释放大量游动孢子。这些游动孢子能够游动，因为它们有两个鞭毛。游动孢子一旦形成细胞壁，就能萌发并产生侵染菌丝。这些菌丝可以感染鱼的皮肤和皮下组织。最初，头部或鳍被感染，后来水霉菌能够蔓延到身体的整个表面。疾病的特点是外部，棉花样外观与新月形或螺纹图案。水霉能够引起细胞坏死以及真皮和表皮损伤。感染似乎不是组织特异性的。菌丝还可以渗透到受感染鱼类的肌肉和血管中。在某些情况下，感染发生得非常迅速，鱼中的炎症反应似乎不存在。这使得一些研究人员认为S。寄生虫能够抑制鱼类的免疫反应。在目前的提案中，我们将进行实验，帮助我们了解这组生物体如何引起疾病。反过来，这将使我们能够开发新的可持续控制疾病的方法。为了在分子水平上分析疾病过程，必须首先确定病原体所有基因的编码区。然后，我们可以使用计算机来识别可能参与入侵鱼类的基因，并进行实验，看看相应的基因产物（蛋白质）有什么作用。此外，我们将利用这些信息来研究相关生物体中的相同基因是否被用来攻击动物和植物。然后，我们将研究哪些基因对感染很重要，通过研究它们在病原体的发育和感染周期中何时被打开。

Watermoulds, or oomycetes, contain some of the most devastating pathogens of animals and plants, causing enormous economic and environmental damage in natural and cultured ecosystems. The most destructive oomycete pathogens on fish are Saprolegnia parasitica and Saprolegnia diclina. These species are present in all fresh water habitats and represent a serious problem for the aquaculture industry, where it has been estimated that these oomycetes alone, kill over 10% of all hatched salmon and eggs. Watermoulds have several fungus-like characteristics but are not 'true fungi'. They belong to a group of organisms called the Stramenopiles or Heterokonts, which also include the golden-brown algae, kelp, and diatoms. Several clearly defined developmental stages are found in the life cycle of oomycetes that are not found in fungal pathogens, which makes them unique and it is becoming clear now that they have evolved different infection strategies compared to other parasites, fungal and bacterial pathogens. The asexual spore or sporangium is formed at the end of hyphal cells and can release many zoospores. These zoospores are able to swim as they have two flagella. Once the zoospore has produced a cell wall, it can germinate and produce infection hyphae. These hyphae can infect the skin and underlying tissue of the fish. Initially the head or the fins become infected and later the watermould is able to spread over the entire surface of the body. Disease is characterised by an external, cotton-like appearance with crescent-shaped or whorled patterns. Saprolegnia is able to cause cellular necrosis as well as dermal and epidermal damage. Infections do not appear to be tissue specific. Hyphae can also penetrate into the muscle and blood vessels of infected fish. In some cases infection takes place very rapidly and inflammatory responses in the fish appear to be absent. This has led several researchers to believe that S. parasitica is able to suppress the immune response in fish. In the current proposal, we will perform experiments that will help us to understand how this group of organisms cause disease. This in return will allow us to develop new sustainable ways of controling the disease. In order to analyse disease processes at the molecular level, it is necessary to first determine the coding regions of all genes of the pathogen. We can then use computers to identify genes likely to be involved in invading the fish and carry out experiments to see what the corresponding gene products (proteins) do. Furthermore we will use this information to see if the same genes in related organisms are used to attack both animals and plants. We will then investigate which genes are important for infection by studying when they are switched on during the development and infection cycles of the pathogen.