Distinctive Expansion of Potential Virulence Genes in the Genome of the Oomycete Fish Pathogen <i>Saprolegnia parasitica</i>

Oomycetes in the class Saprolegniomycetidae of the Eukaryotic kingdom Stramenopila have evolved as severe pathogens of amphibians, crustaceans, fish and insects, resulting in major losses in aquaculture and damage to aquatic ecosystems. We have sequenced the 63 Mb genome of the fresh water fish pathogen, Saprolegnia parasitica. Approximately 1/3 of the assembled genome exhibits loss of heterozygosity, indicating an efficient mechanism for revealing new variation. Comparison of S. parasitica with plant pathogenic oomycetes suggests that during evolution the host cellular environment has driven distinct patterns of gene expansion and loss in the genomes of plant and animal pathogens. S. parasitica possesses one of the largest repertoires of proteases (270) among eukaryotes that are deployed in waves at different points during infection as determined from RNA-Seq data. In contrast, despite being capable of living saprotrophically, parasitism has led to loss of inorganic nitrogen and sulfur assimilation pathways, strikingly similar to losses in obligate plant pathogenic oomycetes and fungi. The large gene families that are hallmarks of plant pathogenic oomycetes such as Phytophthora appear to be lacking in S. parasitica, including those encoding RXLR effectors, Crinkler's, and Necrosis Inducing-Like Proteins (NLP). S. parasitica also has a very large kinome of 543 kinases, 10% of which is induced upon infection. Moreover, S. parasitica encodes several genes typical of animals or animal-pathogens and lacking from other oomycetes, including disintegrins and galactose-binding lectins, whose expression and evolutionary origins implicate horizontal gene transfer in the evolution of animal pathogenesis in S. parasitica.隶属于真核生物界不等鞭毛门（Stramenopila）水霉亚纲（Saprolegniomycetidae）的卵菌（Oomycetes）已演化为两栖类、甲壳类、鱼类及昆虫的严重致病菌，给水产养殖业造成重大损失，同时对水生生态系统带来严重破坏。本研究对淡水鱼类致病菌寄生水霉（Saprolegnia parasitica）的63 Mb基因组完成了测序。组装得到的基因组中约有1/3区域表现为杂合性缺失（heterozygosity），提示其存在高效的新变异显现机制。通过比较寄生水霉与植物致病性卵菌的基因组，研究发现演化过程中宿主细胞环境驱动植物与动物致病菌的基因组呈现出截然不同的基因扩张与丢失模式。寄生水霉拥有真核生物中规模最为庞大的蛋白酶组之一（共270种），结合RNA测序（RNA-Seq）数据分析显示，这些蛋白酶会在感染进程的不同阶段以时序性波次的方式被激活表达。与之形成对比的是，尽管寄生水霉具备腐生生活能力，但寄生生活方式使其丢失了无机氮与硫同化途径，这与专性植物致病性卵菌及真菌的相关途径丢失现象极为相似。作为植物致病性卵菌（如疫霉属（Phytophthora））标志性特征的大型基因家族，在寄生水霉中似乎并不存在，其中包括编码RXLR效应子（RXLR effectors）、Crinkler蛋白（Crinkler's）以及坏死诱导样蛋白（Necrosis Inducing-Like Proteins，NLP）的基因家族。此外，寄生水霉拥有一个规模庞大的激酶组（kinome），共计543种激酶，其中10%的激酶会在感染过程中被诱导表达。进一步而言，寄生水霉还编码了若干仅见于动物或动物致病菌、且在其他卵菌中缺失的典型基因，包括解整合素（disintegrins）与半乳糖结合凝集素（galactose-binding lectins）；对这些基因的表达及进化起源的分析表明，水平基因转移（horizontal gene transfer）在寄生水霉动物致病性的演化过程中发挥了关键作用。