Ceratonova shasta is an important myxozoan pathogen affecting the health of salmonid fishes in the Pacific Northwest of North America. Ceratonova shasta exists as a complex of host-specific genotypes, some with low to moderate virulence, and one that causes a profound, lethal infection in susceptible hosts. High throughput sequencing methods are powerful tools for discovering the genetic basis of these host/virulence differences, but deep sequencing of myxozoans has been challenging due to extremely fast molecular evolution of this group, yielding strongly divergent sequences that are difficult to identify, and unavoidable host contamination. We designed and optimized different bioinformatic pipelines to address these challenges. We obtained a unique set of comprehensive, host-free myxozoan RNA-seq data from C. shasta genotypes of varying virulence from different salmonid hosts. Analyses of transcriptome-wide genetic distances and maximum likelihood multigene phylogenies elucidated the evolutionary relationship between lineages and demonstrated the limited resolution of the established Internal Transcribed Spacer marker for C. shasta genotype identification, as this marker fails to differentiate between biologically distinct genotype II lineages from coho salmon and rainbow trout. We further analyzed the data sets based on polymorphisms in two gene groups related to virulence: cell migration and proteolytic enzymes including their inhibitors. The developed single-nucleotide polymorphism-calling pipeline identified polymorphisms between genotypes and demonstrated that variations in both motility and protease genes were associated with different levels of virulence of C. shasta in its salmonid hosts. The prospective use of proteolytic enzymes as promising candidates for targeted interventions against myxozoans in aquaculture is discussed. We developed host-free transcriptomes of a myxozoan model organism from strains that exhibited different degrees of virulence, as a unique source of data that will foster functional gene analyses and serve as a base for the development of potential therapeutics for efficient control of these parasites.

中文翻译：

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鲑鱼寄生虫Ceratonova s​​hasta宿主相关基因型的转录组范围内的比较和毒力基因多态性。

Ceratonova s​​hasta是一种重要的粘虫病原体，影响北美西北太平洋鲑鱼的健康。Ceratonova s​​hasta它以宿主特异性基因型的复杂形式存在，有些具有低至中毒力，并在易感宿主中引起深刻的致命感染。高通量测序方法是发现这些宿主/毒力差异的遗传基础的有力工具，但是由于该类分子的极快分子进化，产生难以鉴定且不可避免的宿主的高度不同的序列，对粘生动物的深度测序一直具有挑战性污染。我们设计和优化了不同的生物信息管道，以应对这些挑战。我们从C. shasta获得了一套独特的，全面的，无宿主的粘虫RNA-seq数据来自不同鲑鱼宿主的毒力不同的基因型。转录组范围内遗传距离和最大似然多基因系统发育的分析阐明了谱系之间的进化关系，并证明已建立的内部转录间隔子标记对C. shasta的分辨率有限基因型鉴定，因为该标记无法区分银大麻哈鱼和虹鳟鱼生物学上不同的基因型II谱系。我们进一步分析了与毒力相关的两个基因组中基于多态性的数据集：细胞迁移和包括其抑制剂的蛋白水解酶。发达的单核苷酸多态性调用管道确定了基因型之间的多态性，并证明了运动性和蛋白酶基因的变异与沙门氏菌的不同毒力水平相关。在它的鲑鱼宿主中。讨论了蛋白水解酶作为水产养殖中对粘虫的靶向干预的有希望的候选物的潜在用途。我们从表现出不同程度毒力的菌株中开发了无黏附动物模型生物的无宿主转录组，以此作为独特的数据来源，将促进功能基因分析，并为开发有效控制这些寄生虫的潜在疗法奠定基础。