Transcriptome-wide comparisons and virulence gene polymorphisms of host-associated genotypes of the cnidarian parasite Ceratonova shasta in salmonids

Ceratonova shasta is an important myxozoan pathogen affecting the health of salmonid fishes in the Pacific Northwest of North America. C. 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 evolutio...

Ceratonova shasta是一种重要的粘孢子虫病原（myxozoan pathogen），可危害北美太平洋西北地区的鲑形目鱼类健康。该病原以宿主特异性基因型复合体形式存在，其中部分基因型的毒力处于低至中等水平，另有一类可使易感宿主产生严重致死性感染。高通量测序（High throughput sequencing）是解析这类宿主与毒力差异遗传基础的有力工具，但由于粘孢子虫类群分子演化速率极快，导致其序列分化程度极高、难以鉴定，且不可避免地伴随宿主污染，因此对该类群进行深度测序颇具挑战。为此，我们设计并优化了多套生物信息学流程（bioinformatic pipelines）以应对上述难题。我们获取了一套独特的无宿主污染的全面粘孢子虫RNA测序（RNA-seq）数据集，样本取自不同鲑形目宿主体内的不同毒力型Ceratonova shasta基因型。通过对全转录组遗传距离及最大似然多基因系统发育树的分析，我们阐明了其演化……