Gene duplications and novel genes have been shown to play a major role in helminth adaptation to a parasitic lifestyle because they provide the novelty necessary for adaptation to a changing environment, such as living in multiple hosts. Here we present the de novo sequenced and annotated genome of the parasitic trematode Atriophallophorus winterbourni and its comparative genomic analysis to other major parasitic trematodes. First, we reconstructed the species phylogeny, and dated the split of A. winterbourni from the Opisthorchiata suborder to approximately 237.4 Ma (±120.4 Myr). We then addressed the question of which expanded gene families and gained genes are potentially involved in adaptation to parasitism. To do this, we used hierarchical orthologous groups to reconstruct three ancestral genomes on the phylogeny leading to A. winterbourni and performed a GO (Gene Ontology) enrichment analysis of the gene composition of each ancestral genome, allowing us to characterize the subsequent genomic changes. Out of the 11,499 genes in the A. winterbourni genome, as much as 24% have arisen through duplication events since the speciation of A. winterbourni from the Opisthorchiata, and as much as 31.9% appear to be novel, that is, newly acquired. We found 13 gene families in A. winterbourni to have had more than ten genes arising through these recent duplications; all of which have functions potentially relating to host behavioral manipulation, host tissue penetration, and hiding from host immunity through antigen presentation. We identified several families with genes evolving under positive selection. Our results provide a valuable resource for future studies on the genomic basis of adaptation to parasitism and point to specific candidate genes putatively involved in antagonistic host–parasite adaptation.

中文翻译：

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吸虫的基因复制和增益有助于适应寄生


基因重复和新基因已被证明在蠕虫适应寄生生活方式方面发挥着重要作用，因为它们提供了适应不断变化的环境（例如生活在多个宿主中）所需的新颖性。在这里，我们展示了寄生吸虫 Atriophallophorus Winterbourni 的从头测序和注释基因组及其与其他主要寄生吸虫的比较基因组分析。首先，我们重建了该物种的系统发育，并将 A. Winterbourni 从 Opisthorchiata 亚目中分裂的年代确定为大约 237.4 Ma（±120.4 Myr）。然后我们解决了哪些扩展的基因家族和获得的基因可能参与适应寄生的问题。为此，我们使用分层直系同源群在导致 A. Winterbourni 的系统发育上重建了三个祖先基因组，并对每个祖先基因组的基因组成进行了 GO（基因本体论）富集分析，使我们能够表征随后的基因组变化。在 A. Winterbourni 基因组中的 11,499 个基因中，多达 24% 是自 Opisthorchiata 的 A. Winterbourni 物种形成以来通过重复事件产生的，多达 31.9% 似乎是新的，即新获得的。我们发现 A. Winterbourni 中的 13 个基因家族有超过 10 个基因是通过这些最近的复制而产生的；所有这些都具有与宿主行为操纵、宿主组织渗透以及通过抗原呈递隐藏宿主免疫相关的潜在功能。我们鉴定了几个基因在正选择下进化的家族。 我们的结果为未来关于适应寄生的基因组基础的研究提供了宝贵的资源，并指出了可能参与拮抗宿主-寄生虫适应的特定候选基因。