Willemsen Anouk, Manzano-Marín Alejandro, Horn Matthias
Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, University of Vienna, Vienna 1030, Austria.
Genome Biol Evol. 2025 Jan 6;17(1). doi: 10.1093/gbe/evae271.
The need for high-quality protist genomes has prevented in-depth computational and experimental studies of giant virus-host interactions. In addition, our current knowledge of host range is highly biased due to the few hosts used to isolate novel giant viruses. This study presents 6 high-quality amoeba genomes from known and potential giant virus hosts belonging to 2 distinct eukaryotic clades: Amoebozoa and Discoba. We employ their genomic data to investigate the predictability of giant virus host range. Using a combination of long- and short-read sequencing, we obtained highly contiguous and complete genomes of Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba terricola, Naegleria clarki, Vermamoeba vermiformis, and Willaertia magna, contributing to the collection of sequences for the eukaryotic tree of life. We found that the 6 amoebae have distinct codon usage patterns and that, contrary to other virus groups, giant viruses often have different and even opposite codon usage with their known hosts. Conversely, giant viruses with matching codon usage are frequently not known to infect or replicate in these hosts. Interestingly, analyses of integrated viral sequences in the amoeba host genomes reveal potential novel virus-host associations. Matching of codon usage preferences is often used to predict virus-host pairs. However, with the broad-scale analyses performed in this study, we demonstrate that codon usage alone appears to be a poor predictor of host range for giant viruses infecting amoeba. We discuss the potential strategies that giant viruses employ to ensure high viral fitness in nonmatching hosts. Moreover, this study emphasizes the need for more high-quality protist genomes. Finally, the amoeba genomes presented in this study set the stage for future experimental studies to better understand how giant viruses interact with different host species.
对高质量原生生物基因组的需求阻碍了对巨型病毒与宿主相互作用的深入计算和实验研究。此外，由于用于分离新型巨型病毒的宿主较少，我们目前对宿主范围的了解存在很大偏差。本研究展示了来自已知和潜在巨型病毒宿主的6个高质量变形虫基因组，这些宿主属于两个不同的真核生物进化枝：变形虫门和双鞭毛虫门。我们利用它们的基因组数据来研究巨型病毒宿主范围的可预测性。通过结合长读长和短读长测序，我们获得了卡氏棘阿米巴、格里芬棘阿米巴、土栖棘阿米巴、克拉克内格里亚虫、蠕虫形变形虫和大型维拉尔特虫的高度连续和完整的基因组，为真核生物生命树的序列收集做出了贡献。我们发现这6种变形虫具有不同的密码子使用模式，并且与其他病毒群体相反，巨型病毒与其已知宿主的密码子使用往往不同甚至相反。相反，密码子使用匹配的巨型病毒通常不被认为会在这些宿主中感染或复制。有趣的是，对变形虫宿主基因组中整合病毒序列的分析揭示了潜在的新型病毒-宿主关联。密码子使用偏好的匹配通常用于预测病毒-宿主对。然而，通过本研究进行的大规模分析，我们证明仅密码子使用似乎是预测感染变形虫的巨型病毒宿主范围的一个较差指标。我们讨论了巨型病毒为确保在不匹配宿主中的高病毒适应性而采用的潜在策略。此外，本研究强调了对更多高质量原生生物基因组的需求。最后，本研究中展示的变形虫基因组为未来的实验研究奠定了基础，以便更好地理解巨型病毒如何与不同宿主物种相互作用。
