Data_Sheet_1_Genome and Environmental Activity of a Chrysochromulina parva Virus and Its Virophages.PDF

Some giant viruses are ecological agents that are predicted to be involved in the top-down control of single-celled eukaryotic algae populations in aquatic ecosystems. Despite an increased interest in giant viruses since the discovery and characterization of Mimivirus and other viral giants, little is known about their physiology and ecology. In this study, we characterized the genome and functional potential of a giant virus that infects the freshwater haptophyte Chrysochromulina parva, originally isolated from Lake Ontario. This virus, CpV-BQ2, is a member of the nucleo-cytoplasmic large DNA virus (NCLDV) group and possesses a 437 kb genome encoding 503 ORFs with a GC content of 25%. Phylogenetic analyses of core NCLDV genes place CpV-BQ2 amongst the emerging group of algae-infecting Mimiviruses informally referred to as the “extended Mimiviridae,” making it the first virus of this group to be isolated from a freshwater ecosystem. During genome analyses, we also captured and described the genomes of three distinct virophages that co-occurred with CpV-BQ2 and likely exploit CpV for their own replication. These virophages belong to the polinton-like viruses (PLV) group and encompass 19–23 predicted genes, including all of the core PLV genes as well as several genes implicated in genome modifications. We used the CpV-BQ2 and virophage reference sequences to recruit reads from available environmental metatranscriptomic data to estimate their activity in fresh waters. We observed moderate recruitment of both virus and virophage transcripts in samples obtained during Microcystis aeruginosa blooms in Lake Erie and Lake Tai, China in 2013, with a spike in activity in one sample. Virophage transcript abundance for two of the three isolates strongly correlated with that of the CpV-BQ2. Together, the results highlight the importance of giant viruses in the environment and establish a foundation for future research on the physiology and ecology CpV-BQ2 as a model system for algal Mimivirus dynamics in freshwaters.

某些巨型病毒是生态因子，据预测它们参与了对淡水生态系统中单细胞真核藻类种群进行自上而下的控制的进程。尽管自Mimivirus和其他巨型病毒被发现和表征以来，对巨型病毒的兴趣日益增加，但关于它们的生理学和生态学知识仍然有限。在本研究中，我们对一种感染淡水硅藻Chrysochromulina parva的巨型病毒进行了基因组及其功能潜力的表征，该病毒最初从安大略湖中分离出来。这种病毒，CpV-BQ2，属于核质大型DNA病毒（NCLDV）组，具有437 kb的基因组，编码503个开放阅读框，GC含量为25%。核心NCLDV基因的进化分析将CpV-BQ2归类于新兴的藻类感染性Mimiviruses群体，非正式地被称为“扩展的Mimiviridae”，使其成为该组中第一个从淡水生态系统分离的病毒。在基因组分析过程中，我们还捕获并描述了三种与CpV-BQ2共现的独立病毒（virophages）的基因组，这些病毒可能利用CpV进行自身的复制。这些病毒属于多立顿样病毒（PLV）组，包含19-23个预测基因，包括所有核心PLV基因以及一些涉及基因组修饰的基因。我们使用CpV-BQ2和病毒噬菌体参考序列，从可用的环境宏转录组数据中招募读数，以估计它们在淡水中的活性。我们观察到，在2013年中国伊利湖和太湖中微囊藻水华期间获得的样本中，病毒和病毒噬菌体转录本的招募程度适中，其中一个样本的活性显著增加。其中两个独立分离的病毒噬菌体转录本丰度与CpV-BQ2的丰度强烈相关。总之，这些结果突出了巨型病毒在环境中的重要性，并为未来以CpV-BQ2作为淡水藻类Mimivirus动态模型系统的研究奠定了基础。