Olo Ndela Eric, Roux Simon, Henke Christian, Sczyrba Alexander, Sime Ngando Télesphore, Varsani Arvind, Enault François
Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, Clermont-Ferrand F-63000, France.
DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Virus Evol. 2022 Dec 23;9(1):veac123. doi: 10.1093/ve/veac123. eCollection 2023.
Small circular single-stranded DNA viruses of the family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, , has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics data sets from various aquatic ecosystems, of sixteen complete microvirus genomes significantly smaller (2.991-3.692 kb) than known ones. Phylogenetic analysis reveals that these sixteen genomes represent two related, yet distinct and diverse, novel groups of microviruses- being their closest known relatives. We propose that these small microviruses are members of two tentatively named subfamilies and . As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction software, we developed a new methodology to identify all genes based on protein conservation, amino acid composition, and selection pressure estimations. Surprisingly, only four to five genes could be identified per genome, with the number of overprinted genes lower than that in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small number of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and are further evidence that these viruses have explored a wide range of possibilities during their long evolution.
该科的小型环状单链DNA病毒在所有生态系统中既普遍又多样。它们通常拥有4.3至6.3 kb的基因组，最近从海洋α-变形菌中分离出的一种微小病毒是已知最小的DNA噬菌体基因组（4.248 kb）。已提出一个亚科来对这种病毒和其他相关的感染α-变形菌的小型噬菌体进行分类。在此，我们报告在来自各种水生生态系统的宏组学数据集中发现了16个完整的微小病毒基因组，其明显小于已知基因组（2.991 - 3.692 kb）。系统发育分析表明，这16个基因组代表了两个相关但又独特且多样的新型微小病毒组， 是它们已知的最亲近亲属。我们提议将这些小型微小病毒归为两个暂定命名的亚科 和 。由于已知微小病毒基因组编码许多重叠和重叠编码的基因，而这些基因无法通过基因预测软件识别，我们开发了一种基于蛋白质保守性、氨基酸组成和选择压力估计来识别所有基因的新方法。令人惊讶的是，每个基因组只能识别出四到五个基因，重叠编码基因的数量低于φX174中的数量。因此，这些小基因组往往基因数量较少且每个基因的长度较短，没有为可能包含重叠编码基因的可变基因区域留出空间。更令人惊讶的是，这两个 组具有特定且不同的基因内容，以及保守蛋白质序列的主要差异，突出表明这两个相关的小基因组微小病毒组使用非常不同的策略来利用如此少量的基因完成其生命周期。这些基因组的发现以及对其基因组内容的详细预测和注释扩展了我们对自然界中ssDNA噬菌体的理解，并且进一步证明这些病毒在其漫长的进化过程中探索了广泛的可能性。
