Data from: Evolution and diversity of the Microviridae viral family through a collection of 81 new complete genomes assembled from virome reads.

Recent studies suggest that members of the Microviridae (a family of ssDNA bacteriophages) might play an important role in a broad spectrum of environments, as they were found dominant among the viral fraction from seawater and human gut samples. 24 completely sequenced Microviridae have been described so far, divided into three distinct groups named Microvirus, Gokushovirinae and Alpavirinae, this last group being only composed of prophages. In this study, we present the analysis of 81 new complete Microviridae genomes, assembled from viral metagenomes originating from various ecosystems. The phylogenetic analysis of the core genes concludes to the existence of four groups, confirming the three sub-families described so far and exhibiting a new group, named Pichovirinae. The genomic organizations of these viruses are strikingly coherent with their phylogeny, the Pichovirinae being the only group of this family with a different organization of the three core genes. Analysis of the structure of the major capsid protein reveals the presence of mushroom-like insertions conserved within all the groups except for the Microvirus. In addition, a peptidase gene was found in 11 Microviridae and its analysis concludes to a horizontal gene transfer that occurred several times between these viruses and their bacterial hosts. This is the first report of such gene transfer in microviruses. Finally, searches against viral metagenomes revealed the presence of highly similar sequences in a variety of biomes indicating that Microviridae probably have both an important role in these ecosystems and an ancient origin.

近期研究表明，微小噬菌体科（Microviridae，一类单链DNA（ssDNA）噬菌体）的成员可能在多种环境中发挥重要作用，此前研究在海水与人体肠道样本的病毒组分中鉴定到该类群为优势类群。截至目前，已有24条完成测序的微小噬菌体科基因组被报道，它们被划分为三个明确的类群：微病毒属（Microvirus）、极细微病毒亚科（Gokushovirinae）和阿尔帕病毒亚科（Alpavirinae），其中最后一个类群仅由前噬菌体组成。本研究对81条全新的完整微小噬菌体科基因组进行了分析，这些基因组均从不同生态系统来源的病毒宏基因组中组装得到。对核心基因的系统发育分析结果显示，该科可划分为四个类群：既验证了此前报道的三个亚科，同时新增了一个名为皮乔病毒亚科（Pichovirinae）的类群。这些病毒的基因组组织结构与其系统发育关系高度契合，其中皮乔病毒亚科是该科中唯一拥有与其他类群不同的三个核心基因排布方式的类群。对主要衣壳蛋白结构的分析显示，除微病毒属外，其余所有类群均保守存在一类蘑菇状插入序列。此外，在11条微小噬菌体科基因组中发现了肽酶基因，分析表明该基因曾多次在这些病毒与其细菌宿主之间发生水平基因转移，这是首次在微病毒属中报道此类基因转移事件。最后，通过对病毒宏基因组的检索发现，多种生物群系中均存在高度相似的序列，这表明微小噬菌体科不仅在这些生态系统中发挥重要作用，同时拥有古老的演化起源。