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. 2023 Dec 11;13(12):1773.
doi: 10.3390/biom13121773.

Virophages Found in Viromes from Lake Baikal

Sergey Anatoljevich Potapov  1 , Olga Ivanovna Belykh  1
Affiliations

Virophages Found in Viromes from Lake Baikal

Sergey Anatoljevich Potapov et al. Biomolecules. .

Abstract

In this study, a previously little-studied group of viruses-virophages-was searched for and identified in the viromes of the ancient oligotrophic Lake Baikal. Virophages are small dsDNA viruses that parasitize giant viruses (e.g., Mimiviridae), which in turn affect unicellular eukaryotes. We analyzed eight viromes obtained from the deep-water areas of three basins of Lake Baikal and the shallow-water strait Maloye More in different seasons. The sequences of virophages were revealed in all viromes and were dominant after bacteriophages and algal viruses. Sixteen putative complete genomes of virophages were assembled, all of which contained four conserved genes encoding major capsid protein (MCP), minor capsid protein (mCP), maturation cysteine protease (PRO), and FtsK-HerA family DNA-packaging ATPase (ATPase). The MCP-based cluster analysis showed a sequence separation according to seasons, and a dependence on the geographical localization was not detected.

Keywords: Lake Baikal; biodiversity; high-throughput sequencing; virophages; viruses.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Taxonomic representation of viral ORFs at the level of families detected in Lake Baikal according to the NCBI NR database, blastp (e-value 10−5). Virophages are in bold. Others—less than 1%.
Figure 2
Figure 2
Virophage clades based on MCP phylogeny. Best-fit model according to BIC: LG + F + R8.
Figure 3
Figure 3
Cluster dendrogram with p-value (%) based on 294 MCP proteins. AU (Approximately Unbiased) p-value, BP (Bootstrap Probability) value.
Figure 4
Figure 4
Unrooted maximum likelihood trees based on four core proteins. Supports in the nodes are indicated as over 80%. Sequences obtained from putative complete virophage genomes in this study are shown in bold. LBV—Lake Baikal virophage, DSLV—Dishui Lake virophage, YSLV—Yellowstone Lake virophage, OLV—Organic Lake virophage, RV—rumen virophage, ALM—Ace Lake Mavirus, Spezl—Maverick-related virus strain Spezl, QLM—Qinghai Lake virophage.
Figure 5
Figure 5
Genome maps of putative complete/near complete genomes of virophages identified in Lake Baikal viromes. Arrows indicate ORFs, direction indicates synthesis with + or—chains. The arrows below represent ORFs with overlapping reading frames.
Figure 6
Figure 6
Proteomic tree constructed with the online service VipTree. Black branches show the closest relatives; red branches are from this study. For sequences from Lake Baikal, the sample to which the genome corresponds is given in parentheses; for the closest relatives, the accession number is given.
Figure 7
Figure 7
Mapping of reads to 16 putative virophage genomes. The number of aligned reads was normalized. Value—the number of reads. The blue circles show from the reads of which sample the genome was assembled.
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