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, 10 (5), 803-16

Snapshot of Haloarchaeal Tailed Virus Genomes

Affiliations

Snapshot of Haloarchaeal Tailed Virus Genomes

Ana Senčilo et al. RNA Biol.

Abstract

The complete genome sequences of archaeal tailed viruses are currently highly underrepresented in sequence databases. Here, we report the genomic sequences of 10 new tailed viruses infecting different haloarchaeal hosts. Among these, only two viral genomes are closely related to each other and to previously described haloviruses HF1 and HF2. The approximately 760 kb of new genomic sequences in total shows no matches to CRISPR/Cas spacer sequences in haloarchaeal host genomes. Despite their high divergence, we were able to identify virion structural and assembly genes as well as genes coding for DNA and RNA metabolic functions. Interestingly, we identified many genes and genomic features that are shared with tailed bacteriophages, consistent with the hypothesis that haloarchaeal and bacterial tailed viruses share common ancestry, and that a viral lineage containing archaeal viruses, bacteriophages and eukaryotic viruses predates the division of the three major domains of non-viral life. However, as in tailed viruses in general and in haloarchaeal tailed viruses in particular, there are still a considerable number of predicted genes of unknown function.

Keywords: Archaea; bacteriophage; genome; haloarchaea; sequence; tailed virus; virus.

Figures

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Figure 1. Nucleotide sequence comparison of the studied haloarchaeal tailed viruses and earlier described haloviruses HF1 and HF2, represented by a dot plot. The dot plot of concatenated viral nucleotide sequences was generated in Gepard.
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Figure 3. Genome maps of HRTV-5, HRTV-7, HRTV-8, HF1 and HF2. Nucleotide sequence similarity is depicted by shading between the pairs of the genomes according to color spectrum with purple representing the highest identity. Pham and the number of the pham members are outlined above each ORF. TerL, terminase large subunit; RnR, ribonucleotide reductase; Thy, thymidylate.
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Figure 5. Genome maps of HCTV-2 and HHTV-2. Nucleotide sequence similarity is depicted by shading as in Figure 3. Pham and the number of the pham members are outlined above each ORF. TerL, terminase large subunit; AdoMet-MTase, S-adenosylmethionine-dependent methyltransferase; SNase, Staphylococcal nuclease; HJR, Holliday junction resolvase.
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Figure 2. The relationships between the studied haloarchaeal tailed viruses and haloviruses HF1 and HF2, based on their genome contents. The tree was constructed according to the number of phams shared between the different viruses and depicted using SplitsTree program.
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Figure 4. Genome maps of HCTV-1 and HCTV-5. Nucleotide sequence similarity is depicted by shading as in Figure 3. Pham and the number of the pham members are outlined above each ORF. RnR, ribonucleotide reductase; Thy, thymidylate; AdoMet-MTase, S-adenosylmethionine-dependent methyltransferase; RFC, replication factor C; TMP, thymidine monophosphate; TerL, terminase large subunit.
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Figure 6. Conserved nucleotides of aligned HGTV-1 repeats. The repeats are found approximately 60 bp upstream of some HGTV-1 genes. Exact positions of the repeats in HGTV-1 genome and their alignment can be found in Supplemental Material (Fig. S10). WebLogo was used to generate a graph out of the repeats alignment. The conservation of the nucleotides at individual positions is measured in bits. The TATA box-like and inverted repeat sequences found within the HGTV-1 repeats are underlined and indicated below the sequence logo.
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Figure 7. Alignment of the putative Cas4 homologs of haloarchaeal tailed viruses and Haloquadratum walsbyi C23. Accession numbers of the proteins are: YP_005839106.1 (Hqr.walsbyi_Cas4), NP_861634 (HF1_HalHV1gp046), NP_542546 (HF2p052). Cysteine residues predicted to coordinate FeS center are marked in yellow. Putative nuclease active site residues are marked in grey.

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