Virophage discovery pipeline. (A) MCP amino acid sequences from reference isolated genomes and published metagenomic contigs were queried against the IMG/VR database with stringent e value cutoffs. All homologous sequences detected were then clustered together to build four independent MCP profiles. (B) The resulting four MCP models were used to recruit additional homologous sequences from the entire IMG/M system. All new sequences were clustered, and models were built creating a final set of 15 unique MCP HMMs. (C) These 15 unique MCP HMMs were then used to search two different databases for homologous sequences: the IMG/M system and a custom assembled human gut database containing 3771 samples from NCBI’s Sequence Read Archive (SRA). (D) The resulting set of 28,294 non-redundant (NR) sequences with stringent e value cutoffs was filtered by size and (E) by the presence of the four core virophage genes (high-quality genomes; HQ virophages). Finally, completeness of novel metagenomic virophage genomes wsa predicted based on circularity or presence of inverted terminal repeats (ITR). (Figure from Paez-Espino et al. Microbiome (2019) 7:157 https://doi.org/10.1186/s40168-019-0768-5)
Virophages are small viruses with double-stranded DNA genomes that co-infect eukaryotic cells along with giant viruses. Almost all known virophage genomes share only four genes in common: major and minor capsid proteins (MCP and mCP, respectively), ATPase involved in DNA packaging, and PRO, a cysteine protease involved in capsid maturation.
Recently reported in Microbiome, researchers from the US Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science facility, have increased the number of known high quality virophage genome sequences 10-fold through computational approaches. By mining more than 14,000 publicly available metagenomic datasets in JGI’s Integrated Microbial Genomes & Microbiomes (IMG/M) data suite—which includes IMG/VR (for Virus)—for the virophage marker gene MCP, they were able to identify 44,221 total virophage partial sequences, including over 28,000 unique MCP sequences.
Further analysis led to the identification of 328 “high quality” (based on completeness) diverse new virophage genomes containing all four core genes. These virophages were found in diverse habitats including the air, plant rhizosphere, wastewater, and even animal and human (for the first time) gut and taxonomically classified into 27 distinct clades (17 of them without previously known representatives). Of these, 89 contigs were considered to be complete genomes, and their discovery has extended the possible virophage genome size range from 13.8-29.3 kilobases (Kb) to 10.9-42.3 Kb. Additionally, the gene counts have similarly gone up from 13-25 to 12-39. “Overall,” the team concluded, “we provide a global analysis of the diversity, distribution, and evolution of virophages.”
Lead author David Paez-Espino discussed an early version of the paper at the 2018 Viral EcoGenomics & Applications (VEGA) Symposium. Early-bird registration rates currently apply for the 2020 VEGA Symposium, which immediately precedes the 15th Annual JGI Genomics of Energy & Environment Meeting! Register now at https://usermeeting.jgi.doe.gov/vega!
The work also used resources of the National Energy Research Scientific Computing Center (NERSC), which is supported by the Office of Science of the U.S. Department of Energy.
Publication:
- Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC. Diversity, evolution, and classification of virophages uncovered through global metagenomics. Microbiome. 2019 Dec 10;7(1):157. doi: 10.1186/s40168-019-0768-5.
Related Links:
- David Paez-Espino at the 2018 VEGA Symposium: http://bit.ly/JGI2018PaezEspino2VEGA
- VEGA Symposium at the 15th Annual JGI Genomics of Energy & Environment Meeting
- JGI 2017 News Release: Tracking the Viral Parasites of Giant Viruses over Time