Diversity of Virophages in Metagenomic Data Sets

Zhou, Jizhong; Zhang, Weijia; Yan, Shuling; Xiao, Jinzhou; Zhang, Yuanyuan; Li, Bailin; Pan, Yingjie; Wang, Yongjie

doi:10.1128/jvi.03398-12

Cited by 91 publications

(145 citation statements)

References 24 publications

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“…Three complete novel virophage genomes (YSLVs 5 to 7) are presented here and can now be added to the four complete virophage genomes (YSLVs 1 to 4) previously described (6). This was enabled by de novo PCR efforts using virophage-specific PCR primer sets with lake DNA from specific photic-zone samples that were found to contain these novel virophages.…”

Section: Discussionmentioning

confidence: 99%

“…Thus far, five conserved core genes have been detected in all known virophages, including a putative DNA helicase (HEL), packaging ATPase (ATPase), cysteine protease (PRO), major capsid protein (MCP), and minor capsid protein (mCP) (6,20). They were also identified in YSLVs 5 to 7 through BLASTp and PSI-BLAST analyses (see Data Set S1 in the supplemental material).…”

Section: Abundances and Distribution Of Yslvs In Different Yellowstonementioning

confidence: 99%

“…The fourth reported virophage, almost identical to Sputnik and named Sputnik 2, was associated with contact lens fluid of an individual with keratitis (4,5). In 2012, we obtained four complete virophage genomes (Yellowstone Lake Lake virophage 1 [YSLV1] to YSLV4) from Yellowstone Lake and one nearly complete genome (ALM) from Ace Lake in Antarctica (6). In 2014, a virophage named Zamilon was reported to be associated with a Mimiviridae host and closely related to Sputnik (7).…”

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confidence: 99%

“…Yellowstone Lake occupies a dominant space in Yellowstone National Park, USA, and thus far the largest number of distinct virophages were discovered from this lake ecosystem (6). In a major metagenomic survey of this lake, samples were taken at three general different locations, representing the northern region which is rich in lake floor hydrothermal vent activity (9)(10)(11), the West Thumb region where additional lake floor vents occur but that differ in chemistry relative to the northern lake vents (9,12), and the Southeast Arm region of the lake where as yet there is no known lake floor geothermal activity.…”

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confidence: 99%

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Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes

Zhou

Sun

Childers

et al. 2015

J Virol

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Virophages are a unique group of circular double-stranded DNA viruses that are considered parasites of giant DNA viruses, which in turn are known to infect eukaryotic hosts. In this study, the genomes of three novel Yellowstone Lake virophages (YSLVs)-YSLV5, YSLV6, and YSLV7-were identified from Yellowstone Lake through metagenomic analyses. The relative abundance of these three novel virophages and previously identified Yellowstone Lake virophages YSLV1 to -4 were determined in different locations of the lake, revealing that most of the sampled locations in the lake, including both mesophilic and thermophilic habitats, had multiple virophage genotypes. This likely reflects the diverse habitats or diversity of the eukaryotic hosts and their associated giant viruses that serve as putative hosts for these virophages. YSLV5 has a 29,767-bp genome with 32 predicted open reading frames (ORFs), YSLV6 has a 24,837-bp genome with 29 predicted ORFs, and YSLV7 has a 23,193-bp genome with 26 predicted ORFs. Based on multilocus phylogenetic analysis, YSLV6 shows a close evolutionary relationship with YSLV1 to -4, whereas YSLV5 and YSLV7 are distantly related to the others, and YSLV7 represents the fourth novel virophage lineage. In addition, the genome of YSLV5 has a G؉C content of 51.1% that is much higher than all other known virophages, indicating a unique host range for YSLV5. These results suggest that virophages are abundant and have diverse genotypes that likely mirror diverse giant viral and eukaryotic hosts within the Yellowstone Lake ecosystem. IMPORTANCEThis study discovered novel virophages present within the Yellowstone Lake ecosystem using a conserved major capsid protein as a phylogenetic anchor for assembly of sequence reads from Yellowstone Lake metagenomic samples. The three novel virophage genomes (YSLV5 to -7) were completed by identifying specific environmental samples containing these respective virophages, and closing gaps by targeted PCR and sequencing. Most of the YSLV genotypes were associated primarily with photiczone and nonhydrothermal samples; however, YSLV5 had a unique distribution with an occurrence in vent samples similar to that in photic-zone samples and with a higher GC content that suggests a distinct host and habitat compared to other YSLVs. In addition, genome content and phylogenetic analyses indicate that YSLV5 and YSLV7 are distinct from known virophages and that additional as-yet-uncharacterized virophages are likely present within the Yellowstone Lake ecosystem.

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Section: Discussionmentioning

confidence: 99%

Section: Abundances and Distribution Of Yslvs In Different Yellowstonementioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes

Zhou

Sun

Childers

et al. 2015

J Virol

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101

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“…However, these sequenced viruses lack information about their hosts and other biological properties that would guide their assignment into species and genera in the family 10 . Indeed, vast numbers of complete, or nearly complete, genome sequences have been assembled and characterized from metagenomic data for viruses with small [11][12][13][14] , medium [15][16][17][18] and even large 19,20 genomes. The identification of entirely new groups of viruses from such analyses emphasizes the power of metagenomic approaches in discovering viruses, some of which could have key functions in the regulation of ecosystems, whereas others could coexist with their hosts without causing recognizable disease or may even be mutualists 7 .…”

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confidence: 99%

Virus taxonomy in the age of metagenomics

et al. 2017

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| The number and diversity of viral sequences that are identified in metagenomic data far exceeds that of experimentally characterized virus isolates. In a recent workshop, a panel of experts discussed the proposal that, with appropriate quality control, viruses that are known only from metagenomic data can, and should be, incorporated into the official classification scheme of the International Committee on Taxonomy of Viruses (ICTV). Although a taxonomy that is based on metagenomic sequence data alone represents a substantial departure from the traditional reliance on phenotypic properties, the development of a robust framework for sequence-based virus taxonomy is indispensable for the comprehensive characterization of the global virome. In this Consensus Statement article, we consider the rationale for why metagenomic sequence data should, and how it can, be incorporated into the ICTV taxonomy, and present proposals that have been endorsed by the Executive Committee of the ICTV. NATURE REVIEWS | MICROBIOLOGY VOLUME 15 | MARCH 2017 | 161 CONSENSUS STATEMENT © 2 0 1 7 M a c m i l l a n P u b l i s h e r s L i m i t e d , p a r t o f S p r i n g e r N a t u r e . A l l r i g h t s r e s e r v e d .

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