IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

Páez-Espino, David; Chen, I. Min A.; Palaniappan, Krishna; Ratner, Anna; Chu, Ken; Szeto, Ernest; Pillay, Manoj; Huang, Jinghua; Markowitz, Victor; Nielsen, Torben; Huntemann, Marcel; Reddy, T. B. K.; Pavlopoulos, Georgios A.; Sullivan, Matthew B.; Campbell, Barbara J.; Chen, Feng; McMahon, Katherine D.; Hallam, Steve; Denef, Vincent J.; Cavicchioli, Ricardo; Caffrey, Sean; Streit, Wolfgang R.; Webster, J; Handley, Kim M.; Salekdeh, Ghasem Hosseini; Tsesmetzis, Nicolas; Setúbal, João Carlos; Pope, Phillip B.; Liu, Wen Tso; Rivers, Adam R.; Ivanova, Natalia; Kyrpides, Nikos C.

doi:10.1093/nar/gkw1030

Cited by 181 publications

(200 citation statements)

References 33 publications

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“…In accordance with recent research efforts to elucidate the role of the rumen virome, a significant portion of the RUS-refDB proteins (switchgrass: 56; rumen fluid: 62) were assigned to the 913 viral scaffolds we recovered from our switchgrass-associated rumen metagenome 31,56 . Recent studies have demonstrated that some viruses contribute to polysaccharide degradation directly, as they encode glycoside hydrolases 57 , or indirectly through infection of carbohydrate-degrading microorganisms 5 .…”

Section: Virome Activity In Ruminant Biomass-degradationmentioning

confidence: 86%

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Hagen

Brooke

Shaw

et al. 2020

Preprint

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The rumen harbors a complex microbial mixture of archaea, bacteria, protozoa and fungi that efficiently breakdown plant biomass and its complex dietary carbohydrates into soluble sugars that can be fermented and subsequently converted into metabolites and nutrients utilized by the host animal. While rumen bacterial populations have been well documented, only a fraction of the rumen eukarya are taxonomically and functionally characterized, despite the recognition that they contribute to the cellulolytic phenotype of the rumen microbiota. To investigate how anaerobic fungi actively engage in digestion of recalcitrant fiber that is resistant to degradation, we resolved genome-centric metaproteome and metatranscriptome datasets generated from switchgrass samples incubated for 48 hours in nylon bags within the rumen of cannulated dairy cows. Across a gene catalogue covering anaerobic rumen bacteria, fungi and viruses, a significant portion of the detected proteins originated from fungal populations. Intriguingly, the carbohydrate-active enzyme (CAZyme) profile suggested a domain-specific functional specialization, with bacterial populations primarily engaged in the degradation of polysaccharides such as hemicellulose, whereas fungi were inferred to target recalcitrant cellulose structures via the detection of a number of endo-and exo-acting enzymes belonging to the glycoside hydrolase (GH) family 5, 6, 8 and 48. Notably, members of the GH48 family were amongst the highest abundant CAZymes and detected representatives from this family also included dockerin domains that are associated with fungal cellulosomes. A eukaryoteselected metatranscriptome further reinforced the contribution of uncultured fungi in the ruminal degradation of recalcitrant fibers. These findings elucidate the intricate networks of in situ recalcitrant fiber deconstruction, and importantly, suggests that the anaerobic rumen fungi contribute a specific set of CAZymes that complement the enzyme repertoire provided by the specialized plant cell wall degrading rumen bacteria.

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Section: Virome Activity In Ruminant Biomass-degradationmentioning

confidence: 86%

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Hagen

Brooke

Shaw

et al. 2020

Preprint

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“…The same study reported a circularized genome of 630 kbp in length, but this is an assembly artifact (SI and Figure S3 ). The problem of concatenated sequences was sufficiently prominent in IMG/VR (PaezEspino et al , 2017) that we did not include these data in further analyses. We used the complete and circularized genomes from our study and published phage genomes to depict a current view of the distribution of phage genome sizes (Methods).…”

Section: Genome Sizes and Basic Featuresmentioning

confidence: 99%

Clades of huge phage from across Earth’s ecosystems

Al-Shayeb

Sachdeva

Chen

et al. 2019

Preprint

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Phage typically have small genomes and depend on their bacterial hosts for replication. DNA sequenced from many diverse ecosystems revealed hundreds of huge phage genomes, between 200 kbp and 716 kbp in length. Thirtyfour genomes were manually curated to completion, including the largest phage genomes yet reported. Expanded genetic repertoires include diverse and new CRISPRCas systems, tRNAs, tRNA synthetases, tRNA modification enzymes, translation initiation and elongation factors, and ribosomal proteins. Phage CRISPRCas systems have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phageencoded functions. In addition, some phage may repurpose bacterial CRISPRCas systems to eliminate competing phage. We phylogenetically define major clades of huge phage from human and other animal microbiomes, oceans, lakes, sediments, soils and the built environment. We conclude that their large gene inventories reflect a conserved biological strategy, observed over a broad bacterial host range and across Earth's ecosystems.

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“…To determine if the Gossenköllesee PLVs were unique to high mountain lakes, or part of a globally dispersed group of viruses, we interrogated large metagenomic datasets using the novel MCP genes as bait. The complete IMG/VR protein dataset 38 40 . To enhance hits for matching viruses from these viromes, we downloaded all trimmed metagenomic reads from these two BioProjects from the European Bioinformatics Institute (EMBL-EBI; https://www.ebi.ac.uk/), re-assembled each individual metagenome and cross assembled 3 metagenomes (PRJEB19373) using SPAdes (settings: --meta -k 21,33,53,77).…”

Section: Public Metagenome Searchesmentioning

confidence: 99%

Polinton-like viruses and virophages are widespread in aquatic ecosystems

Sommaruga

2019

Preprint

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Polintons are virus-like transposable elements found in the genomes of eukaryotes that are considered the ancient ancestors of most eukaryotic dsDNA viruses 1,2 . Recently, a number of Polinton-Like Viruses (PLVs) have been discovered in algal genomes and environmental metagenomes 3 , which share characteristics and core genes with both Polintons and virophages (Lavidaviridae) 4 . These viruses could be the first members of a major class of ancient eukaryotic viruses, however, only a few complete genomes are known and it is unclear whether most are free viruses or are integrated algal elements 3 . Here we show that PLVs form an expansive network of globally distributed viruses, associated with a range of eukaryotic hosts. We identified PLVs as amongst the most abundant individual viruses present in a freshwater lake virus metagenome (virome), showing they are hundreds of times more abundant in the virus size fraction than in the microbial one. Using the major capsid protein genes as bait, we retrieved hundreds of related viruses from publicly available datasets. A network-based analysis of 976 new PLV and virophage genomes combined with 64 previously known genomes revealed that they represent at least 61 distinct viral clusters, with some PLV members associated with fungi, oomycetes and algae. Our data reveals that PLVs are widespread in predominantly freshwater environments and together with virophages, represent a broad group of eukaryotic viruses which share a number of genes.

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IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses

Cited by 181 publications

References 33 publications

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Proteome specialization of anaerobic fungi during ruminal degradation of recalcitrant plant fiber

Clades of huge phage from across Earth’s ecosystems

Polinton-like viruses and virophages are widespread in aquatic ecosystems

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