Literature DB >> 23896279

The global virome: not as big as we thought?

J Cesar Ignacio-Espinoza1, Sergei A Solonenko, Matthew B Sullivan.   

Abstract

Viruses likely infect all organisms, serving to unknown extent as genetic vectors in complex networks of organisms. Environmental virologists have revealed that these abundant nanoscale entities are global players with critical roles in every ecosystem investigated. Curiously, novel genes dominate viral genomes and metagenomes, which has led to the suggestion that viruses represent the largest reservoir of unexplored genetic material on Earth with literature estimates, extrapolating from 14 mycobacteriophage genomes, suggesting that two billion phage-encoded ORFs remain to be discovered. Here we examine (meta)genomic data available in the decade since this provocative assertion, and use 'protein clusters' to evaluate whether sampling technologies have advanced to the point that we may be able to sample 'all' of viral diversity in nature.
Copyright © 2013 Elsevier B.V. All rights reserved.

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Year:  2013        PMID: 23896279     DOI: 10.1016/j.coviro.2013.07.004

Source DB:  PubMed          Journal:  Curr Opin Virol        ISSN: 1879-6257            Impact factor:   7.090


  28 in total

1.  Illuminating structural proteins in viral "dark matter" with metaproteomics.

Authors:  Jennifer R Brum; J Cesar Ignacio-Espinoza; Eun-Hae Kim; Gareth Trubl; Robert M Jones; Simon Roux; Nathan C VerBerkmoes; Virginia I Rich; Matthew B Sullivan
Journal:  Proc Natl Acad Sci U S A       Date:  2016-02-16       Impact factor: 11.205

Review 2.  Shedding new light on viral photosynthesis.

Authors:  Richard J Puxty; Andrew D Millard; David J Evans; David J Scanlan
Journal:  Photosynth Res       Date:  2014-11-09       Impact factor: 3.573

Review 3.  Viromes, not gene markers, for studying double-stranded DNA virus communities.

Authors:  Matthew B Sullivan
Journal:  J Virol       Date:  2014-12-24       Impact factor: 5.103

Review 4.  Rising to the challenge: accelerated pace of discovery transforms marine virology.

Authors:  Jennifer R Brum; Matthew B Sullivan
Journal:  Nat Rev Microbiol       Date:  2015-02-02       Impact factor: 60.633

5.  Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses.

Authors:  Bonnie L Hurwitz; Anton H Westveld; Jennifer R Brum; Matthew B Sullivan
Journal:  Proc Natl Acad Sci U S A       Date:  2014-07-07       Impact factor: 11.205

6.  Uncovering Earth's virome.

Authors:  David Paez-Espino; Emiley A Eloe-Fadrosh; Georgios A Pavlopoulos; Alex D Thomas; Marcel Huntemann; Natalia Mikhailova; Edward Rubin; Natalia N Ivanova; Nikos C Kyrpides
Journal:  Nature       Date:  2016-08-17       Impact factor: 49.962

Review 7.  Phage diversity, genomics and phylogeny.

Authors:  Moïra B Dion; Frank Oechslin; Sylvain Moineau
Journal:  Nat Rev Microbiol       Date:  2020-02-03       Impact factor: 60.633

8.  efam: an expanded, metaproteome-supported HMM profile database of viral protein families.

Authors:  Ahmed A Zayed; Dominik Lücking; Mohamed Mohssen; Dylan Cronin; Ben Bolduc; Ann C Gregory; Katherine R Hargreaves; Paul D Piehowski; Richard A White; Eric L Huang; Joshua N Adkins; Simon Roux; Cristina Moraru; Matthew B Sullivan
Journal:  Bioinformatics       Date:  2021-06-16       Impact factor: 6.931

9.  Spontaneous Deletion of an "ORFanage" Region Facilitates Host Adaptation in a "Photosynthetic" Cyanophage.

Authors:  Richard J Puxty; Blanca Perez-Sepulveda; Branko Rihtman; David J Evans; Andrew D Millard; David J Scanlan
Journal:  PLoS One       Date:  2015-07-15       Impact factor: 3.240

10.  Informative Regions In Viral Genomes.

Authors:  Jaime Leonardo Moreno-Gallego; Alejandro Reyes
Journal:  Viruses       Date:  2021-06-18       Impact factor: 5.048

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