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Aquatic viral metagenomics: Lights and shadows.
Alberto Rastrojo,Antonio Alcami +1 more
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TLDR
The main steps in the viral metagenomic workflow are described paying special attention to the potential biases introduced by each one, including the purification of virus particles and the preparation of genomic libraries.About:
This article is published in Virus Research.The article was published on 2017-07-15. It has received 19 citations till now. The article focuses on the topics: Viral metagenomics & Metagenomics.read more
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High Diversity of the Viral Community from an
TL;DR: The genetic structure of an Antarctic lake viral community revealed unexpected genetic richness distributed across the highest number of viral families that have been found to date in aquatic viral metagenomes, in contrast to other known aquatic viromes.
Journal ArticleDOI
A Review on Viral Metagenomics in Extreme Environments
Sonia Dávila-Ramos,Hugo G. Castelán-Sánchez,Liliana Martínez-Ávila,María del Rayo Sánchez-Carbente,Raúl Peralta,Armando Hernández-Mendoza,Alan D. W. Dobson,Ramón A. Gonzalez,Nina Pastor,Ramón Alberto Batista-García +9 more
TL;DR: This review critically analyze recent progress in metagenomic based approaches to explore the viromes in extreme environments and discusses the potential for new discoveries, as well as methodological challenges and perspectives.
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Diversity, evolutionary contribution and ecological roles of aquatic viruses.
TL;DR: This review summary and outline main virus species, their evolutionary contribution to aquatic communities through horizontal gene transfer, and their ecological roles for cyanobacterial bloom termination and global biogeochemical cycling in freshwater and marine ecosystems.
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Quito's virome: Metagenomic analysis of viral diversity in urban streams of Ecuador's capital city
Laura Guerrero-Latorre,Brigette Romero,Edison Bonifaz,Natàlia Timoneda,Marta Rusiñol,Rosina Girones,Blanca Ríos-Touma +6 more
TL;DR: The wide diversity of species detected through metagenomics gives key information about the public health risks present in the urban rivers of Quito and describes for the first time the presence of important infectious agents not previously reported in Ecuador and with very little reports in Latin America.
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Critical issues in application of molecular methods to environmental virology.
Ibrahim Ahmed Hamza,Kyle Bibby +1 more
TL;DR: There are many challenges for selecting methods to detect classic and emerging viruses in environmental samples, and further developments are necessary to enable more rapid and accurate methodologies for viral water quality monitoring and regulation.
References
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Journal ArticleDOI
Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction
TL;DR: A new method of total RNA isolation by a single extraction with an acid guanidinium thiocyanate-phenol-chloroform mixture is described, providing a pure preparation of undegraded RNA in high yield and can be completed within 4 h.
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DNA sequencing with chain-terminating inhibitors
TL;DR: A new method for determining nucleotide sequences in DNA is described, which makes use of the 2',3'-dideoxy and arabinon nucleoside analogues of the normal deoxynucleoside triphosphates, which act as specific chain-terminating inhibitors of DNA polymerase.
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Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter,Karin A. Remington,John F. Heidelberg,Aaron L. Halpern,Doug Rusch,Jonathan A. Eisen,Dongying Wu,Ian T. Paulsen,Karen E. Nelson,William C. Nelson,Derrick E. Fouts,Samuel Levy,Anthony H. Knap,Michael W. Lomas,Kenneth H. Nealson,Owen White,Jeremy Peterson,Jeff Hoffman,Rachel Parsons,Holly Baden-Tillson,Cynthia Pfannkoch,Yu-Hui Rogers,Hamilton O. Smith +22 more
TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.
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Marine viruses — major players in the global ecosystem
TL;DR: Viruses are by far the most abundant 'lifeforms' in the oceans and are the reservoir of most of the genetic diversity in the sea, thereby driving the evolution of both host and viral assemblages.
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One Juliet and four Romeos: VeA and its methyltransferases.
TL;DR: Interaction of VeA with at least four methyltransferase proteins indicates a molecular hub function for VeA that questions: Is there a VeA supercomplex or is VeA part of a highly dynamic cellular control network with many different partners?