4.4 Article

Three new clades of putative viral RNA-dependent RNA polymerases with rare or unique catalytic triads discovered in libraries of ORFans from powdery mildews and the yeast of oenological interest Starmerella bacillaris

Related references

Note: Only part of the references are listed.
Article Multidisciplinary Sciences

Petabase-scale sequence alignment catalyses viral discovery

Robert C. Edgar et al.

Summary: Public databases contain a vast amount of nucleic acid sequences, but efficient methods for systematic exploration of this library have been lacking. In this study, we developed a cloud computing infrastructure, Serratus, to enable ultra-high-throughput sequence alignment at the petabase scale. By searching millions of diverse samples, we identified over 10(5) novel RNA viruses and characterized their environmental reservoirs. To facilitate viral discovery, we established a comprehensive database of these data and tools. Expanding the known sequence diversity of viruses has important implications for understanding emerging pathogens and improving pathogen surveillance.

NATURE (2022)

Article Virology

Virome characterization of Cryphonectria parasitica isolates from Azerbaijan unveiled a new mymonavirus and a putative new RNA virus unrelated to described viral sequences

M. Forgia et al.

Summary: In this study, 55 C. parasitica isolates collected in Azerbaijan were investigated to describe associated viruses, leading to the discovery of two new viruses, CpSV1 and CpaV1. The finding of CpaV1 expands our understanding of the RNA virosphere.

VIROLOGY (2021)

Article Genetics & Heredity

Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses

Julie Callanan et al.

Summary: The majority of prokaryotic viruses have double-stranded or single-stranded DNA or RNA genomes. However, recent studies have revealed a much greater diversity of single-stranded positive-sense RNA viruses in prokaryotic soil communities than previously thought. Phylogenetic analysis has led to the reorganization of the class Allassoviricetes into Leviviricetes, with two new orders and a total of six families, 428 genera, and 882 species.

MICROBIAL GENOMICS (2021)

Article Microbiology

Novel Mycoviruses Discovered in the Mycovirome of a Necrotrophic Fungus

Ana Ruiz-Padilla et al.

Summary: The research unveils the composition of mycoviruses in Botrytis cinerea, including 62 new species, with 57 being positive-sense single-stranded RNA viruses. A wide variety of mycoviruses were discovered in vineyards in Italy and Spain, with some being associated with previously unseen viral genera.
Article Multidisciplinary Sciences

Armillaria root rot fungi host single-stranded RNA viruses

Riikka Linnakoski et al.

Summary: Species of Armillaria are globally distributed and some form large long-living clones capable of long-range spore-mediated transfer and vegetative spread. This study identified negative-sense RNA viruses, positive-sense RNA viruses, and new members of virus families infecting Armillaria isolates. Thermal treatment can cure Armillaria isolates of viruses, allowing further research on virus effects using infected and virus-free strains.

SCIENTIFIC REPORTS (2021)

Article Virology

Complexity and Local Specificity of the Virome Associated with Tospovirus-Transmitting Thrips Species

M. Chiapello et al.

Summary: Thrips species Frankliniella occidentalis and Thrips tabaci greatly impact horticultural crops by vectoring viruses, with a study in Italy identifying new viruses and describing a locally persistent core virome specific to distinct geographical locations.

JOURNAL OF VIROLOGY (2021)

Review Microbiology

The Baltimore Classification of Viruses 50 Years Later: How Does It Stand in the Light of Virus Evolution?

Eugene Koonin et al.

Summary: David Baltimore's classification of viruses based on genome expression routes has been fundamental in virology for the past fifty years, providing a conceptual framework for understanding virus diversity. Recent studies have focused on the global ecology and biology of viruses within the context of the Baltimore classes, with an exploration of potential extensions to the original scheme.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2021)

Article Multidisciplinary Sciences

Highly accurate protein structure prediction with AlphaFold

John Jumper et al.

Summary: Proteins are essential for life, and accurate prediction of their structures is a crucial research problem. Current experimental methods are time-consuming, highlighting the need for accurate computational approaches to address the gap in structural coverage. Despite recent progress, existing methods fall short of atomic accuracy in protein structure prediction.

NATURE (2021)

Article Agriculture, Multidisciplinary

Putative new plant viruses associated with Plasmopara viticola-infected grapevine samples

Marco Chiapello et al.

ANNALS OF APPLIED BIOLOGY (2020)

Review Microbiology

Global Organization and Proposed Megataxonomy of the Virus World

Eugene V. Koonin et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2020)

Review Plant Sciences

Deep Roots and Splendid Boughs of the Global Plant Virome

Valerian V. Dolja et al.

ANNUAL REVIEW OF PHYTOPATHOLOGY, VOL 58 (2020)

Article Microbiology

Marine Oomycetes of the GenusHalophytophthoraHarbor Viruses Related to Bunyaviruses

Leticia Botella et al.

FRONTIERS IN MICROBIOLOGY (2020)

Article Virology

A new lineage of segmented RNA viruses infecting animals

Darren J. Obbard et al.

VIRUS EVOLUTION (2020)

Article Biochemistry & Molecular Biology

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Ann C. Gregory et al.

Review Microbiology

Origin of viruses: primordial replicators recruiting capsids from hosts

Mart Krupovic et al.

NATURE REVIEWS MICROBIOLOGY (2019)

Article Biochemistry & Molecular Biology

The EMBL-EBI search and sequence analysis tools APIs in 2019

Fabio Madeira et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

Evan P. Starr et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemical Research Methods

MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization

Kazutaka Katoh et al.

BRIEFINGS IN BIOINFORMATICS (2019)

Article Biochemistry & Molecular Biology

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

Sudhir Kumar et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

SWISS-MODEL: homology modelling of protein structures and complexes

Andrew Waterhouse et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Microbiology

Origins and Evolution of the Global RNA Virome

Yuri I. Wolf et al.

Review Food Science & Technology

Starmerella bacillaris in winemaking: opportunities and risks

Vasileios Englezos et al.

CURRENT OPINION IN FOOD SCIENCE (2017)

Article Multidisciplinary Sciences

Redefining the invertebrate RNA virosphere

Mang Shi et al.

NATURE (2016)

Article Biochemistry & Molecular Biology

W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis

Jana Trifinopoulos et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

The Phyre2 web portal for protein modeling, prediction and analysis

Lawrence A. Kelley et al.

NATURE PROTOCOLS (2015)

Article Biochemistry & Molecular Biology

HMMER web server: 2015 update

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Multidisciplinary Sciences

A novel mycovirus from Aspergillus fumigatus contains four unique dsRNAs as its genome and is infectious as dsRNA

Lakkhana Kanhayuwa et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

Patterns and ecological drivers of ocean viral communities

Jennifer R. Brum et al.

SCIENCE (2015)

Article Biochemistry & Molecular Biology

The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster

Claire L. Webster et al.

PLOS BIOLOGY (2015)

Article Biochemical Research Methods

Fast and sensitive protein alignment using DIAMOND

Benjamin Buchfink et al.

NATURE METHODS (2015)

Review Biochemistry & Molecular Biology

Common and unique features of viral RNA-dependent polymerases

Aartjan J. W. te Velthuis

CELLULAR AND MOLECULAR LIFE SCIENCES (2014)

Article Multidisciplinary Sciences

Fungal negative-stranded RNA virus that is related to bornaviruses and nyaviruses

Lijiang Liu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemical Research Methods

Using Tablet for visual exploration of second-generation sequencing data

Iain Milne et al.

BRIEFINGS IN BIOINFORMATICS (2013)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Biochemistry & Molecular Biology

Primer3-new capabilities and interfaces

Andreas Untergasser et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Biotechnology & Applied Microbiology

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Manfred G. Grabherr et al.

NATURE BIOTECHNOLOGY (2011)

Article Multidisciplinary Sciences

A geminivirus-related DNA mycovirus that confers hypovirulence to a plant pathogenic fungus

Xiao Yu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Plant Sciences

Yeast as a Model Host to Explore Plant Virus-Host Interactions

Peter D. Nagy

Annual Review of Phytopathology (2008)

Article Virology

Structural and functional characterization of sapovirus RNA-dependent RNA polymerase

Stephen W. B. Fullerton et al.

JOURNAL OF VIROLOGY (2007)