4.4 Article

Formal recognition and classification of gene transfer agents as viriforms

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Zoology

The naked truth: An updated review on nudiviruses and their relationship to bracoviruses and baculoviruses

Jirka M. Petersen et al.

Summary: Nudiviruses are enveloped and rod-shaped double-stranded DNA viruses that can infect various insects and aquatic crustaceans, causing different degrees of disease. This literature review aims to provide a comprehensive understanding of nudivirus diversity and phylogeny, as well as the comparison of nudiviruses with related insect viruses.

JOURNAL OF INVERTEBRATE PATHOLOGY (2022)

Article Microbiology

Persulfide-Responsive Transcription Factor SqrR Regulates Gene Transfer and Biofilm Formation via the Metabolic Modulation of Cyclic di-GMP in Rhodobacter capsulatus

Takayuki Shimizu et al.

Summary: Bacterial phage-like particles (gene transfer agents-GTAs) are important genetic vectors in horizontal gene transfer, and the transcription factor SqrR is involved in the regulation of GTA-related genes. Deletion of SqrR increases GTA production and gene transfer activity, and alters intracellular c-di-GMP levels, affecting biofilm formation.

MICROORGANISMS (2022)

Article Virology

Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022)

Peter J. Walker et al.

Summary: This article discusses the changes in virus taxonomy approved by the International Committee on Taxonomy of Viruses (ICTV) in March 2022. The ICTV members voted on 174 taxonomic proposals, all of which were ratified by an absolute majority. The implementation of a new naming rule for virus species has resulted in over 60% of virus species being named in the 'Genus_name species_epithet' format.

ARCHIVES OF VIROLOGY (2022)

Article Biochemistry & Molecular Biology

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

Ivica Letunic et al.

Summary: The Interactive Tree Of Life is an online tool for displaying, manipulating, and annotating phylogenetic and other trees. The latest version 5 introduces a new tree display engine and several new features, such as a new dataset type and expanded annotation options. Users can now also manually annotate trees by hand, providing more flexibility and control.

NUCLEIC ACIDS RESEARCH (2021)

Article Virology

Changes to virus taxonomy and to the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2021)

Peter J. Walker et al.

Summary: This article reports the changes to virus taxonomy approved and ratified by ICTV in March 2021. All proposals and revisions were passed by an absolute majority of ICTV members. ICTV mandated a new uniform rule for virus species naming, abolished the notion of a type species, and clarified its remit through an official definition of 'virus' and other types of mobile genetic elements.

ARCHIVES OF VIROLOGY (2021)

Article Virology

Evolution of DNA packaging in gene transfer agents

Emma S. Esterman et al.

Summary: Gene transfer agents (GTAs) are virus-like particles produced by bacteria and archaea that can transfer genes within communities. GTAs are thought to have evolved from viruses and maintained in prokaryotic genomes due to their DNA transfer capacity. The most-studied GTA, produced by Rhodobacter capsulatus, evolved from a headful packaging virus to be able to package random pieces of the host genome.

VIRUS EVOLUTION (2021)

Article Microbiology

Cyclic di-GMP-Mediated Regulation of Gene Transfer and Motility in Rhodobacter capsulatus

Purvikalyan Pallegar et al.

JOURNAL OF BACTERIOLOGY (2020)

Review Microbiology

Global Organization and Proposed Megataxonomy of the Virus World

Eugene V. Koonin et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2020)

Article Biochemistry & Molecular Biology

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

Bui Quang Minh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Multidisciplinary Sciences

Structure and mechanism of DNA delivery of a gene transfer agent

Pavol Bardy et al.

NATURE COMMUNICATIONS (2020)

Article Biochemistry & Molecular Biology

ClipKIT: A multiple sequence alignment trimming software for accurate phylogenomic inference

Jacob L. Steenwyk et al.

PLOS BIOLOGY (2020)

Review Biology

The dual life of ichnoviruses

Isabelle Darboux et al.

CURRENT OPINION IN INSECT SCIENCE (2019)

Review Biochemistry & Molecular Biology

Polydnaviruses: Evolution and Function

Michael R. Strand et al.

CURRENT ISSUES IN MOLECULAR BIOLOGY (2019)

Article Biochemistry & Molecular Biology

Origin and Evolution of the Bartonella Gene Transfer Agent

Daniel Tamarit et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Biochemistry & Molecular Biology

UFBoot2: Improving the Ultrafast Bootstrap Approximation

Diep Thi Hoang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

Article Evolutionary Biology

Packaging of Dinoroseobacter shibae DNA into Gene Transfer Agent Particles Is Not Random

Juergen Tomasch et al.

GENOME BIOLOGY AND EVOLUTION (2018)

Article Virology

The depths of virus exaptation

Eugene V. Koonin et al.

CURRENT OPINION IN VIROLOGY (2018)

Article Microbiology

Origins and Evolution of the Global RNA Virome

Yuri I. Wolf et al.

Article Biochemical Research Methods

ModelFinder: fast model selection for accurate phylogenetic estimates

Subha Kalyaanamoorthy et al.

NATURE METHODS (2017)

Article Virology

Endogenous viruses of parasitic wasps: variations on a common theme

Jean-Michel Drezen et al.

CURRENT OPINION IN VIROLOGY (2017)

Article Biochemistry & Molecular Biology

Gene Transfer Agent Promotes Evolvability within the Fittest Subpopulation of a Bacterial Pathogen

Maxime Quebatte et al.

CELL SYSTEMS (2017)

Article Biochemistry & Molecular Biology

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

Nuala A. O'Leary et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemistry & Molecular Biology

Functional and Evolutionary Characterization of a Gene Transfer Agent's Multilocus Genome

Alexander P. Hynes et al.

MOLECULAR BIOLOGY AND EVOLUTION (2016)

Article Biochemistry & Molecular Biology

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Kazutaka Katoh et al.

MOLECULAR BIOLOGY AND EVOLUTION (2013)

Article Biochemistry & Molecular Biology

Quorum-sensing regulation of a capsular polysaccharide receptor for the Rhodobacter capsulatus gene transfer agent (RcGTA)

Cedric A. Brimacombe et al.

MOLECULAR MICROBIOLOGY (2013)

Review Biology

When parasitic wasps hijacked viruses: genomic and functional evolution of polydnaviruses

Elisabeth A. Herniou et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2013)

Review Microbiology

Gene transfer agents: phage-like elements of genetic exchange

Andrew S. Lang et al.

NATURE REVIEWS MICROBIOLOGY (2012)

Article Multidisciplinary Sciences

Paleozoic origin of insect large dsDNA viruses

Julien Theze et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Article Multidisciplinary Sciences

High Frequency of Horizontal Gene Transfer in the Oceans

Lauren D. McDaniel et al.

SCIENCE (2010)

Article Biotechnology & Applied Microbiology

Occurrence and expression of gene transfer agent genes in marine bacterioplankton

Erin J. Biers et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2008)

Article Biotechnology & Applied Microbiology

Collateral effects of antibiotics:: Carbadox and metronidazole induce VSH-1 and facilitate gene transfer among Brachyspira hyodysenterae strains

Thaddeus B. Stanton et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2008)

Article Biochemistry & Molecular Biology

Importance of widespread gene transfer agent genes in α-proteobacteria

Andrew S. Lang et al.

TRENDS IN MICROBIOLOGY (2007)

Article Biochemistry & Molecular Biology

Evolutionary implications of phylogenetic analyses of the gene transfer agent (GTA) of Rhodobacter capsulatus

AS Lang et al.

JOURNAL OF MOLECULAR EVOLUTION (2002)

Article Evolutionary Biology

An approximately unbiased test of phylogenetic tree selection

H Shimodaira

SYSTEMATIC BIOLOGY (2002)

Article Microbiology

A bacteriophage-like particle from Bartonella bacilliformis

KD Barbian et al.

MICROBIOLOGY-UK (2000)