4.6 Article

Diversity, distribution, and functional potentials of magroviruses from marine and brackish waters

Related references

Note: Only part of the references are listed.
Article Microbiology

Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome

Rafael Laso-Perez et al.

Summary: This study characterizes a family of ANME-1 archaea and its virome using metagenomics on hydrothermal samples from the Gulf of California. It reveals the diversity, ecology, and evolution of ANME-1 and uncovers the effect of virus-host dynamics. The study also discovers 16 undescribed virus families exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures.

NATURE MICROBIOLOGY (2023)

Article Microbiology

Diverse viruses of marine archaea discovered using metagenomics

Yifan Zhou et al.

Summary: This study assessed the utility of CRISPR spacer targeting, tRNA gene matching, and homology searches for the assignment of archaeal hosts of viruses and validated these approaches on metaviromes from Yangshan Harbor. The results showed a high diversity of archaeal viruses in the YSH virome and proposed three new viral families for the classification of marine archaeal viruses. The study highlights the importance of viral metagenomics in exploring the archaeal virome and provides new insights into the diversity, distribution, and evolution of marine archaeal viruses.

ENVIRONMENTAL MICROBIOLOGY (2023)

Article Multidisciplinary Sciences

A holistic genome dataset of bacteria, archaea and viruses of the Pearl River estuary

Bu Xu et al.

Summary: This study conducted metagenomic sequencing on microbial and viral communities in the Pearl River estuary, one of China's largest estuaries, revealing that many of the microbial and viral genomes in this estuary are novel at the species level. These genomes provide important additions to global marine genome datasets and will greatly enhance our understanding of microbe-virus interactions, evolution, and their implications in estuarine ecosystems.

SCIENTIFIC DATA (2022)

Editorial Material Microbiology

A trove of Asgard archaeal viruses

Tomas Alarcon-Schumacher et al.

NATURE MICROBIOLOGY (2022)

Article Biotechnology & Applied Microbiology

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

Stephen Nayfach et al.

Summary: CheckV is an automated pipeline for identifying closed viral genomes, estimating completeness of genome fragments, and removing host-related regions. By comparing sequences with a large database of complete viral genomes, CheckV assesses the quality of viral genomes assembled from metagenome data. Removing host contamination improves the accurate identification of auxiliary metabolic genes and interpretation of viral-encoded functions.

NATURE BIOTECHNOLOGY (2021)

Article Environmental Sciences

The communities and functional profiles of virioplankton along a salinity gradient in a subtropical estuary

Chen Zhang et al.

Summary: The study found that in a subtropical estuary, viruses are mainly bacteriophages, and their community structure and function vary significantly along a salinity gradient, with carbohydrate-active enzymes being the main functional potential. Viruses have a negative effect on multiple host taxa. Salinity, ammonium, and dissolved oxygen are the dominant factors influencing the community composition of viruses.

SCIENCE OF THE TOTAL ENVIRONMENT (2021)

Article Microbiology

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

Jiarong Guo et al.

Summary: VirSorter2 is a virus identification tool that leverages genome-informed database advances and multiple classifiers to improve accuracy and range of virus sequence detection. It uniquely performs consistently with high accuracy across viral diversity and minimizes errors associated with atypical cellular sequences.

MICROBIOME (2021)

Article Biochemistry & Molecular Biology

Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes

Ying Liu et al.

Summary: This study presents 37 new genomes of haloarchaeal tailed virus isolates, doubling the current number of sequenced arTVs. Analysis of 63 available complete genomes of arTVs proposes to classify them into 14 new families and 3 orders, revealing ancient divergence of archaeal and bacterial tailed viruses and common strategies of virus-host interactions. The survey of metagenomes using viral hallmark genes suggests a global architecture of the arTV community shaped through recurrent transfers between different biomes.

PLOS BIOLOGY (2021)

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 Microbiology

Uncultivated Viral Populations Dominate Estuarine Viromes on the Spatiotemporal Scale

Mengqi Sun et al.

Summary: This study is the first systematic investigation of the spatial and temporal variation of virioplankton communities in estuaries using deep metagenomics sequencing. The results show a large pool of abundant and diverse viruses in estuaries that have not yet been cultivated, with genomes only available thanks to single-cell genomics or single-molecule sequencing. The study highlights the importance of these methods for viral discovery and reveals significant distinctions between estuarine and open ocean viromes.

MSYSTEMS (2021)

Article Biochemical Research Methods

KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold

Takuya Aramaki et al.

BIOINFORMATICS (2020)

Review Microbiology

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems

Amy E. Zimmerman et al.

NATURE REVIEWS MICROBIOLOGY (2020)

Article Mathematical & Computational Biology

Identifying viruses from metagenomic data using deep learning

Jie Ren et al.

QUANTITATIVE BIOLOGY (2020)

Article Biotechnology & Applied Microbiology

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Ho Bin Jang et al.

NATURE BIOTECHNOLOGY (2019)

Article Multidisciplinary Sciences

Spindle-shaped viruses infect marine ammoniaoxidizing thaumarchaea

Jong-Geol Kim et al.

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

Article Biotechnology & Applied Microbiology

Robust taxonomic classification of uncharted microbial sequences and bins with CAT and BAT

F. A. Bastiaan von Meijenfeldt et al.

GENOME BIOLOGY (2019)

Article Geochemistry & Geophysics

Planktonic Marine Archaea

Alyson E. Santoro et al.

Annual Review of Marine Science (2018)

Article Multidisciplinary Sciences

Putative archaeal viruses from the mesopelagic ocean

Dean R. Vik et al.

PEERJ (2017)

Article Biochemistry & Molecular Biology

Novel Abundant Oceanic Viruses of Uncultured Marine Group II Euryarchaeota

Alon Philosof et al.

CURRENT BIOLOGY (2017)

Article Biochemistry & Molecular Biology

The Pfam protein families database: towards a more sustainable future

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biotechnology & Applied Microbiology

Genome Reconstruction from Metagenomic Data Sets Reveals Novel Microbes in the Brackish Waters of the Caspian Sea

Maliheh Mehrshad et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)

Article Multidisciplinary Sciences

Patterns and ecological drivers of ocean viral communities

Jennifer R. Brum et al.

SCIENCE (2015)

Review Microbiology

Marine Group II Archaea, potentially important players in the global ocean carbon cycle

Chuanlun L. Zhang et al.

FRONTIERS IN MICROBIOLOGY (2015)

Article Multidisciplinary Sciences

VirSorter: mining viral signal from microbial genomic data

Simon Roux et al.

PEERJ (2015)

Article Multidisciplinary Sciences

Open science resources for the discovery and analysis of Tara Oceans data

Stephane Pesant et al.

SCIENTIFIC DATA (2015)

Article Biochemical Research Methods

CD-HIT: accelerated for clustering the next-generation sequencing data

Limin Fu et al.

BIOINFORMATICS (2012)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Article Multidisciplinary Sciences

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

Vaughn Iverson et al.

SCIENCE (2012)

Article Biotechnology & Applied Microbiology

Development of phoH as a Novel Signature Gene for Assessing Marine Phage Diversity

Dawn B. Goldsmith et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2011)

Article Biochemistry & Molecular Biology

HMMER web server: interactive sequence similarity searching

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemical Research Methods

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt et al.

BMC BIOINFORMATICS (2010)

Article Multidisciplinary Sciences

FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

Morgan N. Price et al.

PLOS ONE (2010)

Article Biochemical Research Methods

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Salvador Capella-Gutierrez et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Oceanography

Seasonal variability of picoplankton in the northern South China Sea at the SEATS station

Hongbin Liu et al.

DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY (2007)

Article Biochemistry & Molecular Biology

Tolerance and biomarkers as useful tools for assessing environmental quality in the Oued Souss estuary (Bay of Agadir, Morocco)

AA Alla et al.

COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY C-TOXICOLOGY & PHARMACOLOGY (2006)

Article Biochemistry & Molecular Biology

Cytoscape: A software environment for integrated models of biomolecular interaction networks

P Shannon et al.

GENOME RESEARCH (2003)

Article Biochemistry & Molecular Biology

The TIGRFAMs database of protein families

DH Haft et al.

NUCLEIC ACIDS RESEARCH (2003)

Article Biotechnology & Applied Microbiology

A few cosmopolitan phylotypes dominate planktonic archaeal assemblages in widely different oceanic provinces

R Massana et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2000)

Article Biochemistry & Molecular Biology

The COG database: a tool for genome-scale analysis of protein functions and evolution

RL Tatusov et al.

NUCLEIC ACIDS RESEARCH (2000)