ArticlemSystems2022
Long-Read Metagenomics Improves the Recovery of Viral Diversity from Complex Natural Marine Samples.
Article in mSystems, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 39 citations in OpenAlex.
- Perseus: lineage-aware refinement of Kraken2 taxonomic classification for long read metagenomes.Bioinformatics (Oxford, England) · 2026Article
- A hybrid and cost-efficient barcoding strategy for full-length 16S rRNA gene nanopore sequencing of environmental samples.BMC genomics · 2026Article
- Review
- Rolling outMicrobial genomics · 2026Article
- Integrating metagenomics and metatranscriptomics intoThe Journal of general virology · 2026Review
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- Limited consensus of marine viral diversity observed across techniques.Environmental microbiome · 2025Article
- Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations.NAR genomics and bioinformatics · 2025Article
- CLAE: A High-Fidelity Nanopore Sequencing Strategy for Read-Level Viral Variant Detection and Environmental RNA Virus Discovery.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Enriched Long-Read Sequencing of Co-circulating Viruses in Complex Samples.Molecular biology and evolution · 2025Article
- The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity.Environmental microbiome · 2025Article
- Arctic Ocean virus communities and their seasonality, bipolarity, and prokaryotic associations.Nature communications · 2025Article
- Large diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales.mBio · 2025Article
- Article
- Unveiling microbial diversity: harnessing long-read sequencing technology.Nature methods · 2024Review
- The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.Microbial genomics · 2024Article
- Exploring virus-host-environment interactions in a chemotrophic-based underground estuary.Environmental microbiome · 2024Article
- Spatiotemporal dynamics of giant viruses within a deep freshwater lake reveal a distinct dark-water community.The ISME journal · 2024Article
- Assessing RNA integrity by digital RT-PCR: Influence of extraction, storage, and matrices.Biology methods & protocols · 2024Article
- Tools and methodology toFrontiers in microbiology · 2024Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recovery of DNA from viromes is a major obstacle in the use of long-read sequencing to study their genomes. For this reason, the use of cellular metagenomes (>0.2-μm size range) emerges as an interesting complementary tool, since they contain large amounts of naturally amplified viral genomes from prelytic replication. We have applied second-generation (Illumina NextSeq; short reads) and third-generation (PacBio Sequel II; long reads) sequencing to compare the diversity and features of the viral community in a marine sample obtained from offshore waters of the western Mediterranean. We found that a major wedge of the expected marine viral diversity was directly recovered by the raw PacBio circular consensus sequencing (CCS) reads. More than 30,000 sequences were detected only in this data set, with no homologues in the long- and short-read assembly, and ca. 26,000 had no homologues in the large data set of the Global Ocean Virome 2 (GOV2), highlighting the information gap created by the assembly bias. At the level of complete viral genomes, the performance was similar in both approaches. However, the hybrid long- and short-read assembly provided the longest average length of the sequences and improved the host assignment. Although no novel major clades of viruses were found, there was an increase in the intraclade genomic diversity recovered by long reads that produced an enriched assessment of the real diversity and allowed the discovery of novel genes with biotechnological potential (e.g., endolysin genes).
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.