The effect of variant interference on <i>de novo</i> assembly for viral deep sequencing

Castro, Christina J.; Marine, Rachel L.; Ramos, Edward; Ng, Terry Fei Fan

doi:10.1101/815480

Cited by 2 publications

(2 citation statements)

References 46 publications

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“…Standardized bioinformatic pipelines for uncovering viruses via metagenomics are being developed, however assembling eukaryotic viral genomes from uncultured, multicellular, host-based systems is still an uncommon practice (Castro et al, 2019;Ponsero and Hurwitz, 2019;Schulz et al, 2020a). For our dataset, some techniques, such as metagenomic binning using nucleotide composition, contig abundance, and reference genomes (Schulz et al, 2020b), did not work for identifying viral contigs.…”

Section: Metagenomics and Uvig Analysis Suggests Corals Contain A Novmentioning

confidence: 97%

Coral Bleaching Phenotypes Associated With Differential Abundances of Nucleocytoplasmic Large DNA Viruses

et al. 2020

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Eukaryotic viruses and bacteriophage have been implicated in disease and bleaching in corals, but the compositional and functional diversity of these viruses in healthy and compromised hosts remains underexplored. To investigate whether viral assemblages differ in concert with coral bleaching, we collected bleached and non-bleached conspecific pairs of corals during a minor bleaching event in 2016 from reefs on the island of Mo'orea, French Polynesia. Using electron microscopy (EM), we identified several viral particle types, all reminiscent of medium to large-sized nucleocytoplasmic large DNA viruses (NCLDV). We also found that viral metagenomes from bleached corals have significantly more eukaryotic virus sequences, whereas bacteriophage sequences are significantly more abundant in viral metagenomes from non-bleached colonies. In this study, we also initiated the assembly of the first eukaryotic dsDNA coral virus genome. Based on our EM imagery and our taxonomic annotations of viral metagenome sequences, we hypothesize that this genome represents a novel, phylogenetically distinct member of the NCLDVs, with its closest sequenced relative being a distant marine flagellate-associated virus. We also showed that this NCLDV is abundant in bleached corals, but it is also present in apparently healthy corals, suggesting it plays a role in the onset and/or severity of coral bleaching.

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Section: Metagenomics and Uvig Analysis Suggests Corals Contain A Novmentioning

confidence: 97%

Coral Bleaching Phenotypes Associated With Differential Abundances of Nucleocytoplasmic Large DNA Viruses

et al. 2020

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“…Aside from the upstream viral enrichment process, there are several barriers in downstream bioinformatics analysis that limit viral community identification and characterization. High viral complexity and diversity in the environmental samples, particularly sewage samples, often lead to nonuniform sequencing depth resulting in loss of rare viral species signals and poor quality of viral genome recovery [26–28]. Recently, flow cytometry has been coupled with viral metagenomics in marine samples to discover tailed and very large viruses, which could be excluded in routine viral metagenomics [29–31].…”

Section: Introductionmentioning

confidence: 99%

A comparative study of flow cytometry‐sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant

Yang

Mao

et al. 2022

iMeta

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Traditional or "bulk" viral enrichment and amplification methods used in viral metagenomics introduce unavoidable bias in viral diversity. This bias is due to shortcomings in existing viral enrichment methods and overshadowing by the more abundant viral populations. To reduce the complexity and improve the resolution of viral diversity, we developed a strategy coupling fluorescence-activated cell sorting (FACS) with random amplification and compared this to bulk metagenomics. This strategy was validated on both influent and effluent samples from a municipal wastewater treatment plant using the Modified Ludzack-Ettinger (MLE) process as the treatment method.We found that DNA and RNA communities generated using bulk samples were mostly different from those derived following FACS for both treatments before and after MLE. Before MLE treatment, FACS identified five viral families and 512 viral annotated contigs. Up to 43% of mapped reads were not detected in bulk samples. Nucleo-cytoplasmic large DNA viral families were enriched to a greater extent in the FACS-coupled subpopulations compared with bulk samples. FACS-coupled viromes captured a single-contig viral genome associated with Anabaena phage, which was not observed in bulk samples or in FACS-sorted samples after MLE. These short metagenomic reads, which were assembled into a high-quality draft genome of 46 kbp, were found to be highly dominant in one of the pre-MLE FACS annotated virome fractions (57.4%). Using bulk metagenomics, we identified that between Primary Settling Tank and Secondary Settling Tank viromes, Virgaviridae, Astroviridae, Parvoviridae, Picobirnaviridae, Nodaviridae, and Iridoviridae were susceptible to MLE treatment.

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The effect of variant interference on de novo assembly for viral deep sequencing

Cited by 2 publications

References 46 publications

Coral Bleaching Phenotypes Associated With Differential Abundances of Nucleocytoplasmic Large DNA Viruses

Coral Bleaching Phenotypes Associated With Differential Abundances of Nucleocytoplasmic Large DNA Viruses

A comparative study of flow cytometry‐sorted communities and shotgun viral metagenomics in a Singapore municipal wastewater treatment plant

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