dc.contributor.author | Warwick-Dugdale, J | |
dc.contributor.author | Solonenko, N | |
dc.contributor.author | Moore, K | |
dc.contributor.author | Chittick, L | |
dc.contributor.author | Gregory, AC | |
dc.contributor.author | Allen, M | |
dc.contributor.author | Sullivan, MB | |
dc.contributor.author | Temperton, B | |
dc.date.accessioned | 2019-03-19T09:30:47Z | |
dc.date.issued | 2019-04-25 | |
dc.description.abstract | Marine viruses impact global biogeochemical cycles via their influence on host community structure
and function, yet our understanding of viral ecology is constrained by limitations in host culturing and a
lack of reference genomes and ‘universal’ gene markers to facilitate community surveys. Short-read
viral metagenomic studies have provided clues to viral function and first estimates of global viral gene
abundance and distribution, but their assemblies are confounded by populations with high levels of
strain evenness and nucleotide diversity (microdiversity), limiting assembly of some of the most
abundant viruses on Earth. Such features also challenge assembly across genomic islands containing
niche-defining genes that drive ecological speciation. These populations and features may be
successfully captured by single-virus genomics and fosmid-based approaches, at least in abundant
taxa, but at considerable cost and technical expertise. Here we established a low-cost, low-input, high
throughput alternative sequencing and informatics workflow to improve viral metagenomic assemblies
using short-read and long-read technology. The ‘VirION’ (Viral, long-read metagenomics via MinION
sequencing) approach was first validated using mock communities where it was found to be as
relatively quantitative as short-read methods and provided significant improvements in recovery of
viral genomes. We then then applied VirION to the first metagenome from a natural viral community
from the Western English Channel. In comparison to a short-read only approach, VirION: (i) increased
number and completeness of assembled viral genomes; (ii) captured abundant, highly microdiverse
virus populations, and (iii) captured more and longer genomic islands. Together, these findings
suggest that VirION provides a high throughput and cost-effective alternative to fosmid and singlevirus
genomic approaches to more comprehensively explore viral communities in nature. | en_GB |
dc.description.sponsorship | Natural Environment Research Council (NERC) | en_GB |
dc.description.sponsorship | Royal Society (Charity) | en_GB |
dc.description.sponsorship | Simons Foundation | en_GB |
dc.identifier.citation | Published online 25 April 2019 | en_GB |
dc.identifier.doi | 10.7717/peerj.6800 | |
dc.identifier.uri | http://hdl.handle.net/10871/36565 | |
dc.language.iso | en | en_GB |
dc.publisher | PeerJ Inc. | en_GB |
dc.title | Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2019-03-19T09:30:47Z | |
dc.identifier.issn | 2167-8359 | |
dc.description | This is the final version. Available on open access from PeerJ via the DOI in this record | en_GB |
dc.identifier.journal | PeerJ | en_GB |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | en_GB |
dcterms.dateAccepted | 2019-03-14 | |
exeter.funder | ::Natural Environment Research Council (NERC) | en_GB |
exeter.funder | ::Natural Environment Research Council (NERC) | en_GB |
exeter.funder | ::Royal Society (Charity) | en_GB |
exeter.funder | ::Simons Foundation | en_GB |
rioxxterms.version | voR | en_GB |
rioxxterms.licenseref.startdate | 2019-03-18 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2019-03-19T09:17:22Z | |
refterms.versionFCD | AM | |
refterms.dateFOA | 2019-05-14T10:59:16Z | |
refterms.panel | A | en_GB |