Long-read viral metagenomics captures abundant and microdiverse viral populations and their niche-defining genomic islands

PeerJ

article

Joanna Warwick-Dugdale¹  Natalie Solonenko³  Karen Moore²  Lauren Chittick³  Ann C. Gregory³  Michael J. Allen¹  Matthew B. Sullivan³  Ben Temperton² 

[1] Plymouth Marine Laboratory;School of Biosciences, University of Exeter;Department of Microbiology, Ohio State University;Civil, Environmental and Geodetic Engineering, Ohio State University

关键词: Viral Metagenomics;    Virus;    Virome;    Metagenome;    Assembly;    Viral ecology;    Long-read sequencing;    Marine Microbiology;   

DOI  :  10.7717/peerj.6800

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

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 single-virus genomic approaches to more comprehensively explore viral communities in nature.

【 授权许可】

CC BY