Abstract
Sequencing, assembly, and annotation of environmental virome samples is challenging. Methodological biases and differences in species abundance result in fragmentary read coverage; sequence reconstruction is further complicated by the mosaic nature of viral genomes. In this paper, we focus on biocomputational aspects of virome analysis, emphasizing latent pitfalls in sequence annotation. Using simulated viromes that mimic environmental data challenges we assessed the performance of five assemblers (CLC-Workbench, IDBA-UD, SPAdes, RayMeta, ABySS). Individual analyses of relevant scaffold length fractions revealed shortcomings of some programs in reconstruction of viral genomes with excessive read coverage (IDBA-UD, RayMeta), and in accurate assembly of scaffolds ≥50 kb (SPAdes, RayMeta, ABySS). The CLC-Workbench assembler performed best in terms of genome recovery (including highly covered genomes) and correct reconstruction of large scaffolds; and was used to assemble a virome from a copper rich site in the Namib Desert. We found that scaffold network analysis and cluster-specific read reassembly improved reconstruction of sequences with excessive read coverage, and that strict data filtering for non-viral sequences prior to downstream analyses was essential. In this study we describe novel viral genomes identified in the Namib Desert copper site virome. Taxonomic affiliations of diverse proteins in the dataset and phylogenetic analyses of circovirus-like proteins indicated links to the marine habitat. Considering additional evidence from this dataset we hypothesize that viruses may have been carried from the Atlantic Ocean into the Namib Desert by fog and wind, highlighting the impact of the extended environment on an investigated niche in metagenome studies.
Highlights
Viruses are important players in their respective ecological niches
Large scaffolds that are interesting for downstream analyses usually represent a very small fraction of an assembly, and the degree of their misassembly is not discernable based on those values
The CLC Genomics Workbench emerged as the most suitable assembler: it consistently recovered the highest number of genomes, accurately reconstructed large scaffolds, and outperformed most other assemblers in recognition of fragmented genome data (SIM2 virome)
Summary
Viruses are important players in their respective ecological niches Do they drive host adaptation through horizontal gene transfer, they regulate microbial abundance and diversity through predation (reviewed in Kimura et al, 2008). An increasing number of studies investigate virome data obtained from purified viral particles, following a workflow similar to the one established for marine viromes (Solonenko and Sullivan, 2013).
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