Dataset Information

Virome Assembly and Annotation: A Surprise in the Namib Desert.

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.

SUBMITTER: Hesse U

PROVIDER: S-EPMC5253355 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Virome Assembly and Annotation: A Surprise in the Namib Desert.

Hesse Uljana U van Heusden Peter P Kirby Bronwyn M BM Olonade Israel I van Zyl Leonardo J LJ Trindade Marla M

Frontiers in microbiology 20170123

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 assemble ...[more]

PMID: 28167933

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Project description:The fog-basking behavior of the Onymacris unguicularis, a beetle species living in the coastal regions of the Namibian desert, has recently caught the attention of the engineering community, as suggesting a viable biomimetic approach to address the problem of harvesting water in arid regions of the globe. Previous research has focused on observation and analysis of the beetle's elytron properties and how these affect fog-collection rates. The head stance taken by the Onymacris unguicularis when fog basking is well documented. However, how this stance affects droplet collection has not been studied up to now. The present paper addresses this problem from a computational fluid dynamics perspective, where three-dimensional numerical simulations are used to characterize the fog flow properties around a simplified geometry mimicking the beetle's body. The simulations employ two-way coupling between the gas flow and the dispersed fog phase to account for feedback effects of fog droplets on the carrier fluid (air), and assume that droplets are captured after hitting the elytron surface. The study considers several combinations of free-stream velocity and droplet volume fraction. The analysis reveals that there is a range of head-stance angles, corresponding to an inclination of the beetle between 35 deg and 45 deg with respect to the horizon, that maximizes water collection on the beetle's back, in qualitative agreement with observations in nature and laboratory experiments. A rationale is proposed to explain this phenomenon, finding that the specific head stance corresponds to the maximum residence time of fluid particles above the beetle's elytron surface. This, in turn, designates the maximum likelihood for water droplets to be captured in the boundary layer developing over the beetle and subsequently hit the surface where they get captured. The results reveal the importance of the fluid flow pattern around the beetle's body in addition to the microphysical properties of the elytron when reliable predictions of the water droplet collection efficiency are sought.

Dataset Information

Virome Assembly and Annotation: A Surprise in the Namib Desert.

Publications

Virome Assembly and Annotation: A Surprise in the Namib Desert.

Similar Datasets

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