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Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils

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Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils https://t.co/cr5k2m9mxd
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RT @ViralEcology: Soil viromes...let's go!!
Soil viromes...let's go!!
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
RT @gtrubl: Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPr…
Our new paper on ssDNA & dsDNA soil viruses. Protocol has been available for 2yrs @protocolsIO https://t.co/QmOMoRF5Uo @PeerJPreprints https://t.co/gVirimfRnc #Ecology #Microbiology #SoilScience #Virology @simroux_virus @Lab_Sullivan @jrr_microbio @jgi @doescience @doe_isogenie
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils https://t.co/l257iWVZJT https://t.co/emLruiWOCy
43 days ago
Towards optimized viral metagenomes for double-stranded and single-stranded DNA viruses from challenging soils https://t.co/pU6QzoQPzW https://t.co/QbrkBLzMQV
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Supplemental Information

Experiment 1 Bioanalyzer results

Extracted DNA was run on a Bioanalyzer High Sensitivity DNA Assay for all samples and successful libraries (see methods) are shown. Each sample had 15 PCR cycles. Upper marker designated with purple and lower marker with green.

DOI: 10.7287/peerj.preprints.27640v1/supp-1

Relative abundance of vOTUs across 2 bog and 4 fen viromes with variable genome coverage cutoffs (Experiment 1)

Four heatmaps are shown comparing the relative abundances of the 516 vOTUs with different thresholds on the minimum percentage of genome covered (10%, 20%, 30%, and 75%). The relative abundance was normalized per Gbp of metagenome and log10-transformed. All mapping used a minimum nucleotide identify of 90%.

DOI: 10.7287/peerj.preprints.27640v1/supp-2

Relative abundance of vOTUs across 12 palsa viromes with variable genome coverage cutoffs (Experiment 2)

Six heatmaps are shown comparing the relative abundances of the 66 vOTUs with different thresholds on the minimum percentage of genome covered, increasing in increments of 10 (0–60%). The relative abundance was normalized per Gbp of metagenome and log10-transformed. All mapping used a minimum nucleotide identify of 90%.

DOI: 10.7287/peerj.preprints.27640v1/supp-3

Diversity metrics of vOTUs

(A) Richness (R), Pielou's evenness index (J), and Shannon’s Diversity index (H) were calculated for each virome and the viromes are plotted by habitat. Within each habitat the viromes are denoted by a circle, but displayed differently per treatment. For Experiment 1 (bog and fen), viromes are colored green for PowerSoil and blue for Wizard DNA extractions methods. Experiment 2 (palsa) viromes are outlined in red for heat treated samples or blue for bead-beating samples. The marker is filled in for samples that were CsCl purified. (B) A principal coordinate analysis of the viromes by normalized relative abundance of the 66 vOTUs from Experiment 2 based on their Bray-Curtis dissimilarity. Viromes distinguished by soil core, purification (+CsCl outlined in red), and lysis method.

DOI: 10.7287/peerj.preprints.27640v1/supp-4

ssDNA vOTUs from both Experiments

The detected ssDNA virus sequences (see methods) were clustered at 95% average nucleotide identify (ANI) across 85% of their contig length, resulting in 13 vOTUs from the 18 viromes. The ssDNA viruses from each experiment are listed along with their corresponding marker gene and habitat of origin.

DOI: 10.7287/peerj.preprints.27640v1/supp-5

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Gareth Trubl conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Simon Roux analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Natalie Solonenko conceived and designed the experiments, performed the experiments, authored or reviewed drafts of the paper, approved the final draft.

Yueh-Fen Li conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Benjamin Bolduc analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Josué Rodríguez-Ramos analyzed the data, authored or reviewed drafts of the paper, approved the final draft.

Emiley A. Eloe-Fadrosh contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Virginia I. Rich conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Matthew B. Sullivan conceived and designed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Data Deposition

The following information was supplied regarding data availability:

1) IsoGenieDB, 2) Viral Sequencing Data, Trubl Soil Viromes 3) https://isogenie-db.asc.ohio-state.edu/datasources#viral_sequencing

Funding

This study was funded by the Genomic Science Program of the United States Department of Energy Office of Biological and Environmental Research (grants DE-SC0010580 and DE-SC0016440), The Office of Science, Office of Workforce Development for Teachers and Scientists, Office of Science Graduate Student Research (SCGSR) program, and by the Gordon and Betty Moore Foundation Investigator Award (GBMF#3790 to MBS). The SCGSR program is administered by the Oak Ridge Institute for Science and Education (ORISE) for the DOE. ORISE is managed by ORAU under contract number DE‐SC0014664. The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under contract no. DE-AC02-05CH11231. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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