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DNA and RNA viruses in the rhizosphere

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dataset
modified on 2022-04-28, 10:38

This repository contains data used in Muscatt et al. 2022 

Futher details on analysis can be found here 

https://github.com/GeorgeMuscatt/RhizosphereVirome

 

Data is stored in the file RhizosphereVirome.tar 

The following files are stored. See the README for full details:

c1.ntw.gz = vConTACT2 network output file

 core_protein_concatenation_tree = ssRNA phage phylogenetic tree based on aligned core protein concatenations

 CP.faa.gz = fasta amino acid file containing coat protein sequences for 11,222 near-complete ssRNA phage vOTUs

CP_ref_Leviviricetes.faa.gz = fasta amino acid file containing coat protein sequences for 1,868 reference Leviviricetes genomes

dsDNA_gene_annotations.csv.gz = annotations for 20,746 dsDNA vOTU genes

dsDNA_vOTUs.faa.gz = fasta amino acid file containing 20,267 dsDNA vOTU genes

dsDNA_vOTUs.fna.gz = fasta nucleotide file containing 1,059 dsDNA vOTUs

edges.csv.gz = edges for drawing vConTACT2 network

gene_2_genome.csv.gz = input file for vConTACT2 containing gene-to-genome index for 1,059 dsDNA vOTUs and 16,540 ssRNA phage vOTUs

 MP.faa.gz = fasta amino acid file containing maturation protein sequences for 11,222 near-complete ssRNA phage vOTUs

MP_ref_Leviviricetes.faa.gz = fasta amino acid file containing maturation protein sequences for 1,868 reference Leviviricetes genomes

nodes.csv.gz = nodes for drawing vConTACT2 network

RdRp.faa.gz = fasta amino acid file containing RNA-dependent RNA polymerase sequences for 11,222 near-complete ssRNA phage vOTUs

RdRp_ref_Leviviricetes.faa.gz = fasta amino acid file containing RNA-dependent RNA polymerase sequences for 1,868 reference Leviviricetes genomes

ssRNA_vOTUs.faa.gz = fasta amino acid file containing 52,700 ssRNA phage vOTU genes

ssRNA_vOTUs.fna.gz = fasta nucleotide file containing 16,541 ssRNA phage vOTUs

viral_cluster_overview.csv = output file from vConTACT2 containing viral cluster information

Funding

CLIMB-BIG-DATA: A Cloud Infrastructure for Big-Data Microbial Bioinformatics

Medical Research Council

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Roots of decline? Assembly and Function of the Rhizosphere Microbiome in Relation to Yield Decline

Biotechnology and Biological Sciences Research Council

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Warwick Integrative Synthetic Biology Centre

Biotechnology and Biological Sciences Research Council

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EPSRC and BBSRC Centre for Doctoral Training in Synthetic Biology

Engineering and Physical Sciences Research Council

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The MRC Consortium for Medical Microbial Bioinformatics

Medical Research Council

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