DNA and RNA viruses in the rhizosphere
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
Find out more...Roots of decline? Assembly and Function of the Rhizosphere Microbiome in Relation to Yield Decline
Biotechnology and Biological Sciences Research Council
Find out more...Warwick Integrative Synthetic Biology Centre
Biotechnology and Biological Sciences Research Council
Find out more...EPSRC and BBSRC Centre for Doctoral Training in Synthetic Biology
Engineering and Physical Sciences Research Council
Find out more...