DOI: 10.5061/dryad.kd51c5b5v
title: Data for: Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: virus infections of melon, Cucumis melo, crops and adjacent wild communities

description: Emergence of viral diseases results from novel transmission dynamics
 between wild and crop plant communities. The bias of studies towards
 pathogenic viruses of crops has distracted from knowledge of
 non-antagonistic symbioses in wild plants. Here we implemented a high
 throughput approach to compare the viromes of melon (Cucumis melo), and
 wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the
 41-plant species examined was infected by at least one virus. The
 interactions of 104 virus operational taxonomic units (OTUs) with these
 hosts occurred largely within ecological compartments of either Crop or
 Edge, Edge having traits of a reservoir community. The positive
 correlation of virus and plant richness at each site, the tendency for
 increased specialist host use through seasons, and specialist host use by
 OTUs observed only in Melon, characterised local-scale patterns of
 infection. In this study of systematically sampled viromes of crop and
 adjacent wild communities most hosts showed no disease symptoms,
 suggesting non-antagonistic symbioses are common. The coexistence of
 viruses within species-rich ecological compartments of agro-systems might
 promote the evolution of a diversity of virus strategies for survival and
 transmission. These communities, including those suspected as reservoirs,
 are subject to sporadic changes in assemblages, and so too are the
 conditions that favour the emergence of disease.
description: Four sites where <em>Cucumis melo </em>var. Piel de
 Sapo<em> </em>was grown (Crop habitat sites C1, C2, C3, and
 C4, from here, Crop) were compared to relatively permanent communities
 that form the narrow borders (Edge habitat sites E1 and E3, here from
 Edge) that separate crops. At each site, 50 plant samples from a 25 m x 2
 m area were collected systematically at each resampling according to fixed
 itineraries, regardless of plants showing symptoms of virus infection or
 not. Individual RNA extracts from the same plant species and collection
 (i.e. same time, same site) were pooled to obtain a single HTS library.
 Paired-end reads of 125 or 150 nt. were sequenced on Illumina HiSeq
 platforms. Approximately 8.0 x 10^6 reads per library
 were sequenced. Local BLAST queries against reference genomes of plant
 viruses. The following validation criteria were used to subset BLAST query
 output: 1) query coverage of 100%; 2) query length greater or equal to 125
 nt.; 3) paired-read matches only; 4) unique virus matches within each
 library; and 5) the difference between maximum and minimum query start
 positions in the reference genome had to span more than 1% of the virus
 genome length. In this way, at least two pairs of reads were required to
 match the reference. The first two steps of the validation criteria were
 performed to provide a less-restrictive indication of virus presence, then
 the last three steps applied to reduce the potential for the presence of
 false positive detections. Validated OTUs were used to generate
 plant-virus interaction networks.
description: Each data file comprises the following column names:
 "genus" genus of the OTU; "Family", family of the OTU;
 "ncbi reference title", the title of the reference genome for
 the BLAST match; "ncbi accession", the NCBI Accession identifier
 of the reference of the OTU; "virus (OTU)",  the name of the
 virus reference genome of the BLAST read query match;
 "abbreviation",  shows virus segment number when relevant;
 "genome", the genome type of the OTU; "habitat",  the
 vegetation type from where the plant sample was collected; "host
 taxon",  the name of the host species of the OTU; "site",
 the site from where the plant sample was collected; and
 "collection", the code of the plant collection; and
 "library",  the code of the high-throughput read
 library.