Data from: Host genotype and age shape the leaf and root microbiomes of a wild perennial plant

Wagner MR, Lundberg DS, del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T

Date Published: July 13, 2016

DOI: http://dx.doi.org/10.5061/dryad.g60r3

 

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title PRJEB10570
Description Study number PRJEB10570 at the European Nucleotide Archive contains the raw MiSeq reads from high-throughput sequencing of the 16S rRNA gene in hundreds of leaf, root, and soil samples. Note that some of these samples are associated with other experiments and were not analyzed for the Wagner et al. 2016 study.
Download //www.ebi.ac.uk/ena/data/view/PRJEB10570 (0 bytes)
Details View File Details
Title 16S rRNA gene copy number estimates
Downloaded 3159 times
Description Estimates of 16S rRNA gene copy number for OTUs analyzed in the Wagner et al. 2016 study. Created by following Kembel et al. (2012) Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance. PLoS Computational Biology 8 (10), e1002743.
Download Eco_Field_copynumest_forR.txt (1.008 Mb)
Details View File Details
Title Glucosinolate data
Downloaded 24 times
Description Collection of glucosinolate data is described in Supplementary Note 1 of the article. HPLC peaks were called and area under each curve was integrated automatically by Agilent ChemStation software. Columns beginning with "area_" include the area under chromatogram peaks corresponding to the internal standard (Sinigrin) or one of the glucosinolate compounds (2OH1ME, 1ME, 6MSOH, 1MP, or I3M). "Weight" is the mass of air-dried samples, in mg. "Batch" is the identifier for groups of samples measured in the same HPLC run. "HPLC_ID" is a unique identifier for a glucosinolate sample, and "Plant_ID" is a unique identifier for individual plants in the field experiment.
Download Ecotypes_field_glucosinolates.txt (33.30 Kb)
Details View File Details
Title OTU phylogeny
Downloaded 38 times
Description Phylogeny of all OTUs (based on 97% 16S rRNA gene sequence identity). Generated from representative sequences using the midpoint method in QIIME.
Download phylogeny.tre (1.415 Mb)
Details View File Details
Title Field site coordinates
Downloaded 24 times
Description Latitude and longitude of 5 sites where genotypes were collected from natural B. stricta populations / where experimental common gardens were located.
Download site_coords_Ecotypes.txt (129 bytes)
Details View File Details
Title Soil / environmental data
Downloaded 21 times
Description Data on soil & vegetation characteristics from field sites used in this experiment. "PlantDiv" = number of plant morphospecies present in each block; “Veg” = percent of each block covered by vegetation (aggregate of estimated percent cover for 50 10x10cm sub-plots per block). Units are ppm (except for pH, unitless; and conductivity, umho/cm).
Download soildata.txt (4.114 Kb)
Details View File Details
Title Sample metadata
Downloaded 38 times
Description Microbiome sample metadata. "SampleID" = unique identifier for a sequenced 16S rDNA amplicon pool corresponding to a single sample. "Name" = more descriptive unique sample name. "Plant_ID" = unique identifier for individual plants; may correspond to >1 SampleIDs when both roots and leaves were sampled from the same plant; "Experiment" = sub-experiment that a sample belongs to (e.g., "ecotypes" = main field experiment described in Wagner et al. 2016; "ecoGH" = greenhouse experiment described in supplementary information of Wagner et al. 2016; "rilGH" and "fieldBCMA" are not presented in Wagner et al. 2016); "Cohort" = year the individual (Plant_ID) was planted, if applicable; "Harvested" = year sample was harvested; "Treatment" = type of soil the individual was planted in (only applicable to greenhouse experiments); "oldPlate" = identifier of the 96-well plate containing the sample before full randomization; "newPlate" = MiSeq run, i.e., identifier of the amplicon library into which the sample was pooled, i.e., the 96-well plate containing the sample after full randomization; "Analysis" = broadest experimental grouping of samples; either "Ecotypes" (which contains samples described in Wagner et al. 2016) or "BCMA" (containing samples not analyzed or described in Wagner et al. 2016).
Download SMD.txt (168.7 Kb)
Details View File Details
Title OTU table (97%)
Downloaded 28 times
Description OTU table (for OTUs picked based on 97% 16S rRNA gene sequence identity) that forms the basis for most analyses in Wagner et al. 2016. Generated from raw MiSeq reads (see "Bioinformatics pipeline"). Columns are sample names (correspond to "SampleID" column in "Sample metadata" file); rows are OTUs. Decompress file using the Linux/UNIX command ' bunzip2 otuTable97.txt.bz2 '
Download otuTable97.txt.bz2 (6.581 Mb)
Details View File Details
Title Contaminant OTUs
Downloaded 25 times
Description List of OTUs identified as likely contaminants based on comparison to list of known contaminant 16S rRNA gene sequences (generated using custom scripts; see "Bioinformatics pipeline")
Download contaminants.fasta (88.40 Kb)
Details View File Details
Title OTU taxonomic assignments (97%)
Downloaded 53 times
Description Taxonomic assignments of OTUs (binned at 97% 16S rRNA gene sequence identity), generated by comparing representative OTU sequences to the Greengenes database using the RDP classifier in Qiime (see "Bioinformatics pipeline").
Download taxAssignments97.txt (6.022 Mb)
Details View File Details
Title Taxonomic assignments for OTUs binned at 99%
Downloaded 36 times
Description Taxonomic assignments of OTUs (binned at 99% 16S rRNA gene sequence identity), generated by comparing representative OTU sequences to the Greengenes database using the RDP classifier in Qiime. * Note that these are OTUs based on 99% identity, NOT the OTUs that were used for most analyses in Wagner et al. 2016 *
Download taxAssignments99.txt (34.74 Mb)
Details View File Details
Title Representative OTU 16S rRNA gene sequences
Downloaded 20 times
Description Representative sequence for each OTU (based on 97% sequence identity), in FASTA format. Generated from raw MiSeq reads using FLASH and UPARSE software (see "Bioinformatics pipeline")
Download OTUrepSeqs97.fa (12.98 Mb)
Details View File Details
Title OTU table (binned at 99%)
Downloaded 20 times
Description OTU table (for OTUs picked based on 99% 16S rRNA gene sequence identity) that forms the basis for most analyses in Wagner et al. 2016. Generated from raw MiSeq reads. Columns are sample names (correspond to "SampleID" column in "Sample metadata" file); rows are OTUs. Decompress file using the Linux/UNIX command ' bunzip2 otuTable99.txt.bz2 ' ** note that most analyses in this paper used OTUs picked based on 97% sequence similarity-- these are in a different file (otuTable97.txt) **
Download otuTable99.txt.bz2 (21.72 Mb)
Details View File Details
Title Key to Plant IDs
Downloaded 21 times
Description Master list of all individuals originally planted in the field experiment- columns as in the Sample Metadata file (SMD.txt)
Download plant_key.txt (111.7 Kb)
Details View File Details
Title R scripts for data analysis
Downloaded 143 times
Description Archive of R scripts used to produce results in Wagner et al. 2016. See README file for notes on contents and recommendations for use.
Download README.txt (1.912 Kb)
Download R_code_Wagner_etal_2016.tar (327.1 Kb)
Details View File Details
Title Bioinformatics pipeline
Downloaded 93 times
Description A description of the bioinformatics pipeline used to process raw MiSeq data, including parameter values and sample syntax.
Download bioinformatics_pipeline_Wagner_etal_2016.txt (5.972 Kb)
Details View File Details

When using this data, please cite the original publication:

Wagner MR, Lundberg DS, del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T (2016) Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Nature Communications 7: 12151. http://dx.doi.org/10.1038/ncomms12151

Additionally, please cite the Dryad data package:

Wagner MR, Lundberg DS, del Rio TG, Tringe SG, Dangl JL, Mitchell-Olds T (2016) Data from: Host genotype and age shape the leaf and root microbiomes of a wild perennial plant. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.g60r3
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: