Authors: Scott A. Klasek, James E. Crants, Touqeer Abbas, Katherine Ashley, Marian L. Bolton, Madelyn Celovsky, Neil C. Gudmestead, Jianjun Hao, Jorge R. Ibarra Caballero, Courtney E. Jahn, Gilbert Kamgan Nkuekam, Richard A. Lankau, Robert P. Larkin, Eglantina Lopez-Echartea, Jeff Miller, Amber Moore, Julie S. Pasche, Matthew D. Ruark, Brenda K. Schroeder, Shan Shan, Victoria P. Skillman, Ali Srour, Anna K. Stasko, Kurt Steinke, Jane E. Stewart, Mike Thornton, Kim Zitnick-Anderson, Kenneth E. Frost, Carl J. Rosen, Linda L. Kinkel
This work is part of the Potato Soil Health Project, administered by the University of Minnesota and funded by the USDA National Institute of Food and Agriculture Specialty Crops Research Initiative (SCRI).
The manuscript associated with this archived repository is published in Phytobiomes.
Data Availability:
Raw 16S and ITS amplicon sequence reads associated with this study are publicly available as NCBI BioProject PRJNA992073.
Reproducible Workflow:
Code associated with this study is available at this repository.
By topic:
16S sequence processing
cutadapt bash script for processing ITS reads
ITS sequence processing
metadata cleanup
map
ordinations, barplots, and core commuity analysis Note that this is only for ITS, but applies to 16S analysis as well.
upset plots for core and site-specific ASVs
taxonomy barplots
soil chemical and textural analyses
alpha diversity
supplemental tables
more supplemental figures: class-level taxonomy barplots and mean read % abundance distributions of ASVs detected across different numbers of sites