Sequence processing and analysis for multigeneration drought experiment
Belowground plant microbiome resistance and response after two generations of drought exposure in common bean
Abby Sulesky-Grieb, Marie Simonin, A. Fina Bintarti, Brice Marolleau, Matthieu Barret, and Ashley Shade
This work is not published but will soon be available on bioRxiv.
The raw sequence data for this study are available in the NCBI SRA under bioproject PRJNA1058980
Coming soon.
Coming soon.
Code is split up into six directories. Files necessary to run R code are located in R_analysis_files.
The root and rhizosphere samples from Michigan were process separately. Code used for sequence processing including read QC, ASV clustering, taxonomy assignment, can be found under Multigen_Root_processing.Rmd and Multigen_Rhizosphere_processing.Rmd. Scripts were run in QIIME2 using SLURM on the MSU HPCC using slurm batch files with suffix .sb.
Code for sequence decontamination by extraction group was also completed separately for Michigan root and rhizosphere samples: root_OTU_decontam.Rmd and rhizo_OTU_decontam.Rmd. Output ASV table, taxonomy and metadata files from QIIME2 were used to create a Phyloseq object in R.
After decontamination, the datasets were combine and rarefied together. Decontaminated and rarefied phyloseq object is labelled root_rhizo_control_drought_rarefiedphyloseq copy.rds in the R_analysis_files folder.
Formal analysis of the Michigan and France datasets can be found under combined_16s_analysis.Rmd. All analysis was run with R and code was run in Rmarkdown. Input files of R phyloseq oobjects for both datasets can be found in the R_analysis_files folder.
Plant phenotypic measurements are located in the R_analysis_files folder. Analysis code can be found at PlantHealth_analysis.Rmd.
This work was supported by the United States Department of Agriculture award 2019-67019-29305, and by the Michigan State University Plant Resilience Institute.