Analysis for the rhizoplane and rhizosphere assembly project on common bean
Elucidating the recruitment timing and development of the root microbiome over the common bean lifecycle
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 PRJNA1066866
Root photos for this study can be found on Figshare at the following DOIs: doi.org/10.6084/m9.figshare.25054997, doi.org/10.6084/m9.figshare.25055087, doi.org/10.6084/m9.figshare.25055774, doi.org/10.6084/m9.figshare.25057067.
Coming soon.
Coming soon.
Code is split up into four directories: Rhizo_assembly_seq_processing.Rmd, Rhizo_assembly_decontam.Rmd, Rhizo_assembly_analysis.Rmd, and Rhizo_Assembly_health_analysis.Rmd. Files necessary to run R code are located in R_Analysis_Files.
Code used for sequence processing including read QC, ASV clustering, taxonomy assignment, and tree building can be found under Rhizo_assembly_seq_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 can be found in Rhizo_assembly_decontam.Rmd. Output ASV table, taxonomy and metadata files from QIIME2 were used to create a Phyloseq object in R. Decontaminated and rarefied phyloseq object is labelled RA_phyloseq_rarefied.rds. Files are available in R_Analysis_Files folder.
Formal analysis can be found under Rhizo_assembly_analysis.Rmd. All analysis was run with R and code was run in Rmarkdown. Input files for Procrustes analysis can be found in R_Analysis_Files/Procrustes_analysis_files folder.
Above and below-ground plant measurements are located in the R_Analysis_Files folder. Root measurements were performed in ImageJ. Analysis code can be found at Rhizo_Assembly_health_analysis.Rmd.
This work was supported by the Michigan State University Plant Resilience Institute.