Code for analysis of 16S rRNA data and aphid performance data to analyze top-down and bottom-up effects of soil-microbiome-potato aphid interactions
This repository contains all the code necessary to replicate the data analysis and figure generation for the manuscript "Foliar aphid herbivory alters the tomato rhizosphere microbiome, but initial soil community determines the legacy effects" authors: Elizabeth French, Ian Kaplan, Laramy Enders. Front. Sustain. Food Syst., 08 April 2021 | https://doi.org/10.3389/fsufs.2021.629684
To replicate this analysis, first download raw sequence data from NCBI's SRA database, BioProject number PRJNA676117. Then run trim.adapters.rhizo.sub.text script to trim illumina adapters, followed by cutadapt.aphid.sub.txt script to remove primer sequences.
Once these steps have been completed, run AphidRhizoResponse_preprocessing_111020.r code to perform dada2 preprocessing steps (alignment, error correction, chimera removal, taxonomy assignment, non-target seq removal, contaminant removal).
Then run tomatoAphidRhizo_figures_final.R to perform final data analysis and generate figures (please note that paneled figures were joined in inkscape, and some aesthetic-only changes were made to R-generated figures for clarity).
If desired, this script can be run without the previous steps by importing the all.rds object, which contains the phyloseq object of preprocessed data. All additional necessary data files can be downloaded from the data folder in the repository.
