Milkweed-Aphid-Microbiome

Code for analysis of 16S rRNA data to analyze role host specialization on milkweed aphid microbiomes

This repository contains all the code necessary to replicate the data analysis and figure generation for the manuscript "Aphid species specializing on milkweed harbor taxonomically similar bacterial communities that differ in richness and relative abundance of core symbionts" Authors: Laramy Enders, Thorsten Hansen, Kirsten Brichler, John Couture, and Elizabeth French. Scientific Reports 12, 21127 (2022). https://doi.org/10.1038/s41598-022-25554-y

To replicate this analysis, first download raw sequence data from NCBI's SRA database, project number PRJNA635683. Then run trim.adapters.milkweed.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 MilkweedAphid_preprocessing_08182021revised.R code to perform dada2 preprocessing steps (alignment, error correction, chimera removal, taxonomy assignment, non-target seq removal).

Then run MilkweedAphid_figures_final.revised.R to perform final data analysis and generate figures (please note that paneled figures were joined in Adobe Illustrator, 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 mw16.trim.Buchfilt.rds and map.rds objects, which contain the phyloseq object of preprocessed data and sample metadata, respectively. All necessary data files can be downloaded from the data folder in the repository.