This folder contains a serious of R-code used for analyzing the presented RNA-seq dataset.
The work-flow can be found in the main script:Main_Nicotiana_sppRNAseq_NIATTr2.4.R, which calls individual script for detailed analysis.
To run these scripts, you need to install several R packages and unzip InputData.zip file, which contain all of raw data and neccessray information used by each script.
To simply reproduce the main results of the manuscript, you can just excute the last script: AnalyseDuplicationAndMITEs.R, which directly uses the pre-identified M4 module information;

Additonal information on the original data files (in InputData folder):
NIATTr2.4.A1.count.txt is the file contains all of raw count matrix among six Nicotiana species.
NIATTr2.4.A1.count.txt.TMM_normalized.FPKM is the file contains TMM normalized FPKM matrix among six Nicotiana species.
data.all.count.FPKM.M4.txt is the file contains the expression of all genes involved in M4 module.

In all of these three files, each row indicates a gene and each collumn indicates a sample.
Sample IDs are indicated as (species abbreviation)_(treatments abbreviation)_(replicate)
Species abbreviations are:
Nacu: N. acuminata
Natt: N. attenuata
Nmi: N. miersii
Nob: N. obtusifolia
Npau: N. pauciflora
Nlin: N. linearis

Treatments abbreviations are:
WW: wounding + water.
FAC: wounding + FAC.
MS: wounding + oral secretions of Manduca sexta.
SL: wounding + oral secretions of Spodoptera littoralis.

All data were based on N. attenuta genome version r2 (NIATTr2.4).
Questions related to these files should be addressed to Shuqing Xu (sxu@ice.mpg.de)
