This repository contains scripts and data used in the manuscript:
“Transcription factor retention through multiple polyploidisation steps in wheat” by Catherine EB Evans, Ramesh Arunkumar, Philippa Borrill https://doi.org/10.1093/g3journal/jkac147
Data files used across multiple analyses are in data_files. NB additional input files are found in the folders for individual analyses below.
Annotation and analysis of transcription factors in different wheat species: species_comparison (Figure 1)
Analysis of transcription factor family expression levels and tandem duplication: expression_level_and_tandem_duplication (Figure 2)
Analysis of transcription factor expression and co-expression: homoeolog_expression_correlation (Figure 3)
Analysis of SNP variation:
- Prediction of variant effects and plotting these per TF family: variant_effect_prediction (Figure 4b).
- Analysis of mutation load and pi: load_pi (Figure 4a)