Coffee duplicated regions
For the identification of C. canephora duplication, an all-againt-all comparison of the predicted proteins was performed using BLASTP (e-value threshold 1e-20) and by retaining the 10 best hits for each gene (except itself). Paralogous chromosomes segments composed of at least 15 duplicated genes (paralogs) with a maximal gap of 30 genes between syntenic genes were built with an in-house perl script.
Syntenic regions between Coffee, Tomato and Grape
For comparative genome analyses, orthologous gene-pairs were identified using predicted proteomes of Solanum lycopersicum (2.3) and Vitis vinifera (12X). Alignments were performed using BLASTP (e-value 1e−20) and retaining the 10 best hits. Syntenic chromosomes segments composed of at least 10 orthologs with a maximal gap of 30 genes between syntenic genes were built with an in-house perl script.
Gene pairs of syntenic blocks are painted in different colours according to the seven ancestral core eudicot chromosomes (Denoeud et al., 2014)