2.11 Genome duplication and synteny analyses
To estimate the time of whole-genome duplication events (WGD) in the Chinese walnut genome, reciprocal best hit (RBH) gene pairs were identified (Evalue is 1e-5) based on all-vs-all paralogs detected in BLASTP (Altschul et al., 1990). We identified synteny blocks and collinear blocks of gene pairs in the Chinese walnut genome using MCScanX with default parameters (Wang et al., 2012). The synonymous substitution rate (Ks) were calculated using the YN model in KaKs_Calculator v2.0 (Wang et al., 2010). The Ks distributions of orthologues within Chinese walnut and Persian walnut, and between Chinese walnut and Persian walnut were used to compare the relative substitution rates in different species by plotting with the ggplot2 package (Kaori and Murphy et al., 2013).