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).