Whole genome duplication events of T. polyphylla
Three genomes were selected for comparison to investigate the whole genome duplication (WGD) history of T. polyphylla : Vitis vinifera (Vvi), Cercidiphyllum japonicum (Cja), andTiarella polyphylla (Tpo). We identified paralogs (within Vvi, Cja, and Tpo) and orthologs (Tpo/Vvi and Tpo/Cja) using BLASTP (E-value ≤ 1e-5). For each gene pair, the number of synonymous substitutions per synonymous site (Ks ) was calculated using PAML v4.8 (Yang, 2007 ) using the YN00 NG model. MCScanX (Wang et al., 2012 ) was employed to identify syntenic blocks between genomes of Tpo, Vvi, and Cja based on the all-to-all BLASTP results, and a python version of MCScan was used to analyze the synteny (minspan = 100) to further detect whole genome duplication events.