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.