Whole genome duplication events of T. polyphylla
Microsynteny analysis revealed that a typical ancestral region in theT. polyphylla genome could be linearly connected to one region in
the Vitis vinifera and Cercidiphyllum japonicum genomes
(Fig. 2A ). Syntenic depth analyses showed that 45% of theT. polyphylla blocks were covered by one Tpo-Vvi block, 2% were
covered by two Tpo-Vvi blocks, 51% of the V. vinifera blocks
were covered by one Vvi-Tpo block, and 3% were covered by two Vvi-Tpo
blocks. Similarly, we found that 62% of the T. polyphylla blocks
were covered by one Tpo-Cja block, 2% were covered in two Tpo-Cja
blocks, and 67% of the C. japonicum blocks were covered by one
Cja-Tpo block and 1% were covered in two Cja-Tpo blocks (Fig.
2B ). These results suggest a 1:1 syntenic depth pattern for T.
polyphylla versus V. vinifera and T. polyphylla versusC. japonicum . Moreover, the Ksdistribution of paralogs also showed only one dominant peak for T.
polyphylla (1.39; Fig. 2C ), which was the same as V.
vinifera (1.12-1.40) and C. japonicum (0.79). The peak ofT. polyphylla occurred before the divergence peak at 0.77 between
Tpo and Vvi, and was earlier than the speciation peak at 0.46 between
Tpo and Cja, confirming that the WGD event occurred in the ancestor of
the three species. Hence, these results strongly suggest that, as
expected, T. polyphylla experienced the same gamma WGD event asV. vinifera and C. japonicum .