Conclusion
We successfully assembled the genome of Tiarella polyphylla and
reported the first chromosome-level assembly of Saxifragales. We
leveraged this genome to generate a large nuclear gene dataset covering
all superrosid orders, as well as microsynteny data from complete genome
assemblies to resolve relationships. We provided strong support for
Vitales as a sister to core rosids and Saxifragales. We also resolved
the relationships within the core rosids, demonstrating new
circumstances for fabids and malvids. There is a strong discordance
between nuclear and plastid phylogenetic hypotheses for superrosid
relationships, and our work demonstrates that this is best explained by
a combination of incomplete lineage sorting and ancient reticulation.