Whole genome microsynteny of superrosids
Sixteen genomes, including T. polyphylla , representing 14 orders of superrosids, were used for microsynteny network construction (Table S1 ) using an approach described in detail previously (Zhao et al., 2017 ; Zhao et al., 2021 ). Briefly, DIAMOND (v0.9.14.115) (Buchfink et al., 2015 ) was used for all pairwise intra- and inter-genome comparisons using all predicted protein sequences of each genome. Next, MCScanX (Wang et al., 2012 ) was used to detect all pairwise inter- and intra-synteny blocks under default settings. All synteny blocks were integrated into the total synteny network of syntenic genes. The Infomap algorithm (v0.20.0) (Rosvall & Bergstrom, 2008 ) was used for network clustering in the two-level partitioning mode with ten trials (-clu -N 10 -map -2). All synteny clusters identified were phylogenically profiled. A cluster profile recorded the number of nodes in a given cluster for each species. The collection of phylogenomic profiles (of all syntenic clusters) was summarized into a binary data matrix.