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.