Identification of nuclear markers for phylogenetic analyses
To resolve the superrosid phylogeny, 34 transcriptomes and three nuclear genomic datasets were downloaded from GenBank and combined with theT. polyphylla sequences obtained in this study, representing all accepted orders of superrosids and outgroups (Table S2 ). Two species of Buxales (Buxus semperivirens and Buxus sinicavar. insularis ) were selected as outgroups (Chanderbali et al., 2022 ). HybPiper v1.2 (Johnson et al., 2016 ) was used to identify nuclear markers among the Angiosperm-mega 353 gene set (McLay et al., 2021 ) from all the datasets. The identified contigs matching probe can be extract using the following command line “. /reads_first.py -b mega353.fasta -r sample_R1.fastq sample_R2.fastq -prefix sample_result -bwa”, and we selected the genes commonly shared in 38 samples to construct the phylogenetic tree.