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Fig. S1 The workflow applied in this paper.

Fig. S2 Gene copy number of 20 randomly selected low-copy nuclear genes in 15 angiosperms with sequenced genome.

Fig. S3 Single gene tree of 15 species with sequenced genome and information of 20 randomly selected low-copy genes.

Fig. S4 Comparison between the concatenated five good gene tree and the concatenated five bad gene tree.

Fig. S5 Size of SMC1 proteins and sequence identities between species with sequenced genomes.

Fig. S6 Comparison between Arabidopsis thaliana and A.  lyrata of introns of (a) SMC1, (b) SMC2, (c) MCM5, (d) MLH1 and (e) MSH1.

Fig. S7 ML tree inferred by PhyML 3.0 using the nucleotide matrix of (a) SMC1, (b) SMC2, (c) MCM5, (d) MLH1 and (e) MSH1.

Fig. S8 Comparison of five single gene trees with the best ML tree inferred by RAxML using the concatenated 5 genes.

Fig. S9 Comparison of five trees reconstructed by one gene and the concatenated 2–5 genes.

Fig. S10 Cladogram of the best ML tree conducted by RAxML based on the concatenated 5 gene nucleotide sequences.

Fig. S11 Phylogram inferred by MrBayes 3.0 based on the concatenated 5 gene nucleotide sequences of (a) 42 species, (b) eudicot species, (c) eudicot species excluding Saxifragales and Vitaceae species and (d) eudicot species excluding Caryophyllales.

Fig. S12 Phylogram of the best ML tree conducted by RAxML based on the concatenated 5 gene nucleotide matrix excluding the 3rd codon positions.

Methods S1 Supplemental methods.

Table S1 Taxon sampling

Table S2 Degenerate primers used in this study

Table S3 Specific primers used in this study

Table S4 Information of SMC1, four regions were separated to obtain the majority of gene sequences

Table S5 Information of SMC2, four regions were separated to obtain the majority of gene sequence

Table S6 Information of MCM5

Table S7 Information of MLH1

Table S8 Information of MSH1, two regions were separated to obtain gene sequences

Table S9 Evolutionary models inferred by ModelTest

Table S10 AU test results, P values > 0.05 are in bold

Table S11 Divergence time estimation inferred from BEAST analysis, ranges correspond to 95% highest posterior density (HPD). The divergence times of major groups were given

Table S12 Orthogroups identified by genome comparison with the length no < 300 amino acid

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