1. 7 angiosperm genomes OrthoMCL 7 taxa, 7-9 genes HaMStR Physcomitrella patens Orthologous groups (size ≥ 300aa, identity ≥ 60%) GO Ontology 15 genomes 3 angiosperm EST 73 species blast 20 genes with other functions 28 genes with DNA/RNA metabolism Gene copy number Single gene trees Gene copy number SMC1, SMC2, MCM5, MLH1, and MSH1 blast PCR 3 gymnosperm EST blast Phylogenetic analyses Divergence time estimation Fig. S1 The workflow applied in this paper. Arabidopsis thaliana, Populus tricocarpa Prunus persica, Vitis vinifera, Mimulus guttatus Oryza sativa, Sorghum bicolor

2. Glycine max Cucumis sativus Manihot esculenta Ricinus communis Populus trichocarpa Arabidopsis thaliana Arabidopsis lyrata Carica papaya Vitis vinifera Mimulus guttatus Aquilegia coerulea Sorghum bicolor Setaria italica Oryza sativa Brachypodium distachyon 12>=3 AT1G02100AT1G63160AT1G53120AT1G18270 AT2G27680AT2G40760AT3G10370AT3G18140AT4G24270AT4G32910AT4G36390AT3G05040AT5G08400AT5G15920AT5G17620AT5G43710AT5G45380AT5 G1149 0 AT5G67100AT5G52910 Fig. S2 Gene copy number of 20 randomly selected low-copy nuclear genes in 15 angiosperms with whole sequenced genome. The organismal relationships modified from our results were shown on the left. The gene names were provided at the bottom, gene copy numbers were donated by different colors with green, orange, and red indicating only one, two and 3 or more copies, respectively.

3. IDLength (AA) identitiesFunctionIDLength (AA) identitiesFunction AT1G021003320.686MethyltransferaseAT4G329107160.616unkown AT1G1827013930.667Zinc ion bindingAT4G363906400.672Transferase activity AT1G531203200.615RNA bindingAT5G084003330.613unknown AT1G631603330.850DNA replicationAT5G114908500.749adaptin family AT2G276803840.688OxidoreductaseAT5G1592010530.602ATP binding AT2G407604740.606PhosphataseAT5G176203290.754unknown AT3G103706290.773GlycerophosphateAT5G437106240.677Glycosyl hydrolase AT3G181403050.850Nucleotide bindingAT5G453807040.754Sodium symporter AT3G0504012020.594ARM repeatAT5G5291011410.518Circadian rhythm AT4G242708170.439Nucleic acid bindingAT5G6710015240.621DNA-directed DNA polymerase Glycine max Cucumis sativus Manihot esculenta Ricinus communis Populus trichocarpa Arabidopsis thaliana Arabidopsis lyrata Carica papaya Vitis vinifera Mimulus guttatus Aquilegia coerulea Sorghum bicolor Setaria italica Oryza sativa Brachypodium distachyon * * * Fig. S3 Single gene tree of 15 species with sequenced genome and information of 20 randomly selected low-copy genes. The tree was generated by PhyML based on AT5G52910 amino acid sequences using JTT model. If other 19 single gene trees were congruent with the AT5G52910 tree at one node, the bar with corresponding color was placed on the node, asterids indicate all 20 single gene trees supporting this combination. Detailed information on support by single gene trees will be provided upon request.

4. 0.1 96/60 22/48 99/- 100/- 98/- 100/99 99/30 100/98 * Cucumis sativus Glycine max Manihot esculenta Ricinus communis Populus trichocarpa Arabidopsis thaliana Arabidopsis lyrata Carica papaya Vitis vinifera Mimulus guttatus Aquilegia coerulea Brachypodium distachyon Oryza sativa Setaria italica Sorghum bicolor * * * Fig. S4 Comparison between the concatenated five good gene tree and the concatenated five bad gene tree. The phylogram is the best ML tree conducted by PhyML 3.0 using five good genes (AT5G15920, AT5G17620, AT5G43710, AT5G52910, and AT5G67100), the two numbers associated with the branch are the supporting values, with the former and the latter being the one of concatenated five good gene tree and the one of concatenated five bad gene tree ( AT1G02100, AT1G18270, AT2G27680, AT2G40760, AT3G10370 ), respectively. Asterisk indicates 100% bootstrap at this node for both trees. *

5. Fig. S5. Size of SMC1 proteins and sequence identities between species with sequenced genomes. The sizes of amino acid of angiosperm species with whole-sequenced genomes are shown in the diagonal cells of the table. Sequence identities between two proteins are indicated by color. The gene names are abbreviated as follows: Glyma_1, Glycine max_1; Cucsa, Cucumis sativus; Manes, Manihot esculenta; Ricco, Ricinus communis; Poptr, Populus trichocarpa; Arath, Arabidopsis thaliana; Araly, Arabidopsis lyrata; Carpa, Carica papaya; Vitvi, Vitis vinifera; Mimgu, Mimulus guttatus; Aquco, Aquilegia coerulea; Sorbi, Sorghum bicolor; Setit, Setaria italica; Orysa, Oryza sativa; Bradi, Brachypodium distachyon. 1266 1283 1219 1220 1232 1239 1257 1030 1459 1226 1208 1253 1233 1264 1227

6. Aly : tgctcaacgtgagaagaagattgctgagaaaagctcgaaacttggaaaaa Ath : tgctcaacgtgagaagaagattgctgagaaaagctcgaagcttggaaaaa Aly : ttGTGAGTATACCTTGGAAATCTGTGGTTAACAGATTCTATTTTCCCTTT Ath : ttGTGAGTATACCTTGGAAATCTGTGGTTAACAGATTCTATTTTCCCTTT Aly : CAAATATAGCATTAGCATTTCCAGACATCTCTTACAATTTATTTTTTGTT Ath : TAAATATAGCATTTTGAGA-CATGTCTTACATTTTTTTTTATTTTTTGTT Aly : ACCCTCTGGAATTTTACTAA-CGTTCTCACTTGAGTAACTTATATCTGTA Ath : ATCCTCTGGAATTTCACTAAACTTTCTCACTTGAGTAACTTATATCTGTA Aly : CTTTTCCTGTGAGCAGcaacctgagcttctgagatttaaggaggagatag Ath : CCTTTCCTGTGAGCAGcaacctgagcttctgagatttaaggaggagatag Aly : ctcgcattaaagcaaaaattgaga Ath : ctcgcattaaagcaaaaattgaga 1 234567891011121314151617 Arabidopsis lyrata 1021041634214224531819574174834606048026436993 Arabidopsis thaliana 14610516348442246618195741748347661481281390114 Identity (%)66.482.684.777.191.990.393.990.595.595.496.491.491.295.188.388.266.7 intronLength Species (bp) Fig. S6a. Comparison of introns of SMC1 between Arabidopsis thaliana and A. lyrata. The table shows the length of each intron from Arabidopsis thaliana and A. lyrata and the percentage of identity for every intron. The alignment of intron 3 of SMC1 is shown below. The conserved gene sequences are represented by black characters, while the variable regions are shown by red ones. Exon and intron regions are shown by lower case letters and upper case letters, respectively.

7. 12345678910111213141516171819 Arabidopsis lyrata 10891877581841652781082091181528039112997122164107 Arabidopsis thaliana 99908875808412132390204115153793871208511915692 Identity (%)63.987.989.790.787.795.264.878.376.995.789.892.196.392.194.683.587.784.877.6 intronLength Species (bp) Aly : ggcattgcttctcttcaaaccggctcctctttatatattagacgagGTAC Ath : ggcattgcttctcttcaaaccggctcctctttatatattagatgagGTAC Aly : GTCTCTGCTTTTCGATTTTTGATT-CTCAGTTCCCAACTGATATTTCAAA Ath : ATCTCTGCTTTTCAATTTCAGATTTCTCAGTTTCCAATTGATATTTCAAA Aly : TTACCATAGAAGATCTCAAGGGTTTGTTTATGTTTTTGATGTGGA----- Ath : TTATCATAGAAGATCTATAGGGTTGGTTTATGTTTCCGATGTGGAACACT Aly : --TTTTCAATAAACAATCAGCGAGTGAAGAGAGAAAATACTCATGATTTTG Ath : GATTTTGCATTAACAATCAGCGAGTGAAGAGAGAAAATACTCATGATTTTG Aly : ATTTATTTCAGgttgatgcagctcttgatctcagtcacacacagaacatag Ath : AATTATATCAGgttgatgcagctcttgatctcagtcacacacagaacatag Aly : gaagaatg Ath : gaagaatg Fig. S6b. Comparison of introns of SMC2 between Arabidopsis thaliana and A. lyrata. The table shows the length of each intron from Arabidopsis thaliana and A. lyrata and the percentage of identity for every intron. (b), The alignment of intron 18 of SMC2 is shown below. The conserved gene sequences are represented by black characters, while the variable regions are shown by red ones. Exon and intron regions are shown by lower case letters and upper case letters, respectively.

8. 1 234567891011121314151617 Arabidopsis lyrata 141778675993128720681801011478683848882 Arabidopsis thaliana 68708071902948520592851031499082777982 Identity (%)32.666.286.076.081.886.2 89.380.488.291.289.985.689.283.386.495.1 intronLength Species (bp) Aly : tggaagacacaaatgaggccagttcccgtggccctgccaacttcactcct Ath : tggaagacacaaatgaggccagttcccgtggccctgccaacttcactcct Aly : gacgaaGTTAGTATCGCATCATTTGGATCATTTTTTT-CTTCATTTGATA Ath : gacgaaGTTAGTATCGCATCATTTGGTTCTTTTTGTTTTCTCATTTGATA Aly : GCCTATGCCATCCATGGTTTCACAATGGACTGTTAAAGTCAACATGCCTG Ath : GCCTATGTCATCCATGGTTTCACAATGAACTATTAAAGTTAACATGGCTG Aly : AACTACTGTTACTGGAAACCAAATGCCTTACGTAGCTGTTGGCTTTATGA Ath : AATTATTGTTACTGGAAACCAAATGCCTTAGGTAGCTGTTGGCTCTATGA Aly : AATTTGATTCTTTATGTAACTCCCAAATGGATGTGATGGTGTTTTCAGGA Ath : AATT-----CTTTATGTAACTCCCAAATGAATGTGATGGTGTTTTCTGGA Aly : AACATACTCTGTGCTATTAGTTTACTATGAACCATTTAGGCCTGCTTGGA Ath : AATATTCTCTGTGCTACTAGTTTACTATGAAACATTTAGGCCTGCTTGGA Aly : ACATCACTTTATACAGCCTTGTTGTACAATTCCATTTATCAGTTTTGCCT Ath : A--------------GCCTAGTTGTACAATTCCATTTATCAGTTTTGTCT Aly : TTCCTAATATTACTTTTAGgaggaagaattcaaaaagtttgctgatagtc Ath : TCCATAATATTACTTTTAGgaggaagaattcaaaaagtttgctgatagtc Aly : aagatgtatacaagaacatttg Ath : aagatgtatacaagaacatttg Fig. S6c. Comparison of introns of MCM5 between Arabidopsis thaliana and A. lyrata. (a), The table shows the length of each intron from Arabidopsis thaliana and A. lyrata and the percentage of identity for every intron. (b), The alignment of intron 6 of MCM5 is shown below. The conserved gene sequences are represented by black characters, while the variable regions are shown by red ones. Exon and intron regions are shown by lower case letters and upper case letters, respectively.

9. 1 23456789101112131415 Arabidopsis lyrata 988280929017596113214858914811296120 Arabidopsis thaliana 126969210496180961142228513914511094118 % Identity70.676.075.076.986.583.389.688.678.485.946.889.089.396.993.3 intron Length Species (bp) Aly : ggttacatgcctttttgcaacccaagccacaaagtctccctgacaaggtt Ath : ggttacatgcctttttgcaacccaagccacataatctccctgacaaggtt Aly : tctagtttgagtgtagtaagGTAAGACCCCACCTGATACAAGACGTGTAG Ath : tctagtctgagtgtagttagGTAAGACCTCATGTGATACCGGATATGTAG Aly : TTACATATAAACAACATTGGATCCCATGTCATTACTGTATTCAAAACTCT Ath : TTTCATACAAACAAAATTGGATCCCGAGTCATCACTT--TTCAAAAATCG Aly : CATCTTATTTACCAGTAGATGTTCACTCCTTTAATTTCCGTGAAAATTGT Ath : CATCTTATTTACCAAA-GATGTGCACTCCTTTGATTTCCTTGAAAAGTAT Aly : TTCCTGCAGGTGTTTCTTTGGCATGATTCTTTATTGGTTAGATGTGTTGC Ath : TTGCTGCCGGTGTTACTATGGCTTGATA-----TTTCTTTTATTTTTTAC Aly : GCAACTGCAGTATATTC–ACTTGATCT–TATTACGGAA-TTGCAGgtctt Ath : ---ACTTCATTATATTCCACATGATATATATTACTGAACTTGCAGgtctt Aly : ctgtaaggcaaagaagaaacccaaaggaaactgctgatctttctag Ath : cggtaaggcaaagaagaaacccaaaggaaactgctgatctttctag Fig. S6d. Comparison of introns of MLH1 between Arabidopsis thaliana and A. lyrata. (a), The table shows the length of each intron from Arabidopsis thaliana and A. lyrata and the percentage of identity for every intron. (b), The alignment of intron 9 of MLH1 is shown below. The conserved gene sequences are represented by black characters, while the variable regions are shown by red ones. Exon and intron regions are shown by lower case letters and upper case letters, respectively.

10. 1234567891011121314151617181920 Arabidopsis lyrata 355297152451108136133249989112810215022013392741339895 Arabidopsis thaliana 182260133454891301112659296839310719112891731269795 Identity (%)33.071.769.184.663.975.778.983.075.581.332.072.539.370.577.483.789.285.795.984.2 intron Length Species (bp) Aly : gctgtcatcatctattcttacatgcatcgttgaggcacaatgcatcagGT Ath : gctgtcatcatcttttcttacatgcatcgttgaggcacaatgcatcagGT Aly : TTTGTATACAATCT------CTACATTGTATTAGCACCTCTGAACTGT-G Ath : TTTGAATACTATCTTCAATTCTACATTGTATTAGCATCTCTGAACTGTTG Aly : AAGATAATGCCAA-------ATGTGGACAGTGTGCAATTTTAACATCACA Ath : AAGATAGTGCCAATAATAGAATGTAGACGG-GTGCCATTTTATCCTCACA Aly : TGAACATAAGTACGCCCAGGTGGCAGCATATGATCTAGCAGTCTATTTAA Ath : TGAACATAAGTATTCTCAGGTGGTAGCATATGATCTAGCAAATACTTTAG Aly : AGTGTCAGGAGACTGTTAGAAGCAAAATACTATTCATGATTTTT--CAAC Ath : AGAGTCTGGAGACAGTTACAAGAGAAATACGATTCATGTTTTGTGTCAAC Aly : TTAATTAGCTTTTGAGCTTTATTGTCTTTTACGATAACAATTCTTGAAAA Ath : TTAATTGACTTTTGAGCTTTGTGGTCTTTTCTGATA-CAATTCTTGTTAA Aly : TTAT—-GGTATGCAGggacgtgccgctggggagagtttggggaagggggt Ath : TTTTTTATTATGCAGggacgtgccgctggggagagtttggggaagggggt Aly : cttctctgggg Ath : cttctctgggg Fig. S6e. Comparison of introns of MSH1 between Arabidopsis thaliana and A. lyrata. (a), The table shows the length of each intron from Arabidopsis thaliana and A. lyrata and the percentage of identity for every intron. (b), The alignment of intron 8 of MSH1 is shown below. The conserved gene sequences are represented by black characters, while the variable regions are shown by red ones. Exon and intron regions are shown by lower case letters and upper case letters, respectively. Gunnera manicata

11. Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Hibiscus syriacus Stachyurus yunnanensis Arabidopsis lyrata Arabidopsis thaliana Carica papaya Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Pelargonium hortorum Ulmus macrocarpa Morus alba Photinia serrulata Glycine max_2 Glycine max_1 Cyclobalanopsis glauca Oenothera erythrosepala Lagerstroemia limii Cucumis sativus Stellaria media Phytolacca americana Polygonum runcinatum Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Vinca major Nerium oleander Galium aparine Solanum lycopersicum Pharbitis nil Ilex purpurea Aucuba japonica Lonicera japonica Pittosporum tobira Hedera nepalensis Ligusticum chuanxiong Lactuca sativa Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Diospyros kaki Rhododendron pulchrum Cercidiphyllum japonicum Distylium buxifolium Paeonia lactiflora Vitis vinifera Gunnera manicata Buxus sinica Pachysandra terminalis Platanus acerifolia Meliosma parviflora Aquilegia coerulea Ranunculus muricatus Nandina domestica Dicentra spectabilis Sorghum bicolor Setaria italica Brachypodium distachyon Oryza sativa Dioscorea opposita Canna indica Musa basjoo Asparagus officinalis Yucca filamentosa Iris japonica Lilium brownii Pinellia ternata Cinnamomum camphora Acorus calamus Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Liriodendron chinese x L. tulipifera Magnolia denudata Chimonanthus praecox Chloranthus elatior & C. spicatus Ceratophyllum demersum Illicium henryi Schisandra propinqua & S. sphenanthera Nuphar advena_2 Nuphar advena_1 Cabomba caroliniana Amborella trichopoda Pinus Picea Zamia fischeri 100 95 99 91 100 97 100 96 15 100 89 99 85 100 84 100 37 100 99 87 100 93 5 100 48 92 100 15 100 79 63 100 82 100 61 95 100 78 97 100 94 99 100 98 48 86 99 96 100 99 100 74 100 94 99 88 96 90 100 50 52 9 100 56 96 100 36 99 100 59 90 68 100 0.1 Fig. S7a. ML tree of SMC1 inferred by PhyML 3.0 using the nucleotide matrix. Numbers associated with branches are SH aLRT supporting values. If two copies are found in one species, the gene that evolved faster is marked by gray background, then it will be excluded from further analyses. 100

12. Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Arabidopsis thaliana_2 Arabidopsis thaliana_1 Arabidopsis lyrata Hibiscus syriacus Carica papaya Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa_2 Populus tricocarpa_1 Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max_2 Glycine max_1 Cucumis sativus Cyclobalanopsis glauca Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Vitis vinifera Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Pharbitis nil Solanum lycopersicum Vinca major Nerium oleander Galium aparine Lactuca sativa Pittosporum tobira Hedera nepalensis Ligusticum chuanxiong Lonicera japonica Ilex purpurea Aucuba japonica Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Phytolacca americana Stellaria media Polygonum runcinatum Gunnera manicata Buxus sinica Pachysandra terminalis Aquilegia coerulea Ranunculus muricatus Nandina domestica Meliosma parviflora Platanus acerifolia Dicentra spectabilis Sorghum bicolor Setaria italica Oryza sativa Brachypodium distachyon Canna indica Musa basjoo Trachycarpus fortunei Yucca filamentosa Asparagus officinalis Iris japonica Lilium brownii Alisma plantago-aquatica Pinellia ternata Acorus calamus Chimonanthus praecox Cinnamomum camphora Asarum heterotropoides Liriodendron chinese x L. tulipifera Magnolia denudata Chloranthus elatior & C. spicatus Aristolochia fimbriata Houttuynia cordata Ceratophyllum demersum Illicium henryi Schisandra propinqua & S. sphenanthera Nuphar advena Amborella trichopoda Picea Pinus 89 99 100 55 100 99 63 100 99 92 2 100 99 92 35 100 37 99 100 73 81 100 55 100 34 92 100 85 100 64 53 80 99 100 32 65 99 100 99 97 100 82 100 37 99 100 17 100 99 0 100 83 100 86 98 100 82 84 44 97 99 12 100 85 0 100 59 99 49 57 99 100 49 99 50 100 0.1 Fig. S7b. ML tree of SMC2 inferred by PhyML 3.0 using the nucleotide matrix. Numbers associated with branches are SH aLRT supporting values. If two copies are found in one species, the gene that evolved faster is highlighted by gray background, then it will be excluded from further analyses. Cabomba caroliniana

13. Poncirus trifoliata Rhus chinensis Sapindus mukorossi Euonymus carnosus Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Manihot esculenta Ricinus communis Populus tricocarpa _2 Populus tricocarpa _1 Hypericum chinense Stachyurus yunnanensis Cyclobalanopsis glauca Ulmus macrocarpa Photinia serrulata Morus alba Glycine max_2 Glycine max_1 Lagerstroemia limii Oenothera erythrosepala Cucumis sativus Pelargonium hortorum Cercidiphyllum japonicum Distylium buxifolium Paeonia lactiflora Gunnera manicata Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Vinca major Nerium oleander Galium aparine Ligusticum chuanxiong Pittosporum tobira Hedera nepalensis Lonicera japonica Lactuca sativa Diospyros kaki Actinidia arguta Aucuba japonica Ilex purpurea Cornus officinalis Cornus wisoniana Philadelphus incanus Phytolacca americana Polygonum runcinatum Stellaria media Dicentra spectabilis Buxus sinica Pachysandra terminalis Aquilegia coerulea Ranunculus muricatus Nandina domestica Platanus acerifolia Meliosma parviflora Sorghum bicolor Setaria italica Brachypodium distachyon Oryza sativa Canna indica Musa basjoo Trachycarpus fortunei Asparagus officinalis Yucca filamentosa Iris japonica Dioscorea opposita Lilium brownii Alisma plantago-aquatica Pinellia ternata Acorus calamus Liriodendron chinese x L. tulipifera Magnolia denudata Chimonanthus praecox Illicium henryi Schisandra propinqua & S. sphenanthera Chloranthus elatior & C. spicatus Nuphar advena Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Amborella trichopoda Pinus Picea Zamia fischeri 49 3 0 82 100 30 20 100 85 98 97 20 100 98 53 99 52 100 77 99 77 100 77 82 97 98 59 57 99 56 5 95 38 100 86 82 96 95 89 100 81 41 68 100 95 41 98 77 53 97 75 47 98 76 17 96 85 100 70 100 80 88 74 90 92 85 90 81 69 35 99 81 93 24 95 78 94 100 82 92 97 100 0.1 Fig. S7c. ML tree of MCM5 inferred by PhyML 3.0 using the nucleotide matrix. Numbers associated with branches are SH aLRT supporting values. If two copies are found in one species, the gene that evolved faster is highlighted by gray background, then it will be excluded from further analyses. Cabomba caroliniana

14. Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Stachyurus yunnanensis Arabidopsis lyrata Arabidopsis thaliana Hypericum chinense Hibiscus syriacus Carica papaya Manihot esculenta Ricinus communis Populus tricocarpa Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Cyclobalanopsis glauca Lagerstroemia limii Glycine max Pelargonium hortorum Cucumis sativus Cercidiphyllum japonicum Paeonia lactiflora Distylium buxifolium Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Pharbitis nil Solanum lycopersicum Nerium oleander Vinca major Galium aparine Lactuca sativa Ligusticum chuanxiong Pittosporum tobira Hedera nepalensis Lonicera japonica Ilex purpurea Aucuba japonica Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Gunnera manicata Phytolacca americana Stellaria media Polygonum runcinatum Pachysandra terminalis Buxus sinica Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Aristolochia fimbriata Houttuynia cordata Liriodendron chinese x L. tulipifera Magnolia denudata Cinnamomum camphora Chimonanthus praecox Illicium henryi Schisandra propinqua & S. sphenanthera Amborella trichopoda Sorghum bicolor Setaria italica Brachypodium distachyon Oryza sativa Canna indica Trachycarpus fortunei Lilium brownii Dioscorea opposita Yucca filamentosa Asparagus officinalis Iris japonica Alisma plantago-aquatica Pinellia ternata Acorus calamus Ceratophyllum demersum Nuphar advena Zamia fischeri Pinus 100 92 38 92 95 96 6 100 87 100 66 70 95 59 99 87 84 32 37 69 84 83 92 75 89 100 14 100 70 60 8 96 99 11 99 98 62 93 31 30 97 90 83 99 100 99 96 11 89 99 100 93 100 43 97 90 93 99 87 94 5 100 90 12 3 95 99 100 71 0 50 78 100 73 99 0.1 Fig. S7d. ML tree of MLH1 inferred by PhyML 3.0 using the nucleotide matrix. Numbers associated with branches are SH aLRT supporting values.

15. Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Hibiscus syriacus Stachyurus yunnanensis Euonymus carnosus Arabidopsis lyrata Arabidopsis thaliana Carica papaya Manihot esculenta Ricinus communis Hypericum chinense Populus tricocarpa Ulmus macrocarpa Morus alba Photinia serrulata Cucumis sativus Glycine max Cyclobalanopsis glauca Lagerstroemia limii Oenothera erythrosepala Cercidiphyllum japonicum Paeonia lactiflora Distylium buxifolium Vitis vinifera Callicarpa bodinieri Mimulus guttatus Pittosporum tobira Jassminum nudiflorum Nerium oleander Vinca major Galium aparine Pharbitis nil Solanum lycopersicum Aucuba japonica Ilex purpurea Ligusticum chuanxiong Hedera nepalensis Lonicera japonica Lactuca sativa Actinidia arguta Rhododendron pulchrum Diospyros kaki Cornus officinalis Cornus wisoniana Philadelphus incanus Stellaria media Phytolacca americana Polygonum runcinatum Gunnera manicata Buxus sinica Pachysandra terminalis Platanus acerifolia Meliosma parviflora Aquilegia coerulea Ranunculus muricatus Nandina domestica Dicentra spectabilis Sorghum bicolor Setaria italica Brachypodium distachyon Oryza sativa Canna indica Musa basjoo Trachycarpus fortunei Yucca filamentosa Asparagus officinalis Iris japonica Dioscorea opposita Lilium brownii Alisma plantago-aquatica Pinellia ternata Acorus calamus Chloranthus elatior & C. spicatus Aristolochia fimbriata Houttuynia cordata Asarum heterotropoides Magnolia denudata Liriodendron chinese x L. tulipifera Cinnamomum camphora Chimonanthus praecox Nuphar advena Ceratophyllum demersum Illicium henryi Schisandra propinqua & S. sphenanthera Amborella trichopoda 70 99 92 99 100 91 66 72 97 57 17 63 100 93 41 100 98 0 99 72 99 92 100 98 99 51 95 100 99 100 99 89 100 94 80 38 97 98 100 24 100 35 98 99 88 100 97 39 93 99 92 100 99 6 6 84 100 78 60 100 85 33 83 89 88 94 99 100 23 78 99 100 96 84 100 97 0.1 Fig. S7e. ML tree of MSH1 inferred by PhyML 3.0 using the nucleotide matrix. Numbers associated with branches are SH aLRT supporting values. Cabomba caroliniana

16. Poncirus trifoliata Tetradium ruticarpum Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Stellaria media Phytolacca americana Polygonum runcinatum Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Nerium oleander Vinca major Galium aparine Ilex purpurea Aucuba japonica Hedera nepalensis Ligusticum chuanxiong Pittosporum tobira Lonicera japonica Lactuca sativa Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Gunnera manicata Buxus sinica Pachysandra terminalis Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis Oryza sativa Brachypodium distachyon Setaria italica Sorghum bicolor Musa basjoo Canna indica Trachycarpus fortunei Dioscorea opposita Yucca filamentosa Asparagus officinalis Iris japonica Lilium brownii Pinellia ternata Alisma plantago-aquatica Acorus calamus Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Cinnamomum camphora Chimonanthus praecox Magnolia denudata Liriodendron chinese x L. tulipifera Ceratophyllum demersum Chloranthus elatior & C. spicatus Schisandra propinqua & S. sphenanthera Illicium henryi Nuphar advena Amborella trichopoda Pinus Picea Zamia fischeri 1/2/-/4/5 1/2/3/4/- 1/2/-/4/5 1/2/3/4/5 1/-/3/-/5 -/2/3/4/- 1/2/-/-/- 1/2/3/4/5 1/2/-/4/- 1/2/3/-/5 1/-/-/-/- 1/2/3/4/5 1/2/-/4/5 1/2/3/4/5 1/-/-/-/ 1/-/-/-/- -/2/-/-/5 -/2/3/-/- 1/2/-/?/5 1/2/-/?/- 1/2/-/4/5 1/2/3/4/5 1/-/-/-/- 1/2/3/-/- 1/2/3/-/5 1/-/-/4/5 -/2/-/-/- 1/2/3/4/5 -/2/-/-/- 1/2/3/4/5 1/2/-/-/- 1/-/-/-/- -/-/-/-/5 1/2/3/4/? 1/2/3/4/5 1/-/3/-/5 1/2/-/-/5 1/2/3/4/5 1/-/3/-/5 -/2/-/4/5 1/2/-/-/- 1/2/3/4/5 1/-/-/-/- 1/2/-/4/5 1/2/3/4/5 1/-/-/?/5 1/-/-/-/5 1/2/3/4/5-/-/3/-/5 1/2/-/-/5 1/2/3/4/5 1/2/3/?/5 -/-/-/4/5 ?/2/-/4/5 1/-/-/-/- 1/2/3/4/5 1/2/3/-/5 -/2/-/-/5 1/2/3/4/5 ?/-/-/-/5 -/2/3/-/5 1/-/3/?/- 1/-/3/4/5 -/2/?/4/5 1/2/3/4/5 -/-/3/-/5 1/-/-/?/- -/-/-/-/- 1/-/-/-/- 1/2/-/-/- 1/2/3/4/5 1/2/3/-/5 1/2/3/?/? 1/-/-/-/- -/2/3/-/5 -/2/-/-/5 Fig. S8. Comparison of five single gene trees with the concatenated 5 gene tree. The tree is the best ML tree inferred by RAxML using the concatenated five genes. Numbers above the branch indicate different genes, with 1, 2, 3, 4, and 5 indicating SMC1, SMC2, MCM5, MLH1 and MSH1, respectively. If the single gene tree is congruent with the concatenated gene tree, the corresponding number was placed on the branch. The gap (-) indicates different topology at this node when compared with the concatenated tree. Question mark (?) indicates missing data at this node for one single gene tree. Cabomba caroliniana 1/?/3/4/? 1/2/3/4/5 -/2/-/4/5 1/2/3/4/5 BP_RM_N: SMC1/SMC2/MCM5/MLH1/MSH1

17. Poncirus trifoliata Tetradium ruticarpum Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Stellaria media Phytolacca americana Polygonum runcinatum Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Nerium oleander Vinca major Galium aparine Ilex purpurea Aucuba japonica Hedera nepalensis Ligusticum chuanxiong Pittosporum tobira Lonicera japonica Lactuca sativa Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Gunnera manicata Buxus sinica Pachysandra terminalis Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis Oryza sativa Brachypodium distachyon Setaria italica Sorghum bicolor Musa basjoo Canna indica Trachycarpus fortunei Dioscorea opposita Yucca filamentosa Asparagus officinalis Iris japonica Lilium brownii Pinellia ternata Alisma plantago-aquatica Acorus calamus Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Cinnamomum camphora Chimonanthus praecox Magnolia denudata Liriodendron chinese x L. tulipifera Ceratophyllum demersum Chloranthus elatior & C. spicatus Schisandra propinqua & S. sphenanthera Illicium henryi Nuphar advena Amborella trichopoda Pinus Picea Zamia fischeri */97/*/*/* 78/68/64/91/* */97/*/*/* */*/*/*/* 52/95/*/*/* 43/66/95/99/* -/-/-/-/59 -/-/-/-/82 83/99/*/*/* -/-/-/88/81 -/72/*/*/* -/42/-/93/81 41/56/74/*/* 99/*/*/*/* 57/81/95/88/* -/-/-/-/84 -/-/-/-/80 -/24/22/22/* 50/-/49/-/44 -/*/*/*/* -/-/-/-/35 -/76/96/88/* */*/*/*/* 98/*/*/*/* -/-/-/35/78 -/-/72/99/* 64/99/*/*/* 63/77/50/88/* -/-/-/43/76 */*/*/*/* 99/43/*/*/* 89/*/*/*/* -/32/-/-/51 */*/*/*/* 98/*/*/*/* 99/32/99/*/* -/-/-/-/74 -/18/61/64/* -/81/-/-/51 99/31/97/*/* -/-/-/-/63 24/25/85/98/* 51/88/93/*/* */*/*/*/* 56/99/99/98/* 97/99/99/93/* -/-/-/62/* 90/90/97/*/* -/-/-/62/70 -/-/-/*/* 98/87/*/98/* 99/*/*/*/* 98/*/*/*/* -/97/98/*/* 65/81/98/89/* 97/87/*/*/* 28/82/96/98/84 -/-/35/53/87 */99/*/*/* ?/99/*/*/* 41/25/97/-/81 -/19/82/-/85 -/-/23/33/62 */95/*/*/* 83/95/*/*/* 17/12/-/-/54 -/36/*/*/* -/20/75/75/* 55/81/78/93/* 56/22/71/98/* -/50/52/90/87 17/74/99/*/* 68/99/*/*/* */*/*/*/* -/59/60/-/* ?/-/-/68/59 13/-/-/31/42 34/-/-/66/59 56/-/-/97/* */88/*/*/* ?/96/*/*/* ?/?/*/*/* 29/-/-/98/94 80/91/98/91/83 39/-/-/51/92 Fig. S9. Comparison of five trees reconstructed by one gene and the concatenated 2-5 genes. The tree is the best ML tree inferred by RAxML using the concatenated five genes. Numbers above the branch are bootstrap (BP) values estimated by RAxML using one gene (MLH1), concatenated two genes (MLH1 and MSH1), three genes (MLH1, MSH1 and MCM5), four genes (MLH1, MSH1, MCM5 and SMC1), five genes (MLH1, MSH1, MCM5, SMC1 and SMC2), respectively. Asterisk (*) indicates BP = 100%. The gap (-) indicates different topology at this node when compared with the concatenated five genes. Question mark (?) indicates missing data at this node for one tree. Cabomba caroliniana */*/*/*/* BP_RM_N: 1 gene/2 genes/3 genes/4 genes/5genes

18. Poncirus trifoliata Tetradium ruticarpum Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Stellaria media Phytolacca americana Polygonum runcinatum Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Nerium oleander Vinca major Galium aparine Ilex purpurea Aucuba japonica Hedera nepalensis Ligusticum chuanxiong Pittosporum tobira Lonicera japonica Lactuca sativa Cornus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Gunnera manicata Buxus sinica Pachysandra terminalis Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis Oryza sativa Brachypodium distachyon Setaria italica Sorghum bicolor Musa basjoo Canna indica Trachycarpus fortunei Dioscorea opposita Yucca filamentosa Asparagus officinalis Iris japonica Lilium brownii Pinellia ternata Alisma plantago-aquatica Acorus calamus Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Cinnamomum camphora Chimonanthus praecox Magnolia denudata Liriodendron chinese x L. tulipifera Ceratophyllum demersum Chloranthus elatior & C. spicatus Schisandra propinqua & S. sphenanthera Illicium henryi Nuphar advena Amborella trichopoda Pinus Picea Zamia fischeri */*/*/* */*/*/87 */*/*/* */0.99/*/42 */-/59/- */-/82/- */*/*/* */-/81/- */-/*/- */-/81/28 */*/*/* */-/84/- */-/80/- */*/*/89 0.9/-/44/35 */*/*/* 0.9/*/35/- */*/*/* */0.98/78/70 */*/*/* */*/*/56 */-/76/- */*/*/* 0.86/*/51/72 */*/*/* 0.99/-/74/- */-/*/- 0.92/-/51/- */*/*/* 0.99/-/63/65 */*/*/* */*/*/71 */*/*/* */*/*/90 */*/*/* 0.96/*/70/* */*/*/* */*/*/89 */*/*/* */-/84/- */*/87/74 */*/*/* */*/81/90 */*/85/87 0.94/*/62/60 */*/*/* 0.85/0.98/54/46 */*/*/* */*/*/89 */*/*/* */0.99/87/73 */*/*/* */*/*/93 */*/59/65 */-/42/- */*/59/64 */*/*/* */*/94/* */*/83/* */*/*/* */*/92/89 */*/*/* 0.99/-/*/90 0.99/*/*/* */*/*/* 0.99/*/*/* 0.99/-/*/58 0.99/0.66/56/- 0.99/-/76/28 */*/*/* 0.5/0.42/68/- */*/*/- 0.99/-/76/32 0.98/*/*/* */*/*/* */0.99/*/* 0.77/0.76/76/39 0.99/*/87/72 0.45/-/35/- */*/*/* -/-/31/- 0.98/*/*/* */0.99/*/* 0.88/0.99/55/48 0.99/*/*/* */*/*/* 0.99/0.72/*/46 0.97/-/56/- */*/*/* 0.48/0.93/53/66 */*/*/* -/-/72/- -/-/86/52 0.37/-/57/- */*/*/* 0.58/0.72/68/72 */*/88/84 */*/*/* */0.99/*/76 0.99/*/*/* 0.99/0.99/*/* 0.99/0.84/*/91 0.99/0.99/*/* */*/*/* 0.98/*/*/* 0.94/0.62/63/46 */*/*/* 0.98/*/*/* 0.66/-/68/- 0.97/0.87/83/89 0.97/*/*/* */*/*/* 0.99/*/90/* 0.5/-/76/65 0.98/*/*/* */*/*/* 0.97/0.97/73/82 0.98/0.99/76/76 0.56/0.71/46/60 */*/*/* 0.98/*/*/* -/0.5/41/45 0.92/0.61/82/70 0.98/0.99/*/92 */*/*/* 0.96/0.55/89/66 */*/*/* 0.98/*/*/* */*/*/* 0.98/*/*/93 0.97/0.99/94/63 0.86/0.81/42/- 0.91/-/31/- 0.97/0.77/37- 0.97/*/93/86 0.98/*/*/* 0.97/*/*/* 0.98/*/*/* 0.97/0.99/89/91 0.81/0.99/69/92 0.98/*/*/* -/-/81/39 Fig. S10. Cladogram of the best ML tree conducted by RAxML based on the concatenated 5 gene nucleotide sequences. Asterisks indicate supporting values of posterior probabilities (PP) = 1 or bootstrap (BP) > 95.Totally, 8 kinds of supporting values were shown. The first two numbers above the branch are PPs estimated by MrBayes using nucleotide and amino acid matrixes, respectively. While the latter ones are BPs estimated by RAxML using nucleotide and amino acid matrixes, respectively. The first two numbers below the branches are PPs estimatated by PhyloBayes using nucleotide and amino acid matrixes, respectively. The latter ones are BPs estimated by PhyML using nucleotide and amino acid matrixes, respectively. Gap indicates different topology at this node when compared with the best ML tree shown here. Scale bar indicates number of changes per site. Different colors of species names indicate different sources of data, red indicates that data was generated by PCR in this study, black and blue indicate genomic data and EST data retrieved from public databases, respectively. PP_MB_N/PP_MB_P/BP_RM_N/BP_RM_P PP_PB_N/PP_PB_P/BP_PM_N/BP_PM_P Cabomba caroliniana

19. Fig. S11a. Phylogram of 42 species inferred by MrBayes 3.0 based on the concatenated 5 gene nucleotide sequences. Number associate with branches are supporting values with the former and the latter being posterior possibilities give by Mrbayes 3.0 and bootstrap values estimated by RAxML, respectively. When PP = 1.0 and bootstrap value > 95 at the same time, asterisk is placed on the node. The gap indicates that difference exists between ML tree and Bayes tree. Cucumis sativus Ulmus macrocarpa Populus tricocarpa Sapindus mukorossi Lagerstroemia limii Mimulus guttatus Solanum lycopersicum Pittosporum tobira Cornus wisoniana Actinidia arguta Gunnera manicata Pachysandra terminalis Buxus sinica Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis Musa basjoo Canna indica Trachycarpus fortunei Dioscorea opposita Asparagus officinalis Yucca filamentosa Iris japonica Lilium brownii Pinellia ternata Alisma plantago-aquatica Acorus calamus Asarum heterotropoides Aristolochia fimbriata Houttuynia cordata Magnolia denudata Liriodendron chinese X L. tulipifera Cinnamomum camphora Chimonanthus praecox Chloranthus elatior & C. spicatus Ceratophyllum demersum Schisandra propinqua & S. sphenanthera Illicium henryi Nuphar advena Amborella trichopoda 1.0/89 1.0/88 0.98/36 0.98/27 0.84/30 0.59/21 0.98/80 0.9/27 * 0.52/- 0.05 * * * * * * * * * * * * * * * * * * * * * * * * * Eudicots Monocots Magnoliids Chloranthaceae Ceratophyllaceae Early-diverging angiosperms * * * Cabomba caroliniana

20. Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Stellaria media Phytolacca americana Polygonum runcinatum Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Vinca major Nerium oleander Galium aparine Aucuba japonica Ilex purpurea Ligusticum chuanxiong Hedera nepalensis Pittosporum tobira Lonicera japonica Lactuca sativa Cornus wisoniana Conus officinalis Philadelphus incanus Rhododendron pulchrum Actinidia arguta Diospyros kaki Gunnera manicata Pachysandra terminalis Buxus sinica Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis 1.0/69 1.0/81 0.99/85 1.0/87 * 1.0/52 1.0/86 0.99/33 0.99/25 1.0/51 1.0/46 0.97/76 0.96/65 1.0/91 0.71/54 0.98/93 1.0/88 0.76/57 0.05 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Rosidae Caryophyllales Saxifragales Vitaceae Asteridae Basal eudicots Fig. S11b. Phylogram of eudicot species inferred by MrBayes 3.0 based on the concatenated 5 gene nucleotide sequences. Number associate with branches are supporting values with the former and the latter being posterior possibilities give by Mrbayes and bootstrap values estimated by RAxML, respectively. When PP =1.0 and bootstrap value > 95 at the same time, asterisk is placed on the node. The gap indicates that difference exists between ML tree and Bayes tree * * * * *

21. Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Stellaria media Phytolacca americana Polygonum runcinatum Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Vinca major Nerium oleander Galium aparine Aucuba japonica Ilex purpurea Ligusticum chuanxiong Hedera nepalensis Pittosporum tobira Lonicera japonica Lactuca sativa Cornus wisoniana Conus officinalis Philadelphus incanus Rhododendron pulchrum Actinidia arguta Diospyros kaki Gunnera manicata Pachysandra terminalis Buxus sinica Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis 1.0/70 0.98/82 1.0/87 1.0/76 * 1.0/52 1.0/89 0.97/41 0.71/- 0.98/74 0.98/84 0.61/55 0.99/81 0.65/- 0.05 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Rosidae Caryophyllales Asteridae Basal eudicots Fig. S11c. Phylogram of eudicot species excluding Saxifragales and Vitaceae species inferred by MrBayes 3.0 based on the concatenated 5 gene nucleotide sequences. Number associate with branches are supporting values with the former and the latter being posterior possibilities give by Mrbayes 3.0 and bootstrap values estimated by RAxML, respectively. When PP =1.0 and bootstrap value > 95 at the same time, asterisk is placed on the node. The gap indicates that difference exists between ML tree and Bayes tree. * * * * * * *

22. Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Distylium buxifolium Cercidiphyllum japonicum Paeonia lactiflora Vitis vinifera Callicarpa bodinieri Mimulus guttatus Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Vinca major Nerium oleander Galium aparine Aucuba japonica Ilex purpurea Ligusticum chuanxiong Hedera nepalensis Pittosporum tobira Lonicera japonica Lactuca sativa Cornus wisoniana Conus officinalis Philadelphus incanus Rhododendron pulchrum Actinidia arguta Diospyros kaki Gunnera manicata Pachysandra terminalis Buxus sinica Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis 1.0/71 1.0/83 0.99/91 1.0/90 * 1.0/60 1.0/87 0.74/25 0.72/14 1.0/86 0.99/81 0.95/59 0.53/63 0.99/72 1.0/82 0.79/59 0.05 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Rosidae Saxifragales Vitaceae Asteridae Basal eudicots Fig. S11d. Phylogram of eudicot species excluding Caryophyllales inferred by MrBayes 3.0 based on the concatenated 5 gene nucleotide sequences. Number associate with branches are supporting values with the former and the latter being posterior possibilities give by Mrbayes 3.0 and bootstrap values estimated by RAxML, respectively. When PP =1.0 and bootstrap value > 95 at the same time, asterisk is placed on the node. The gap indicates that difference exists between ML tree and Bayes tree. * * * * *

23. Tetradium ruticarpum Poncirus trifoliata Rhus chinensis Sapindus mukorossi Arabidopsis thaliana Arabidopsis lyrata Carica papaya Hibiscus syriacus Stachyurus yunnanensis Manihot esculenta Ricinus communis Populus tricocarpa Hypericum chinense Euonymus carnosus Ulmus macrocarpa Morus alba Photinia serrulata Glycine max Cyclobalanopsis glauca Cucumis sativus Oenothera erythrosepala Lagerstroemia limii Pelargonium hortorum Cercidiphyllum japonicum Distylium buxifolium Paeonia lactiflora Vitis vinifera Mimulus guttatus Callicarpa bodinieri Jassminum nudiflorum Solanum lycopersicum Pharbitis nil Vinca major Nerium oleander Galium aparine Aucuba japonica Ilex purpurea Ligusticum chuanxiong Hedera nepalensis Pittosporum tobira Lonicera japonica Lactuca sativa Conus officinalis Cornus wisoniana Philadelphus incanus Actinidia arguta Rhododendron pulchrum Diospyros kaki Stellaria media Phytolacca americana Polygonum runcinatum Gunnera manicata Pachysandra terminalis Buxus sinica Platanus acerifolia Meliosma parviflora Ranunculus muricatus Aquilegia coerulea Nandina domestica Dicentra spectabilis Sorghum bicolor Setaria italica Oryza sativa Brachypodium distachyon Musa basjoo Canna indica Trachycarpus fortunei Dioscorea opposita Yucca filamentosa Asparagus officinalis Iris japonica Lilium brownii Alisma plantago-aquatica Pinellia ternata Acorus calamus Aristolochia fimbriata Asarum heterotropoides Houttuynia cordata Chimonanthus praecox Cinnamomum camphora Magnolia denudata Liriodendron chinese x L. tulipifera Chloranthus elatior & C. spicatus Ceratophyllum demersum Schisandra propinqua & S. sphenanthera Illicium henryi Nuphar advena Amborella trichopoda Picea Pinus Zamia fischeri 38/0.88 58/0.99 50/0.7 93/1.0 73/1.0 43/0.83 67/1.0 88/0.99 47/0.63 38/0.66 29/- 27/- 92/1.0 80/0.98 76/0.95 74/1.0 48/0.86 58/0.74 68/0.99 23/- 30/- 51/0.70 62/0.6 89/1.0 81/0.9 92/1.0 93/1.0 92/1.0 86/1.0 84/1.0 49/1.0 45/1.0 * 65/0.87 0.02 Eudicots Monocots Magnoliids Chloranthaceae Ceratophyllaceae Early-diverging angiosperms Fig. S12. Phylogram of the best ML tree conducted by RAxML based on the concatenated 5 gene nucleotide matrix excluding the 3 rd codon positions. Asterisks indicate supporting values of posterior probabilities (PP) = 1 and bootstrap (BP) > 95. Numbers associated with internal branches are also supporting values (BP/PP). The gap indicates that difference exists between ML tree and Bayes tree. Scale bar represents number of changes per site. Basal eudicots Rosidae Asteridae Pentapetalae * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Cabomba caroliniana