Eud! Mag! Chl! Cer! Mon! outgroup! g 88. Eud! Cer! <50. Chl! Mag! Mon! outgroup! Eud! Mon! Cer! Mag! Chl! outgroup!
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- Crystal Nicholson
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1 a < Eud! Chl! Mag! Cer! Mon! outgroup! b Eud! Mag! Chl! Cer! Mon! outgroup! c *.73 Eud! Cer! Mon! Chl! Mag! outgroup! d < 5 Eud! Cer! Mag! Chl! Mon! outgroup! Barkman et al., 2! Zanis et al., 22! Qiu et al., 999, 25! Hilu et al., 23! Qiu et al., 25! Qiu et al., 25! e Qiu et al., 25! Eud! Mag! Cer! Chl! Mon! outgroup! f Qiu et al., 25! Eud! Cer! Chl! Mag! Mon! outgroup! g 88 <5 <5 Eud! Cer! Mon! Mag! Chl! outgroup! Qiu et al., 25,! Moore et al, 2! h < 5 < 5 < 5 Eud! Qiu et al., 26! Cer! Mag! Mon! Chl! outgroup! i.6 <.5 Eud! j Cer! Mon! Chl! Mag! outgroup! Eud! Mon! Cer! Mag! Chl! outgroup! Moore et al., 27! Goremykin et al., 22! Supplementary Fig.. Ten additional alternative topologies among eudicots (Eud), monocots (Mon), magnoliids (Mag), Ceratophyllaceae (Cer) and Chloranthaceae (Chl) modified from previous studies. An asterisk indicates that the bootstrap value or posterior probability reached % or., respectively. Other bootstrap values (<BS<) or posterior probabilities (<PP<.) are indicated.!
2 Raw reads of 26 transcriptome data Angiosperms phylogeny Trinity & TGICL Unigenes! (contigs + singletons)! HaMStR & OrthoMCL 3 Genomes and 5 EST data RAxML & MrBayes! Supermatrix concatenate! BLAST filter 93 Putative core OGs discard species specific inparalogs! coverage ( 8%)! & length ( 8%) 59 Optimal OGs 349 Candidate OGs MUSCLE! Aligned OGs trimal! Trimmed alignments 5 effective genes (SMC, SMC2, MCM5, MSH, MLH) discard spurious sequences! discard obviously mistranslated regions! discard genes with topologies conflicting with established relationships! Construct 349 Single gene trees with 2 representative species construct single gene trees! Manually evaluated alignments Supplementary Fig. 2. Flowchart of data analysis.!
3 a!! 46! 55! 57! 65!! Arabidopsis thaliana! 7! Thellungiella parvula! 77! Ricinus communis! 86! Medicago truncatula!! Mimulus guttatus! Solanum lycopersicum! Aquilegia coerulea! Magnolia denudata! Aristocochia tagala! Magnoliids! 85! 9! 96! 95! 8! 44!. substitution per site! Chimonanthus praecox!! Oryza sativa! Sorghum bicolor! Asparagus officinalis! Canna indica! Dioscorea opposita! Pinellia ternata! calamus! henryi! caroliniana! Ginkgo biloba! Monocots! Eudicots! b! 9! 36! 9! 52! 54! 68! 9!! A. thaliana! 99! T. parvula! 74! R. communis! M. truncatula! M. guttatus! 64! S. lycopersicum! A. coerulea! M. denudata! A. tagala! Magnoliids! C. praecox! 99! 88! 8! 99! 45! I. henryi! C. caroliniana! G. biloba!.5 substitution per site!! O. sativa! S. bicolor! C. indica! D. opposita! A. officinalis! P. ternata! A. calamus! Eudicots! Monocots! 3! c! 26! 32!!! 5! 44! 63! 38! 92! 94! 96! 9!! A. thaliana! T. parvula! R. communis! M. truncatula! M. guttatus! S. lycopersicum! A. coerulea! Eudicots! M. denudata! C. praecox! Magnoliids! A. tagala! A. officinalis! D. opposita!! O. sativa! S. bicolor! A. calamus! I. henryi! C. caroliniana! G. biloba! Monocots! 9! 58! 56! d!! 9! 64! 4! 74! 88! 86! 63!! 98! 5!!! A. thaliana! T. parvula! R. communis! M. truncatula! M. guttatus! S. lycopersicum! A. coerulea! O. sativa! S. bicolor! C. indica! D. opposita! A. officinalis! P. ternata! A. calamus! M. denudata! C. praecox! A. tagala! I. henryi! C. caroliniana! G. biloba! Magnoliids! Eudicots! Monocots!. substitution per site!. substitution per site! Supplementary Fig. 3 (a-d). Examples of single gene trees of selected marker genes in accordance with species trees of 2 representative species with established relationships. Taxa in different major groups of mesangiosperms are shown in different colors as indicated. Numbers in each nodes are ML bootstrap values obtained by RAxML.!
4 e!! Arabidopsis thaliana!! 26! Thellungiella parvula! 75! 28! Ricinus communis! 36! Magnolia denudata! 38! 52! Mimulus guttatus! 25! 26! Solanum lycopersicum! 22! 28! Medicago truncatula! 8!! 59! Aquilegia coerulea! Chimonanthus praecox! 33! henryi! 26! Aristocochia tagala! 69! Dioscorea opposita! 9! 53! Pinellia ternata! 69! 3! Canna indica! 86! 65! Asparagus officinalis! 46! calamus! caroliniana! 45! 8! 99! Sorghum bicolor! Oryza sativa! Ginkgo biloba! f! A. thaliana! T. parvula! S. lycopersicum! M. guttatus! R. communis! M.truncatula! 57! 58! 86! 88! C. praecox! M. denudata! I. henryi! A. coerulea! G. biloba!! S. bicolor! O. sativa! C. indica! D. opposita! A. officinalis! P. ternata! A. tagala! A. calamus! C. caroliniana!.5 substitution per site!. substitution per site! g! 53! G. biloba! 45! 58! 25! 27! 72! 64! 93! 46! 26! 6! 38! 58! 95! M.truncatula!! A. thaliana! T. parvula! M. guttatus! S. lycopersicum! A. coerulea! A. tagala! 98! O. sativa! S. bicolor! 6! C. indica! P. ternata! D. opposita! P. ternata! A. calamus! C. praecox! M. denudata! I. henryi! C. caroliniana! R. communis! 96! h!! T. parvula! 6! A. thaliana! 4! R. communis! 99! 75! M. guttatus! S. lycopersicum! 56! 49! A. coerulea! M.truncatula! A. calamus! 76! C. indica! 4! O. sativa! 52!! S. bicolor! 78! P. ternata! 97! 49! D. opposita! P. ternata! 64! A. tagala! C. praecox! M. denudata! I. henryi! C. caroliniana! G. biloba!.2 substitution per site!. substitution per site! Supplementary Fig. 3 (e-h). Examples of single gene trees for excluded candidate genes conflicting with species trees of 2 representative species with established relationships. Numbers in each nodes are ML bootstrap obtained by RAxML. Species in purple, green and red are from eudicots, monocots and magnoliids, respectively.!
5 / Mesodicots 5/ Mesangiospermae 98/ 93/ 6/ Carica papaya! Theobroma cacao! Malvales! Gossypium raimondii! Citrus sinensis! Sapindales! Citrus clementina! Manihot esculenta! Ricinus communis! Malpighiales! 84/ Populus trichocarpa! Glycine max! Phaseolus vulgaris! Fabales! Medicago truncatula! Prunus persica! Rosales! Fragaria vesca! 92/ Eucalyptus grandis! Myrtales! Solanum tuberosum! Solanales! Solanum lycopersicum! Mimulus guttatus! Lamiales! Lactuca sativa! Asterales! Artemisia annua! Vitis vinifera! Vitales! Buxus sinica! Buxales! x acerifolia! Proteales! Aquilegia coerulea! Ranunculales! glabra! japonicus! Chloranthaceae oryzetorum! demersum! Cinnamomum camphora! Persea americana! Laurales! Chimonanthus praecox! Magnolia denudata! Magnoliales! tulipifera! Saruma henryi! Aristolochia tagala! Piperales! Houttuynia cordata! Ceratophyllaceae Sorghum bicolor! Zea mays! Setaria italica! Panicum virgatum! Brachypodium distachyon! Canna indica! Musa acuminata! Zingiberales! 75/ Trachycarpus fortunei! Yucca filamentosa! Arecales! 97/ Asparagus officinalis! Iris japonica! Asparagales! 9/ Lilium brownii! Liliales! Pandanus utilis! Pandanales! Dioscorea opposita! Dioscoreales! Pinellia ternata! Alisma plantago-aquatica! Alismatales! calamus! Acorales! henryi! les! caroliniana! advenda! Nymphaeales! trichopoda! les! Ginkgo biloba! Arabidopsis lyrata! Arabidopsis thaliana! Capsella rubella! Thellungiella parvula! Brassicales! Magnoliids Poales! basal! angiosperms Eudicots Monocots.5 substitution per site! Supplementary Fig. 4. The ML tree reconstructed using 59 genes of 6 species without gene partition. Numbers associated with nodes are the bootstrap value (BS, on the left) obtained by RAxML and the posterior probability (PP, on the right) obtained by MrBayes based on concatenated 59 genes. Asterisks indicate BS of % or PP of.. Diamonds indicate BS of % and PP of..!
6 Mesodicots */*/97/94! 92/86/84/86! 92/98/96/84! 86/94/94/79! Mesangiospermae 98/*/99/99! 96/92/92//94! 93/89/85/86! */99/96/86! 82/77/79/57! 82/82/76/8! 84/86/82/67! */*/98/98! Arabidopsis lyrata! Arabidopsis thaliana! Capsella rubella! Thellungiella parvula! Carica papaya! Theobroma cacao! Gossypium raimondii! Citrus sinensis! Citrus clementina! Manihot esculenta! Ricinus communis! Populus trichocarpa! Glycine max! Phaseolus vulgaris! Medicago truncatula! Prunus persica! Fragaria vesca! Eucalyptus grandis! Solanum tuberosum! Solanum lycopersicum! Mimulus guttatus! Lactuca sativa! Artemisia annua! Vitis vinifera! Buxus sinica! x acerifolia! Aquilegia coerulea! Supplementary Fig. 5. Trees based on different evolutionary models. This cladogram was inferred by RAxML based on concatenated 59-gene amino acid sequences. Taxa in different major groups of mesangiosperms are shown in different colors as indicated. Numbers associated with branches are bootstrap values (BS) based on JTT + CAT, JTT + G, WAG + CAT, and DAYHOFF + CAT from left to right; BS of % is indicated by asterisk; a diamond indicates that all four BS values are %.! Eudicots! glabra! japonicus! Chloranthaceae! oryzetorum! demersum! Ceratophyllaceae! Cinnamomum camphora! Persea americana! Chimonanthus praecox! Magnolia denudata! tulipifera! Saruma henryi! Aristolochia tagala! Houttuynia cordata! Sorghum bicolor! Zea mays! Setaria italica! Panicum virgatum! Brachypodium distachyon! Canna indica! Musa acuminata! Trachycarpus fortunei! Yucca filamentosa! Asparagus officinalis! Iris japonica! Lilium brownii! Pandanus utilis! Dioscorea opposita! Pinellia ternata! Alisma plantago-aquatica! calamus! henryi! caroliniana! advenda! trichopoda! Ginkgo biloba! Magnoliids! Monocots! Early-diverging! angiosperms
7 86/93/96/97/79/94/-! */.92/.96/.96/*/*/.64! 85/86/8/88/86/7/82! */*/.93/.97/ 99/*/ Mesodicots 77/83/8/87/92/85/87! */.99/*/.97/.99/.93/ Mesangiospermae */*/*/*/*/*/99! */.99/*/*/*/*/ 99/*/*/*/*/*/96! */.98/*/*/*/*/ 88/8/82/77/89/6/74! */.97/*/*/*/.97/ */*/*/*/99/*/ */*/*/*/*/*/ 9/98/95/*/97/99/84! */*/*/*/*/*/ 96/93/99/96/98/9/56! */.98/*/*/*/*/*/ 94/*/89/94/87/88/89! */*/.93/.97/.99/*/ */*/*/*/*/99/99!.98/*/*/*/*/*/ 78/84/88/9/83/92/82! */*/*/*/*/*/ */*/98/96/93/79/48! */*/*/*/*/*/.99! */*/*/*/*/*/77! */*/*/*/*/*/ 95/93/*/*/96/95/97! */*/*/*/*/*/ 84/8/87/93/92/79/-! */*/*/*/*/*/.63! 84/74/85/82/63/-/-!.93/.9/.97/*/.78/-/.53! 99/94/*/99/94/95! */*/*/*/*/ Arabidopsis lyrata! Arabidopsis thaliana! Capsella rubella! Thellungiella parvula! Carica papaya! Theobroma cacao! Gossypium raimondii! Citrus sinensis! Citrus clementina! Manihot esculenta! Ricinus communis! Populus trichocarpa! Glycine max! Eudicots! Phaseolus vulgaris! Medicago truncatula! Prunus persica! Fragaria vesca! Eucalyptus grandis! Solanum tuberosum! Solanum lycopersicum! Mimulus guttatus! Lactuca sativa! Artemisia annua! Vitis vinifera! Buxus sinica! x acerifolia! Aquilegia coerulea! glabra! japonicus! Chloranthaceae! oryzetorum! demersum! Ceratophyllaceae! Cinnamomum camphora! Persea americana! Chimonanthus praecox! Magnolia denudata! tulipifera! Magnoliids! Saruma henryi! Aristolochia tagala! Houttuynia cordata! Sorghum bicolor! Zea mays! Setaria italica! Panicum virgatum! Brachypodium distachyon! Canna indica! Musa acuminata! Trachycarpus fortunei! Yucca filamentosa! Monocots! Asparagus officinalis! Iris japonica! Lilium brownii! Pandanus utilis! Dioscorea opposita! Pinellia ternata! Alisma plantago-aquatica! calamus! henryi! caroliniana! advenda! trichopoda! Ginkgo biloba! Early-diverging! angiosperms Supplementary Fig. 6. Trees based on different numbers of genes. A cladogram inferred using RAxML based on concatenated 59-gene amino acid sequences. Numbers associated with branches are bootstrap values (above) obtained by RAxML and posterior probability (below) obtained by MrBayes based on 55, 5, 46, 4, 33, 25 and 6 genes from left to right, respectively. A diamond indicates all seven bootstrap values and posterior possibilities on this node reaching % and.. A dash indicates different topology at this node when compared with the 59-gene tree.!
8 a Density Bandwidth: genes b Density genes Bandwidth: Mean value of upper quartile of LB scores Standard deviation of LB scores Supplementary Fig. 7. Density plots generated with R of different genespecific long-branch indices for the 59 genes. (a) Average of the upper quartile of LB scores representing the genes with the longest branches. (b) Standard deviation of LB scores measuring heterogeneity. Dashed line indicates starting shoulder value. Red areas in the right-hand side indicate deviations from the normal distribution and comprise genes might be long branches.
9 Mesodicots Mesangiospermae 95/8! 99/99! 85/89! 89/9! 94/95! 88/87! 96/97! 96/96! 8/7! 67/75! 96/98! 97/ Arabidopsis lyrata! Arabidopsis thaliana! Capsella rubella! Thellungiella parvula! Carica papaya! Theobroma cacao! Gossypium raimondii! Citrus sinensis! Citrus clementina! Manihot esculenta! Ricinus communis! Populus trichocarpa! Glycine max! Eudicots! Phaseolus vulgaris! Medicago truncatula! Prunus persica! Fragaria vesca! Eucalyptus grandis! Solanum tuberosum! Solanum lycopersicum! Mimulus guttatus! Lactuca sativa! Artemisia annua! Vitis vinifera! Buxus sinica! x acerifolia! Aquilegia coerulea! glabra! japonicus! Chloranthaceae! oryzetorum! demersum! Ceratophyllaceae Cinnamomum camphora! Persea americana! Chimonanthus praecox! Magnolia denudata! tulipifera! Magnoliids! Saruma henryi! Aristolochia tagala! Houttuynia cordata! Sorghum bicolor! Zea mays! Setaria italica! Panicum virgatum! Brachypodium distachyon! Canna indica! Musa acuminata! Trachycarpus fortunei! Yucca filamentosa! Monocots! Asparagus officinalis! Iris japonica! Lilium brownii! Pandanus utilis! Dioscorea opposita! Pinellia ternata! Alisma plantago-aquatica! calamus! henryi! caroliniana! advenda! trichopoda! Ginkgo biloba! Early-diverging! angiosperms Supplementary Fig. 8. ML Trees inferred by removing genes with high long branch scores. A cladogram inferred using RAxML based on concatenated 55-gene amino acid sequences. Numbers associated with branches are bootstrap (BS) values obtained by RAxML based on 55 and 5 genes, which excluded four (gene ID: , , and MCM5) and eight (gene ID: , , , MCM5, 4322, 43723, and 43486) genes according to gene-specific long-branch scores, from left to right, respectively. A diamond indicates both BS values of % at this node. An asterisk indicates one of the BS values at this node being %. Other BS values are indicated.!
10 8 8 Count Count Color Key Color key density andand Histogram LB scores Value MCM ! MCM MCM5! MSH 43273! MSH 4328 MSH! ! ! MLH ! MLH MLH! ! ! ! SMC ! SMC SMC2! ! SMC ! SMC SMC! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! ! Zea Zea mays! Zea Sorghum Sorghum bicolor! Sorghum Panicum Panicum virgatum! Panicum Setaria Setaria italica Setaria! Brachypodium Brachypodium distachyon! Brachypodium caroliniana advenda Arath Arabidopsis Arath thaliana Araly Arabidopsis Araly lyrata Capsella Capsella rubella Capsella Thellungiella Thellungiella parvula Thellungiella Alisma Alisma plantago aquatica! Alisma Iris Iris japonica Iris Ceratophyory oryzetorum Ceratophyory Ceratophyde demersum Ceratophyde Artemisia Artemisia annua! Artemisia Lactuca Lactuca sativa! Lactuca Lilium Lilium brownii! Lilium Mimulus Mimulus guttatus! Mimulus Medicago Medicago Medicago truncatula calamus! Fragaria Fragaria Fragaria vesca Houttuynia Houttuynia Houttuynia cordata Aristolochia Aristolochia Aristolochia tagala Eucalyptus Eucalyptus Eucalyptus grandis Phaseolus Phaseolus Phaseolus vulgaris Glycine Glycine Glycine max Solly Sollylycopersicum Solanum Soltu Soltutuberosum Solanum Ginkgo Ginkgo Ginkgo biloba trichopoda Carica Carica Carica papaya Buxus Buxus Buxus sinica Citrsi Citrus sinensis Citrsi Citcl Citcl Citrus clementina Canna Canna indica Canna Musa Musa acuminata Musa Pinellia Pinellia ternata Pinellia Saruma Saruma Saruma henryi Asparagus Asparagus Asparagus officinalis Yucca Yucca filamentosa Yucca Dioscorea Dioscorea opposita Dioscorea Pandanus Pandanus utilis Pandanus henryi Persea Persea americana Persea Trachycarpus Trachycarpus fortunei Trachycarpus Gossypium Gossypium raimondii Gossypium Theobroma Theobroma cacao Theobroma Populus Populus trichocarpa Populus Prunus Prunus Prunus persica Aquilegia Aquilegia Aquilegia coerulea Ricinus Ricinus communis Ricinus Manihot Manihot Manihot esculenta Vitis Vitis Vitvi vinifera x acerifolia Chimonanthus Chimonanthus Chimonanthus praecox Cinnamomum Cinnamomum Cinnamomum camphora japonicus glabra Magnolia Magnolia Magnolia denudata tulipifera Supplementary Fig. 9. Heat map in combination with hierarchical clustering generated with R of the taxon-specific long-branch scores for 59 genes of 6 species. Row show taxa and columns genes. Color key and density plot of long-branch (LB) scores are shown in the upper left corner of the heat map. White cells in the map indicate that the taxon was lacking in that gene. Orange cells indicate that the taxon with low LB scores indicate that the taxon in that gene might be not affected by long-branch attraction. Dark green cells (genes with ID of in Carica papaya, in trichopoda and in Ginkgo biloba) with high LB scores indicate that the taxon in that gene might be a long-branch.
11 96/ Mesodicots 9/ Mesangiospermae 99/ 6/ 85/ 77/ 94/ 89/ 98/ Vitis vinifera! Buxus sinica! x acerifolia! Aquilegia coerulea! glabra! japonicus! Citrus clementina! Manihot esculenta! Ricinus communis! Populus trichocarpa! Glycine max! Phaseolus vulgaris! Medicago truncatula! Prunus persica! Fragaria vesca! Eucalyptus grandis! Solanum tuberosum! Solanum lycopersicum! Mimulus guttatus! Lactuca sativa! oryzetorum! demersum! Cinnamomum camphora! Persea americana! Chimonanthus praecox! Magnolia denudata! tulipifera! Saruma henryi! Aristolochia tagala! Houttuynia cordata! 84/ Arabidopsis lyrata! Arabidopsis thaliana! Capsella rubella! Thellungiella parvula! Carica papaya! Theobroma cacao! Gossypium raimondii! Malvales! Citrus sinensis! Canna indica! Artemisia annua! Vitales! Buxales! Proteales! Sapindales! Ceratophyllaceae Zingiberales! Musa acuminata! Trachycarpus fortunei! Arecales! Yucca filamentosa! Asparagus officinalis! Asparagales! Iris japonica! Lilium brownii! Liliales! Pandanus utilis! Pandanales! Dioscorea opposita! Dioscoreales! Pinellia ternata! Alisma plantago-aquatica! Alismatales! calamus! Acorales! henryi! les! caroliniana! advenda! Nymphaeales! trichopoda! les! Ginkgo biloba! Malpighiales! Rosales! Myrtales! Fabales! Solanales! Lamiales! Asterales! Ranunculales! Chloranthaceae Magnoliales! Laurales! Piperales! Brassicales! Magnoliids Sorghum bicolor! Zea mays! Setaria italica! Panicum virgatum! Brachypodium distachyon! Poales! Eudicots Monocots Early-diverging! angiosperms.5 substitution per site! Supplementary Fig.. A phylogram of the best ML tree inferred using RAxML based on concatenated 59- gene amino acid sequences from 6 species. Genes with ID of in Carica papaya, in trichopoda and in Ginkgo biloba with the highest LB scores according to Supplementary Fig 9 were excluded in this analysis. Numbers associated with branches are bootstrap value (BS) and posterior probability (PP) inferred by RAxML and MrBayes, respectively. An asterisk indicates PP of.. A diamond indicates BS of % and PP of. at the same time.!
12 a Density Bandwidth: genes. b Density Bandwidth: genes Slope of linear regression R 2 of linear regression Supplementary Fig. Density plots (distribution) of different gene-specific saturation indices for the 59 genes generated with R. (A) Slopes of the linear regression between patristic and uncorrected pairwise distances. (B) R 2 of the linear regression between patristic and uncorrected pairwise distances. Dashed line indicates starting shoulder value. Red areas in the left-hand side comprise genes that might be saturated.
13 Mesodicots 94/92! Mesangiospermae 85/92! 9/! 88/87! /99! /88! 85/85! 79/62! 88/94! 94/98! /85! /99! 82/78! 94/97! Vitis vinifera! Buxus sinica! x acerifolia! Aquilegia coerulea! glabra! japonicus! Citrus clementina! Manihot esculenta! Ricinus communis! Populus trichocarpa! Glycine max! Phaseolus vulgaris! Medicago truncatula! Prunus persica! Fragaria vesca! Eucalyptus grandis! Solanum tuberosum! Solanum lycopersicum! Mimulus guttatus! Lactuca sativa! oryzetorum! demersum! Cinnamomum camphora! Persea americana! Chimonanthus praecox! Magnolia denudata! tulipifera! Saruma henryi! Aristolochia tagala! Houttuynia cordata! Arabidopsis lyrata! Arabidopsis thaliana! Capsella rubella! Thellungiella parvula! Carica papaya! Theobroma cacao! Gossypium raimondii! Malvales! Citrus sinensis! Canna indica! Artemisia annua! Vitales! Buxales! Proteales! Sapindales! Ceratophyllaceae Zingiberales! Musa acuminata! Trachycarpus fortunei! Arecales! Yucca filamentosa! Asparagus officinalis! Asparagales! Iris japonica! Lilium brownii! Liliales! Pandanus utilis! Pandanales! Dioscorea opposita! Dioscoreales! Pinellia ternata! Alisma plantago-aquatica! Alismatales! calamus! Acorales! henryi! les! caroliniana! advenda! Nymphaeales! trichopoda! les! Ginkgo biloba! Malpighiales! Rosales! Myrtales! Fabales! Solanales! Lamiales! Asterales! Ranunculales! Chloranthaceae Magnoliales! Laurales! Piperales! Brassicales! Magnoliids Sorghum bicolor! Zea mays! Setaria italica! Panicum virgatum! Brachypodium distachyon! Poales! Eudicots Monocots Early-diverging! angiosperms.5 substitution per site! Supplementary Fig. 2. A phylogram of the best ML tree inferred using RAxML based on unsaturated genes amino acid sequences from 6 species. Numbers associated with branches are bootstrap (BS) values obtained by RAxML based on 54 and 57 genes, which excluded five genes (gene ID: , MCM5, 43358, and MSH) with Slope. and two genes (gene ID: and MCM5) with R 2.5 according to Supplementary Fig, respectively, from 59-gene dataset. An asterisk indicates BS of % and a diamond indicates both two BS on this node of %.!
14 a! Vitis vinifera! Buxus sinica! x acerifolia! Carica papaya! Theobroma cacao! Gossypium raimondii! Citrus sinensis! Citrus clementina! Manihot esculenta! Ricinus communis! Arabidopsis lyrata! Arabidopsis thaliana! Capsella rubella! Thellungiella parvula! Populus trichocarpa! Glycine max! Phaseolus vulgaris! Medicago truncatula! Prunus persica! Fragaria vesca! Eucalyptus grandis! Solanum tuberosum! Solanum lycopersicum! Mimulus guttatus! Lactuca sativa! Artemisia annua! Eudicots! 65/.! Aquilegia coerulea! Mesodicots glabra! japonicus! Chloranthaceae! 95/.! 9/.99! demersum! oryzetorum! Ceratophyllaceae! Cinnamomum camphora! Persea americana! Chimonanthus praecox! Magnoliids! Magnolia denudata! tulipifera! Mesangiospermae Sorghum bicolor! Zea mays! Setaria italica! Panicum virgatum! Brachypodium distachyon! Canna indica! Musa acuminata! 79/.! Trachycarpus fortunei! Yucca filamentosa! Asparagus officinalis! /.97! 77/.96! Iris japonica! Lilium brownii! Pandanus utilis! Dioscorea opposita! 92/.7! Pinellia ternata! Alisma plantago-aquatica! calamus! 97/.!.5 substitution per site! 89/.! 95/.! henryi! advenda! caroliniana! trichopoda! Ginkgo biloba! Supplementary Fig. 3a. A phylogram of the best ML tree inferred using RAxML based on concatenated 59-gene amino acid sequences from 58 species. Three species from Piperales of magnoliids were excluded in this analysis; numbers associated with branches are bootstrap values (BS) and posterior probability (PP) inferred by RAxML and MrBayes, respectively; an asterisk indicates BS of % and PP of. at the same time.! Early-diverging! angiosperms Monocots!
15 b! /.98! 99/.9! 72/.99! Mesodicots 7/.99! Mesangiospermae 98/.! 94/.! 8/.96! 7/.99!.5 substitution per site! 96/.! 97/.! 88/.! 99/.! Vitis vinifera! Buxus sinica! xacerifolia! Carica papaya! Theobroma cacao! Gossypium raimondii! Citrus sinensis! Citrus clementina! Manihot esculenta! Ricinus communis! Arabidopsis lyrata! Arabidopsis thaliana! Capsella rubella! Thellungiella parvula! Populus trichocarpa! Glycine max! Phaseolus vulgaris! Medicago truncatula! Prunus persica! Fragaria vesca! Eucalyptus grandis! Solanum tuberosum! Solanum lycopersicum! Mimulus guttatus! Lactuca sativa! Artemisia annua! Supplementary Fig. 3b. A phylogram of the best ML tree inferred using RAxML based on concatenated 59-gene amino acid sequences from 58 species. Three species from basal monocots ( calamus, Alisma plantago-aquatica, and Pinellia ternata) were excluded in this analysis; numbers associated with branches are bootstrap values (BS) and posterior probability (PP) inferred by RAxML and MrBayes, respectively; an asterisk indicates BS of % and PP of. at the same time.! Eudicots! Aquilegia coerulea! glabra! Chloranthaceae! japonicus! demersum! Ceratophyllaceae! oryzetorum! Cinnamomum camphora! Persea americana! Chimonanthus praecox! Magnolia denudata! Magnoliids! tulipifera! Saruma henryi! Aristolochia tagala! Houttuynia cordata! 99/.! 85/.99! Canna indica! Musa acuminata! Trachycarpus fortunei! Yucca filamentosa! Asparagus officinalis! Iris japonica! Lilium brownii! Pandanus utilis! Dioscorea opposita! henryi! advenda! caroliniana! trichopoda! Ginkgo biloba! Sorghum bicolor! Zea mays! Setaria italica! Panicum virgatum! Brachypodium distachyon! Early-diverging! angiosperms Monocots!
16 c! Citrus clementina Citrus sinensis Ricinus commnis Manihot esculenta 85/. Populus trichocarpa Glycine max Phaseolus vulgaris Medicago truncatula Prunus persica Fragaria vesca 92/. Eucalyptus grandis Solanum tuberosum Solanum lycopersicum Mimulus guttatus Artemisia annua Lactuca sativa 97/. Vitis vinifera Buxus sinica x acerifolia 94/.99 Aquilegia formosa Mesodicots glabra japonicus 98/.99 demersum 89/.99 oryzetorum Cinnamomum camphora Persea americana Chimoanthus parecox Magnolia denudata tulipifera 85/.96 Mesangiospermae 94/.99 99/.5 substitution per site henryi advenda caroliniana trichopoda Picea sitchensis Picea glauca Pinus taeda Ginkgo biloba Arabidopsis thaliana Arabidopsis lyrata Capsella rubella Thellungiella parvula Carica papaya Gossypium raimondii Theobroma cacao Saruma henryi Aristolochia tagala Houttuynia cordata Supplementary Fig. 3c. A phylogram of the best ML tree inferred using RAxML based on concatenated 59- gene amino acid sequences from 64 species. Three Pinaceae species (Picea sitchensis, Picea glauca, and Pinus taeda) were included in this analysis; numbers associated with branches are bootstrap values (BS) and posterior probability (PP) inferred by RAxML and MrBayes, respectively; an asterisk indicates BS of % and PP of. at the same time.! Eudicots! Chloranthaceae! Ceratophyllaceae! Magnoliids! Setaria italica Panicum virgatum Zea mays Sorghum bicolor Brachypodium distachyon Musa acuminata Canna indica 8/. Trachycarpus fortunei Yucca filamentosa Asparagus officinalis 8/. Iris japonica Lilium brownii Pandanus utilis Dioscorea opposita Pinellia ternata Alisma plantago-aquatica calamus Early-diverging! angiosperms Monocots!
17 Arabidopsis lyrata d! Arabidopsis thaliana Capsella rubella Thellungiella parvula Carica papaya Theobroma cacao Gossypium raimondii Citrus clementina Citrus sinensis Manihot esculenta Ricinus communis! 89 Populus trichocarpa Glycine max Phaseolus vulgaris! Medicago truncatula Prunus persica Fragaria vesca 98 Eucalyptus grandis! Solanum tuberosum! Solanum lycopersicum Mimulus guttatus Artemisia annua Lactuca sativa Vitis vinifera Buxus sinica! 99 x acerifolia nucifera! 93 Meliosma parviflora! 92 Aquilegia coerulea! Eschscholzia californica! Mesodicots glabra! japonicus! 96 demersum 82 oryzetorum Cinnamomum camphora! Persea americana! Chimonanthus praecox! Magnolia denudata! 77 tulipifera! Saruma henryi! Magnoliids! Aristolochia tagala! Mesangiospermae Houttuynia cordata! Sorghum bicolor! Zea mays! Panicum virgatum! Setaria italica! Brachypodium distachyon! Musa acuminata! Canna indica! 9 Trachycarpus fortunei! Yucca filamentosa! Pinellia ternata! calamus! henryi advenda caroliniana trichopoda Ginkgo biloba! Eudicots! Chloranthaceae! Ceratophyllaceae! Asparagus officinalis! Iris japonica! Lilium brownii! Pandanus utilis! Dioscorea opposita! Alisma plantago-aquatica! Early-diverging! angiosperms Monocots!.5 substitution per site Supplementary Fig. 3d. An ML tree inferred by RAxML based on concatenated 59-gene amino acid sequences from 63 species. Three basal eudicot species ( nucifera, Meliosma parviflora and Eschscholzia californica) were included in this analysis; numbers associated with branches are bootstrap values inferred by RAxML; an asterisk indicates BS of %.!
18 a! substitution per site Supplementary Fig. 4a. The ML tree inferred by RAxML based on concatenated 83 plastid genes of 86 species. Numbers associated with branches are bootstrap values; an asterisk indicates bootstrap of %. Species from eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae are in purple, green, orange, violet and blue, respectively.! 9 Aucuba japonica Gunnera manicata Buxus microphylla aralioides nucifera occidentalis 74 Meliosma cuneifolia Nandina domestica Ranunculus macranthus demersum 99 Drimys granadensis Calycanthus floridus tulipifera spicatus oligandrum Nymphaea alba advena trichopoda Arabidopsis thaliana Brassica rapa Gossypium hirsutum Citrus sinensis Staphylea colchica Oenothera elata Eucalyptus globulus Ficus sp. Morus indica Cucumis sativus Quercus nigra Pelargonium x hortorum Medicago truncatula Lotus corniculatus Phaseolus vulgaris Glycine max Passiflora biflora Polulus alba Manihot esculenta Euonymus americanus Oxalis latifolia Bulnesia arborea Heuchera sanguinea Liquidambar styraciflua Vitis vinifera Dillenia indica Ipomoea purpurea Solanum lycopersicum Atropa belladonna Nicotiana tabacum Nerium oleander Coffea arabica Ehretia acuminata Antirrhinum majus Jasminum nudiflorum Helianthus annuus Lactuca sativa Anethum graveolens Daucus carota Cuscuta exaltata Scaevola aemula Trachelium caeruleum Panax ginseng Lonicera japonica Ilex cornuta Rhododendron simsii Cornus florida Spinacia oleracea Plumbago auriculata Berberidopsis corallina Ximenia americana Typha latifolia Musa acuminata Elaeis oleifera Phalaenopsis aphrodite Yucca schidigera Dioscorea elephantipes Lemna minor americanus Piper cenocladum Epifagus virginiana Phoradendron leucarpum Oryza sativa Triticum aestivum Zea mays Cycas micronesica Ginkgo biloba Pinus thunbergii
19 b!. substitution per site Arabidopsis thaliana Brassica rapa Gossypium hirsutum Citrus sinensis Staphylea colchica Eucalyptus globulus Polulus alba Manihot esculenta Oxalis latifolia Euonymus americanus Oenothera elata Pelargonium x hortorum Passiflora biflora Lotus corniculatus Glycine max Phaseolus vulgaris Cucumis sativus Quercus nigra Ficus sp. Morus indica Heuchera sanguinea Liquidambar Vitis vinifera styraciflua Helianthus annuus Lactuca sativa Daucus carota Anethum graveolens Panax ginseng Lonicera japonica Bulnesia arborea Ilex cornuta Jasminum nudiflorum Epifagus virginiana Antirrhinum majus Nicotiana tabacum Atropa belladonna Solanum lycopersicum Ipomoea purpurea Cuscuta exaltata Nerium oleander Coffea arabica Ehretia acuminata Aucuba japonica Rhododendron simsii Cornus florida Berberidopsis corallina Spinacia oleracea Plumbago auriculata Ximenia americana Phoradendron leucarpum Dillenia indica Gunnera manicata aralioides Buxus microphylla nucifera occidentalis Meliosma cuneifolia Nandina domestica Ranunculus macranthus demersum spicatus Calycanthus floridus tulipifera Drimys granadensis Piper cenocladum Typha latifolia Musa acuminata Elaeis oleifera Phalaenopsis aphrodite Yucca schidigera Dioscorea elephantipes Lemna minor americanus oligandrum trichopoda Nymphaea alba advena Oryza sativa Triticum aestivum Zea mays Cycas micronesica Ginkgo biloba Medicago truncatula Scaevola aemula Trachelium caeruleum Pinus thunbergii Supplementary Fig. 4b. The ML tree inferred by RAxML based on 4 concatenated plastid inverted repeat genes of 86 species. Numbers associated with branches are bootstrap values; an asterisk indicates bootstrap of %. Species from eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae are in purple, green, orange, violet and blue, respectively.!
20 c! Aucuba japonica Berberidopsis corallina Dillenia indica Gunnera manicata aralioides 99 Buxus microphylla occidentalis nucifera Meliosma cuneifolia 47 Ranunculus macranthus Nandina domestica demersum Typha latifolia Musa acuminata 9 Elaeis oleifera Phalaenopsis aphrodite 37 Yucca schidigera 95 Dioscorea elephantipes Lemna minor americanus 84 tulipifera Calycanthus floridus Piper cenocladum Drimys granadensis spicatus oligandrum Nymphaea alba advena trichopoda Ginkgo biloba Cycas micronesica Pinus thunbergii.2 substitution per site Supplementary Fig. 4c. The ML tree inferred by RAxML based on concatenated 34 plastid genes of 86 species with percentage of parsimony informative sites less than 4%. Numbers associated with branches are bootstrap values; an asterisk indicates bootstrap of %. Species from eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae are in purple, green, orange, violet and blue, respectively.!! Arabidopsis thaliana Brassica rapa Gossypium hirsutum Citrus sinensis Staphylea colchica Oenothera elata Eucalyptus globulus Pelargonium x hortorum Medicago truncatula Lotus corniculatus Phaseolus vulgaris Glycine max Ficus sp. Morus indica Cucumis sativus Quercus nigra Passiflora biflora Polulus alba Manihot esculenta Euonymus americanus Oxalis latifolia Bulnesia arborea Vitis vinifera Heuchera sanguinea Liquidambar styraciflua Ehretia acuminata 62 Cuscuta exaltata Ipomoea purpurea Solanum lycopersicum Atropa belladonna Nicotiana tabacum Coffea arabica Nerium oleander Antirrhinum majus Jasminum nudiflorum Helianthus annuus Lactuca sativa Scaevola aemula Trachelium caeruleum Anethum graveolens Daucus carota Panax ginseng Lonicera japonica Ilex cornuta Rhododendron simsii Cornus florida Spinacia oleracea Plumbago auriculata Ximenia americana Phoradendron leucarpum Triticum aestivum Oryza sativa Zea mays Epifagus virginiana
21 d!.2 substitution per site Arabidopsis thaliana Brassica rapa Gossypium hirsutum Citrus sinensis Staphylea colchica Oenothera elata Eucalyptus globulus Heuchera sanguinea Liquidambar styraciflua Vitis vinifera Ehretia acuminata Pelargonium x hortorum Medicago truncatula Lotus corniculatus Phaseolus vulgaris Glycine max Quercus nigra Cucumis sativus Ficus sp. Morus indica Passiflora biflora Polulus alba Manihot esculenta Euonymus americanus Oxalis latifolia Bulnesia arborea Dillenia indica Ipomoea purpurea Cuscuta exaltata 99 Solanum lycopersicum Atropa belladonna Nicotiana tabacum Coffea arabica Nerium oleander Aucuba japonica Antirrhinum majus Jasminum nudiflorum Helianthus annuus Lactuca sativa Scaevola aemula Trachelium caeruleum Anethum graveolens Daucus carota Panax ginseng Lonicera japonica Ilex cornuta Rhododendron simsii Cornus florida Spinacia oleracea Plumbago auriculata Ximenia americana Berberidopsis corallina Gunnera manicata aralioides Buxus microphylla occidentalis nucifera Meliosma cuneifolia Nandina domestica Ranunculus macranthus demersum Typha latifolia Musa acuminata Elaeis oleifera Phalaenopsis aphrodite Yucca schidigera Dioscorea elephantipes Lemna minor americanus tulipifera Calycanthus floridus Piper cenocladum Drimys granadensis spicatus oligandrum Nymphaea alba advena trichopoda Ginkgo biloba Cycas micronesica Pinus thunbergii Phoradendron leucarpum Triticum aestivum Oryza sativa Zea mays Epifagus virginiana Supplementary Fig. 4d. The ML tree inferred by RAxML based on concatenated 46 plastid genes of 86 species with percentage of parsimony informative sites less than 5%. Numbers associated with branches are bootstrap values; an asterisk indicates bootstrap of %. Species from eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae are in purple, green, orange, violet and blue, respectively.!
22 Supplementary Fig. 4e. The ML tree inferred by RAxML based on concatenated 66 plastid genes of 86 species with percentage of parsimony informative sites less than 6%. Numbers associated with branches are bootstrap values; an asterisk indicates bootstrap of %. Species from eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae are in purple, green, orange, violet and blue, respectively.!! e!.2 substitution per site Berberidopsis corallina Ximenia americana 43 Aucuba japonica Arabidopsis thaliana Brassica rapa Gossypium hirsutum Citrus sinensis Staphylea colchica Oenothera elata Eucalyptus globulus Ficus sp. Morus indica Cucumis sativus Quercus nigra Pelargonium x hortorum Medicago truncatula Lotus corniculatus Phaseolus vulgaris Glycine max Passiflora biflora Polulus alba Manihot esculenta Euonymus americanus Oxalis latifolia Bulnesia arborea Heuchera sanguinea Liquidambar styraciflua Vitis vinifera Dillenia indica Ipomoea purpurea Solanum lycopersicum Atropa belladonna Nicotiana tabacum Antirrhinum majus Jasminum nudiflorum Coffea arabica Nerium oleander Ehretia acuminata Helianthus annuus Lactuca sativa Anethum graveolens Daucus carota Panax ginseng Lonicera japonica Ilex cornuta Rhododendron simsii Cornus florida Spinacia oleracea Gunnera manicata aralioides Buxus microphylla occidentalis nucifera Meliosma cuneifolia Ranunculus macranthus Nandina domestica demersum Typha latifolia Musa acuminata Elaeis oleifera Phalaenopsis aphrodite Yucca schidigera Dioscorea elephantipes Lemna minor americanus tulipifera Calycanthus floridus Drimys granadensis Piper cenocladum spicatus oligandrum Nymphaea alba advena trichopoda Cuscuta exaltata Scaevola aemula Trachelium caeruleum Plumbago auriculata Phoradendron leucarpum Triticum aestivum Oryza sativa Zea mays Epifagus virginiana Ginkgo biloba Cycas micronesica Pinus thunbergii
23 Supplementary Fig. 4f. The ML tree inferred by RAxML based on concatenated 7 plastid genes of 86 species with percentage of parsimony informative sites greater than 6%. Numbers associated with branches are bootstrap values; an asterisk indicates bootstrap of %. Species from eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae are in purple, green, orange, violet and blue, respectively.!! f! substitution per site Aucuba japonica Arabidopsis thaliana Brassica rapa Gossypium hirsutum Citrus sinensis Staphylea colchica Oenothera elata Eucalyptus globulus Ficus sp. Morus indica Quercus nigra Cucumis sativus Heuchera sanguinea Liquidambar styraciflua Vitis vinifera Dillenia indica Polulus alba Manihot esculenta Euonymus americanus Oxalis latifolia Solanum lycopersicum Atropa belladonna Nicotiana tabacum Nerium oleander Coffea arabica Ehretia acuminata Pelargonium x hortorum Medicago truncatula Lotus corniculatus Phaseolus vulgaris Glycine max Bulnesia arborea Passiflora biflora Ipomoea purpurea Cuscuta exaltata Antirrhinum majus Jasminum nudiflorum Helianthus annuus Lactuca sativa Epifagus virginiana Scaevola aemula Trachelium caeruleum Anethum graveolens Daucus carota Panax ginseng Lonicera japonica Ilex cornuta Cornus florida Rhododendron simsii Spinacia oleracea Plumbago auriculata 97 Berberidopsis corallina Phoradendron leucarpum Ximenia americana Gunnera manicata 92 Buxus microphylla aralioides nucifera occidentalis Meliosma cuneifolia Nandina domestica Ranunculus macranthus Oryza sativa 45 Triticum aestivum 67 Zea mays Typha latifolia 96 Musa acuminata Elaeis oleifera Yucca schidigera Phalaenopsis aphrodite 9 Dioscorea elephantipes Lemna minor americanus tulipifera Calycanthus floridus Piper cenocladum Drimys granadensis demersum spicatus oligandrum advena Nymphaea alba trichopoda Cycas micronesica Ginkgo biloba Pinus thunbergii
24 g!.2 substitution per site americanus tulipifera Calycanthus floridus Piper cenocladum Drimys granadensis demersum spicatus oligandrum advena Nymphaea alba trichopoda Supplementary Fig. 4g. The ML tree inferred by RAxML based on concatenated 37 plastid genes of 86 species with percentage of parsimony informative sites greater than 5%. Numbers associated with branches are bootstrap values; an asterisk indicates bootstrap of %. Species from eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae are in purple, green, orange, violet and blue, respectively.!! Solanum lycopersicum Atropa belladonna Nicotiana tabacum Coffea arabica Nerium oleander Ehretia acuminata Aucuba japonica Arabidopsis thaliana Brassica rapa Gossypium hirsutum Citrus sinensis Staphylea colchica Oenothera elata Eucalyptus globulus Heuchera sanguinea Liquidambar styraciflua Vitis vinifera Dillenia indica Pelargonium x hortorum Medicago truncatula Lotus corniculatus Phaseolus vulgaris Glycine max Ficus sp. Morus indica Cucumis sativus Quercus nigra Euonymus americanus Oxalis latifolia Passiflora biflora Polulus alba Manihot esculenta Bulnesia arborea Ipomoea purpurea Cuscuta exaltata Antirrhinum majus Jasminum nudiflorum Helianthus annuus Lactuca sativa Anethum graveolens Daucus carota Epifagus virginiana Scaevola aemula Trachelium caeruleum Panax ginseng Lonicera japonica Ilex cornuta Rhododendron simsii Cornus florida Plumbago auriculata Spinacia oleracea Berberidopsis corallina Ximenia americana Gunnera manicata Buxus microphylla aralioides occidentalis nucifera 67 Meliosma cuneifolia Nandina domestica Ranunculus macranthus Typha latifolia Musa acuminata Elaeis oleifera Phalaenopsis aphrodite Yucca schidigera Dioscorea elephantipes Lemna minor Ginkgo biloba Cycas micronesica Phoradendron leucarpum Triticum aestivum Oryza sativa Zea mays Pinus thunbergii
25 h!.2 substitution per site Supplementary Fig. 4h. The ML tree inferred by RAxML based on concatenated 49 plastid genes of 86 species with percentage of parsimony informative sites greater than 4%. Numbers associated with branches are bootstrap values; an asterisk indicates bootstrap of %. Species from eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae are in purple, green, orange, violet and blue, respectively.!! Arabidopsis thaliana Brassica rapa Gossypium hirsutum Citrus sinensis Staphylea colchica Oenothera elata Eucalyptus globulus Quercus nigra Cucumis sativus Ficus sp. Morus indica Pelargonium x hortorum Medicago truncatula Lotus corniculatus Phaseolus vulgaris Glycine max Passiflora biflora Polulus alba Manihot esculenta 9 99 Euonymus americanus 83 Oxalis latifolia Bulnesia arborea Heuchera sanguinea Liquidambar styraciflua Vitis vinifera 66 Dillenia indica Ipomoea purpurea Cuscuta exaltata Atropa belladonna Solanum lycopersicum Nicotiana tabacum Antirrhinum majus Jasminum nudiflorum Coffea arabica Nerium oleander Ehretia acuminata Aucuba japonica Helianthus annuus Lactuca sativa Anethum graveolens Daucus carota Epifagus virginiana Scaevola aemula Trachelium caeruleum Panax ginseng Lonicera japonica Ilex cornuta Rhododendron simsii Cornus florida Spinacia oleracea Plumbago auriculata Berberidopsis corallina Ximenia americana Phoradendron leucarpum Gunnera manicata Buxus microphylla aralioides occidentalis nucifera 45 7 Meliosma cuneifolia Ranunculus macranthus Nandina domestica demersum Triticum aestivum Oryza sativa 45 Zea mays Typha latifolia Musa acuminata Elaeis oleifera Phalaenopsis aphrodite Yucca schidigera Dioscorea elephantipes Lemna minor americanus tulipifera Calycanthus floridus Piper cenocladum 5 Drimys granadensis spicatus oligandrum Nymphaea alba advena trichopoda Cycas micronesica Ginkgo biloba Pinus thunbergii
26 i! 94.2 substitution per site Aucuba japonica Supplementary Fig. 4i. The ML tree inferred by RAxML based on concatenated 3 plastid genes of 86 species with percentage of parsimony informative sites ranging from 4% to 5%. Numbers associated with branches are bootstrap values; an asterisk indicates bootstrap of %. Species from eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae are in purple, green, orange, violet and blue, respectively.!! Gossypium hirsutum Citrus sinensis Staphylea colchica Oenothera elata Eucalyptus globulus Arabidopsis thaliana Brassica rapa Pelargonium x hortorum Medicago truncatula Lotus corniculatus Phaseolus vulgaris Glycine max Quercus nigra Cucumis sativus Ficus sp. Morus indica Passiflora biflora Polulus alba Manihot esculenta Euonymus americanus Oxalis latifolia Bulnesia arborea Heuchera sanguinea Liquidambar styraciflua Vitis vinifera Dillenia indica Ipomoea purpurea Cuscuta exaltata 48 Atropa belladonna Nicotiana tabacum Solanum lycopersicum 9 Antirrhinum majus Jasminum nudiflorum Nerium oleander Coffea arabica Ehretia acuminata Helianthus annuus Lactuca sativa Scaevola aemula Trachelium caeruleum Anethum graveolens Daucus carota Panax ginseng Lonicera japonica Ilex cornuta Rhododendron simsii Cornus florida Plumbago auriculata Ximenia americana Spinacia oleracea Plumbago auriculata Berberidopsis corallina 36 Gunnera manicata aralioides Buxus microphylla Meliosma cuneifolia nucifera occidentalis Ranunculus macranthus Nandina domestica demersum Typha latifolia Musa acuminata Elaeis oleifera Yucca schidigera Phalaenopsis aphrodite Dioscorea elephantipes Lemna minor americanus Piper cenocladum 73 Drimys granadensis Calycanthus floridus 56 tulipifera spicatus oligandrum advena Nymphaea alba trichopoda 2 Cycas micronesica Ginkgo biloba Oryza sativa Triticum aestivum Zea mays Pinus thunbergii Epifagus virginiana
27 j! Ranunculus macranthus Arabidopsis thaliana Brassica rapa Gossypium hirsutum Citrus sinensis Staphylea colchica Oenothera elata Eucalyptus globulus Pelargonium x hortorum Medicago truncatula Lotus corniculatus Phaseolus vulgaris Glycine max Ficus sp Morus indica Cucumis sativus 7 Quercus nigra 88 Passiflora biflora Polulus alba Manihot esculenta 79 Euonymus americanus 79 Oxalis latifolia 57 Bulnesia arborea Liquidambar styraciflua Heuchera sanguinea Vitis vinifera Dillenia indica Ipomoea purpurea Cuscuta exaltata 96 Solanum lycopersicum 52 Atropa belladonna Nicotiana tabacum Ehretia acuminata Epifagus virginiana Antirrhinum majus Jasminum nudiflorum 4 Nerium oleander Coffea arabica Aucuba japonica Helianthus annuus Lactuca sativa Anethum graveolens Daucus carota Scaevola aemula Trachelium caeruleum Panax ginseng Lonicera japonica Ilex cornuta Rhododendron simsii Cornus florida Spinacia oleracea Plumbago auriculata Berberidopsis corallina Ximenia americana Gunnera manicata aralioides Buxus microphylla Meliosma cuneifolia nucifera occidentalis Nandina domestica 8 93 Typha latifolia Musa acuminata Elaeis oleifera Yucca schidigera Phalaenopsis aphrodite Dioscorea elephantipes Lemna minor 99 americanus tulipifera 4 Calycanthus floridus 99 Piper cenocladum 98 Drimys granadensis demersum spicatus oligandrum advena Nymphaea alba trichopoda Phoradendron leucarpum Triticum aestivum Oryza sativa Zea mays Ginkgo biloba Cycas micronesica Pinus thunbergii.2 substitution per site Supplementary Fig. 4j. The ML tree inferred by RAxML based on concatenated 2 plastid genes of 86 species with percentage of parsimony informative sites ranging from 5% to 6%. Numbers associated with branches are bootstrap values; an asterisk indicates bootstrap of %. Species from eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae are in purple, green, orange, violet and blue, respectively.!!
28 k! substitution per site Supplementary Fig. 4k. The ML tree inferred by RAxML based on concatenated 2 plastid genes of 86 species. Numbers associated with branches are bootstrap values; an asterisk indicates bootstrap of %. Species from eudicots, monocots, magnoliids, Chloranthaceae and Ceratophyllaceae are in purple, green, orange, violet and blue, respectively.!! Arabidopsis thaliana Brassica rapa Gossypium hirsutum Citrus sinensis Staphylea colchica Oenothera elata Eucalyptus globulus Polulus alba Manihot esculenta Euonymus americanus Oxalis latifolia Cucumis sativus Quercus nigra Morus indica Ficus sp. Liquidambar styraciflua Heuchera sanguinea Vitis vinifera Dillenia indica Helianthus annuus Lactuca sativa Pelargonium x hortorum Passiflora biflora Medicago truncatula Lotus corniculatus Glycine max Phaseolus vulgaris Bulnesia arborea Scaevola aemula Trachelium caeruleum Anethum graveolens Daucus carota Panax ginseng Lonicera japonica Ilex cornuta Ipomoea purpurea Cuscuta exaltata Atropa belladonna Solanum lycopersicum Nicotiana tabacum Nerium oleander Coffea arabica Ehretia acuminata 99 Antirrhinum majus Aucuba japonica Cornus florida Jasminum nudiflorum Rhododendron simsii Spinacia oleracea Plumbago auriculata Berberidopsis corallina Ximenia americana Gunnera manicata Buxus microphylla aralioides nucifera occidentalis Meliosma cuneifolia Nandina domestica Ranunculus macranthus demersum Typha latifolia Musa acuminata Elaeis oleifera Phalaenopsis aphrodite Yucca schidigera Dioscorea elephantipes Lemna minor americanus Calycanthus floridus tulipifera Drimys granadensis spicatus oligandrum advena Nymphaea alba trichopoda Piper cenocladum Phoradendron leucarpum Oryza sativa Triticum aestivum Zea mays Epifagus virginiana Ginkgo biloba Cycas micronesica Pinus thunbergii
Supplementary Figure 3
Supplementary Figure 3 7.0 Col Kas-1 Line FTH1A 8.4 F3PII3 8.9 F26H11 ATQ1 T9I22 PLS8 F26B6-B 9.6 F27L4 9.81 F27D4 9.92 9.96 10.12 10.14 10.2 11.1 0.5 Mb T1D16 Col % RGR 83.3 101 227 93.5 75.9 132 90 375
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Number of CC- NBS and CC- NBS- LRR R- genes Number of TIR- NBS and TIR- NBS- LRR R- genes 0 50 100 150 200 250 0 50 100 150 200 250 300 350 400 450 mir482 and mir2118 Cajanus cajan Glycine max Hevea brasiliensis
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