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Additional File 4: Supplementary Fig. S6 Additional file 4: supplementary Fig. S6 Mitochondrial genomes of two parasitic Cuscuta species show little ​ ​ evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes ​ Anderson, Benjamin M; Krause, Kirsten; and Petersen, Gitte Fig. S6. Phylogenetic trees for mitochondrial genes across angiosperms, with particular focus (red) on Cuscuta species. Bootstrap support >60% is shown adjacent to nodes. Gene trees ​ ​ are divided as (a) atp1, atp4, atp6, atp8, atp9; (b) ccmB, ccmC, ccmFC, ccmFN, cob; (c) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ cox1, cox2, cox3, matR, mttB; (d) nad1, nad2, nad3, nad4, nad4L; (e) nad5, nad6, nad7, ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ nad9; (f) rrn5, rrn18, rrn26, rpl5, rpl16; and (g) rps1, rps3, rps4, rps12, rps13. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ a atp1 atp4 atp6 Cycas taitungensis Cycas taitungensis Cycas taitungensis 100 Pinus taeda 98 Ginkgo biloba 75 Ginkgo biloba Ginkgo biloba Pinus taeda Pinus taeda Nymphaea colorata 100Nymphaea colorata Amborella trichopoda Schisandra sphenanthera Nymphaea colorata2 Schisandra sphenanthera Amborella trichopoda 100 Schisandra sphenanthera 100 Nymphaea colorata 100 Schisandra sphenanthera2 Liriodendron tulipifera Liriodendron tulipifera Amborella trichopoda 74 Allium cepa Spirodela polyrhiza Liriodendron tulipifera Gastrodia elata 100 Tripsacum dactyloides Gastrodia elata Phoenix dactylifera 99 Saccharum officinarum Allium cepa 100 Sorghum bicolor Phoenix dactylifera 84 100 Butomus umbellatus Eleusine indica 98 99 Cynodon dactylon2 Stratiotes aloides Zea perennis 98 Zostera marina Lolium perenne Cynodon dactylon Lolium perenne 79 100 Eleusine indica 77 77 73 75 Hordeum vulgare 88 99 Aegilops speltoides 72 99 Triticum timopheevii 76 Aegilops speltoides 97 99 Triticum timopheevii Hordeum vulgare 70 76 Triticum timopheevii 92 Hordeum vulgare Aegilops speltoides Bambusa oldhamii 94 Lolium perenne 90 76 Oryza sativa 67 Oryza sativa 100 Oryza sativa 99 Bambusa oldhamii Allium cepa 100 Sorghum bicolor 76 Sorghum bicolor Cocos nucifera 87 100 Saccharum officinarum Saccharum officinarum 99Phoenix dactylifera 65 98 Tripsacum dactyloides 98 99 Zea perennis 100100 Butomus umbellatus Zea perennis Tripsacum dactyloides 76 Stratiotes aloides Bambusa oldhamii 83 Eleusine indica Zostera marina Cocos nucifera Cocos nucifera Nelumbo nucifera Spirodela polyrhiza Spirodela polyrhiza Vitis vinifera 96 87 Butomus umbellatus Nelumbo nucifera 85 Vaccinium macrocarpon 100 Stratiotes aloides Vitis vinifera 69 Monotropa hypopitys 64 Zostera marina 76 Nepenthes ventricosa Camellia sinensis Nelumbo nucifera Fallopia multiflora Ilex pubescens 68Beta vulgaris 96 94 Beta vulgaris Daucus carota Chenopodium quinoa 100 Chenopodium quinoa Fallopia multiflora 97 Sesuvium portulacastrum 96 Spinacia oleracea 87 Silene vulgaris 71 Spinacia oleracea 100 Silene vulgaris 85 78Beta vulgaris 78 Silene vulgaris 76 Spinacia oleracea Fallopia multiflora Sesuvium portulacastrum 62 Chenopodium quinoa Nepenthes ventricosa Eucalyptus grandis Sesuvium portulacastrum Camellia sinensis Lagerstroemia indica 65 Nepenthes ventricosa 100 Cynanchum wilfordii Geranium maderense Cynomorium coccineum 98 Cynanchum wilfordii2 100 Salix suchowensis 64 Rhazya stricta Rhazya stricta Populus tremula Asclepias syriaca 100 Platycodon grandiflorus 67Lactuca serriola Erythranthe guttata Codonopsis lanceolata 86 Paraprenanthes diversifolia Ajuga reptans 81Olea europaea 100 Diplostephium hartwegii 82 Castilleja paramensis 84Chionanthus rupicola Chrysanthemum boreale Salvia miltiorrhiza Ligustrum quihoui Helianthus annuus Utricularia reniformis Hesperelaea palmeri 100 Platycodon grandiflorus 87 Haberlea rhodopensis Utricularia reniformis 100 Codonopsis lanceolata Dorcoceras hygrometricum Salvia miltiorrhiza Prunus avium Olea europaea Ajuga reptans Eriobotrya japonica 77 Erythranthe guttata 100 69 Hesperelaea palmeri Castilleja paramensis Malus domestica Chionanthus rupicola Capsicum annuum Batis maritima 99 Ligustrum quihoui 100 69 Physochlaina orientalis 100 Citrullus lanatus 69Paraprenanthes diversifolia Hyoscyamus niger 84 Cucumis sativus Chrysanthemum boreale Nicotiana tabacum Cucurbita pepo 95 Lactuca serriola Solanum tuberosum Morus notabilis Diplostephium hartwegii Ilex pubescens Cannabis sativa Helianthus annuus Carica papaya Hemiptelea davidii 62 Ziziphus jujuba Corchorus olitorius Ziziphus jujuba 100 Prunus avium Batis maritima Arabis alpina 100Malus domestica Spondias tuberosa 100 Schrenkiella parvula Eriobotrya japonica Xanthoceras sorbifolium Eruca vesicaria Cannabis sativa 89 Cucurbita pepo Brassica rapa 95Morus notabilis 94 Cucumis sativus Capsella rubella 88 Hemiptelea davidii 76 Citrullus lanatus 100 Turritis glabra Styphnolobium japonicum Lagerstroemia indica Boechera stricta Cercis canadensis 100Leucaena trichandra Arabidopsis thaliana Citrullus lanatus 70 Acacia ligulata Sinapis arvensis 88 Cucumis sativus Lophophytum mirabile 100 Raphanus sativus Cucurbita pepo Castanospermum australe Lagerstroemia indica Senna tora 79Capsicum annuum Geranium maderense 86 Libidibia coriaria 98 Hyoscyamus niger Spondias tuberosa Haematoxylum brasiletto 100 Physochlaina orientalis Peganum harmala Lotus japonicus Solanum tuberosum Glycine soja 63 Nicotiana tabacum Citrus sinensis 93 Ipomoea nil Hibiscus cannabinus 69 Phaseolus vulgaris 100 100 Corchorus olitorius 97 Vigna radiata 98 Cuscuta australis Gossypium trilobum Millettia pinnata Cuscuta campestris 92 Bombax ceiba Bupleurum falcatum2 Cuscuta gronovii 99 Gastrodia elata 88 Bupleurum falcatum 100 Hesperelaea palmeri Gastrodia elata2 81Vicia faba Chionanthus rupicola 100 Codonopsis lanceolata 68 Medicago truncatula 65 Ligustrum quihoui Platycodon grandiflorus Styphnolobium japonicum 98 Olea europaea Epirixanthes elongata Tamarindus indica Haberlea rhodopensis Carica papaya 99 Haberlea rhodopensis Dorcoceras hygrometricum 100 63 Erythranthe guttata 85 Manihot esculenta 99 Salvia miltiorrhiza Hevea brasiliensis 100 97 Bombax ceiba 94 74 Ajuga reptans Ricinus communis Gossypium trilobum 97 Utricularia reniformis Eucalyptus grandis Hibiscus cannabinus Castilleja paramensis Xanthoceras sorbifolium 99 Ammopiptanthus nanus Dorcoceras hygrometricum 100Salix suchowensis Sophora flavescens 100 Populus tremula Geranium maderense 100 Cynanchum wilfordii Citrus sinensis Asclepias syriaca Arabidopsis thaliana Cercis canadensis Rhazya stricta 99 Arabis alpina Diplostephium hartwegii Ilex pubescens Boechera stricta Chrysanthemum boreale Epirixanthes elongata Turritis glabra 99Paraprenanthes diversifolia Carica papaya Capsella rubella Lactuca serriola Peganum harmala 98 69 Sinapis arvensis Epirixanthes elongata Spondias tuberosa 79 Raphanus sativus Cannabis sativa 97 Cynomorium coccineum 77 Brassica rapa 96 Capsella rubella Eruca vesicaria Turritis glabra Citrus sinensis Batis maritima Xanthoceras sorbifolium 71 Arabidopsis thaliana 71 Camellia sinensis 100 Lophophytum mirabile Raphanus sativus 100 100 Vaccinium macrocarpon Acacia ligulata 78Brassica rapa Monotropa hypopitys Leucaena trichandra 60 Sinapis arvensis Gossypium trilobum Tamarindus indica 100 Eruca vesicaria 67 92Senna tora Boechera stricta 99 Hibiscus cannabinus 70 Senna tora2 74 61 Arabidopsis thaliana2 Bombax ceiba 96 Ammopiptanthus nanus Arabis alpina Corchorus olitorius Sophora flavescens Peganum harmala Manihot esculenta Castanospermum australe Helianthus annuus 99 Hevea brasiliensis 0.1 Millettia pinnata Hemiptelea davidii Ricinus communis Vigna radiata 93 Cynomorium coccineum2 95 Vigna radiata 98 Vicia faba Cynomorium coccineum 100 Phaseolus vulgaris Medicago truncatula 100 Populus tremula Glycine soja Phaseolus vulgaris 0.1 Salix suchowensis Millettia pinnata Glycine soja Eucalyptus grandis 0.2 Lotus japonicus Lotus japonicus 98 Ipomoea nil 78 Styphnolobium japonicum Bupleurum falcatum 97 Cuscuta gronovii 97 Castanospermum australe 100 Libidibia coriaria 92Cuscuta campestris 82 Sophora flavescens 95 Haematoxylum brasiletto Cuscuta australis 68 Ammopiptanthus nanus Cynanchum wilfordii Ricinus communis 76 Medicago truncatula 62 Solanum tuberosum Hevea brasiliensis Bupleurum falcatum Hyoscyamus niger 88 Manihot esculenta Tamarindus indica 91 Physochlaina orientalis Daucus carota Cercis canadensis Capsicum annuum Monotropa hypopitys Lophophytum mirabile 86 Nicotiana tabacum Vitis vinifera 74 88 Ipomoea nil Ziziphus jujuba Leucaena trichandra 100 100 Prunus avium 94 Acacia ligulata 100 Cuscuta australis 90 97Eriobotrya japonica Haematoxylum brasiletto Cuscuta campestris 90 96 Libidibia coriaria Cuscuta gronovii Malus domestica atp8 atp9 Cycas taitungensis Cycas taitungensis 95 Pinus taeda 98 Ginkgo biloba Ginkgo biloba Pinus taeda 98 Schisandra sphenanthera Amborella trichopoda Schisandra sphenanthera2 Nymphaea colorata Nymphaea colorata 100 Stratiotes aloides 99 Liriodendron tulipifera Zostera marina Amborella trichopoda Butomus umbellatus Nelumbo nucifera 90 Gastrodia elata Spirodela polyrhiza 100 Cocos nucifera Cocos nucifera Phoenix dactylifera 87Hordeum vulgare Oryza sativa Aegilops speltoides 67 Sorghum bicolor Triticum timopheevii 100 Bambusa oldhamii 83 Eleusine indica Saccharum officinarum Cynodon dactylon 10088 Cynodon dactylon Oryza sativa Eleusine indica 69 67 Tripsacum dactyloides Zea perennis 60 89 Zea perennis Tripsacum dactyloides Sorghum bicolor 83 Lolium perenne 84 Saccharum officinarum 98 Hordeum vulgare Bambusa oldhamii Triticum timopheevii Phoenix dactylifera 100 82Rhazya stricta 97 Aegilops speltoides 62 100 Cynanchum wilfordii Allium
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