Additional file 3: supplementary Fig. S5 Mitochondrial genomes of two parasitic Cuscuta show little ​ ​ evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes ​ Anderson, Benjamin M; Krause, Kirsten; and Petersen, Gitte

Fig. S5. Phylogenetic for nuclear candidate copies of mitochondrial genes in Cuscuta ​ australis and C. campestris in relation to known mitochondrial copies in other . ​ ​ ​ Bootstrap support >60% is shown adjacent to nodes.

rps2 rps10 rps11 rps14 Cycas taitungensis Cycas taitungensis Cycas taitungensis 74 Ginkgo biloba Cycas taitungensis Pinus taeda Pinus taeda Ginkgo biloba Ginkgo biloba Nymphaea colorata Schisandra sphenanthera Amborella trichopoda 61 99 Amborella trichopoda 96 Phoenix dactylifera Pinus taeda Pinus taeda Cocos nucifera 74 Cocos nucifera Nicotiana tabacum Gastrodia elata 93 Capsicum annuum Lolium perenne Amborella trichopoda Hyoscyamus niger 100 Nymphaea colorata Physochlaina orientalis Ginkgo biloba Liriodendron tulipifera Solanum tuberosum Schisandra sphenanthera Olea europaea Nymphaea colorata Nelumbo nucifera 100 100 Hesperelaea palmeri Vitis vinifera Ligustrum quihoui 83 79 Bombax ceiba Chionanthus rupicola Schisandra sphenanthera Utricularia reniformis Gossypium trilobum 93 Salvia miltiorrhiza Lagerstroemia indica 93 Castilleja paramensis 68 63 65 Eucalyptus grandis Cuscuta australis Erythranthe guttata Ipomoea nil 100 Lagerstroemia indica Nepenthes ventricosa Vitis vinifera Populus tremula Cuscuta campestris Carica papaya 100 Camellia sinensis Bombax ceiba Fallopia multiflora 73 70 Hibiscus cannabinus Erythranthe guttata 71 72 Liriodendron tulipifera Gossypium trilobum Castilleja paramensis Corchorus olitorius Nepenthes ventricosa Haberlea rhodopensis Batis maritima Ligustrum quihoui Cynomorium coccineum 62 Nelumbo nucifera Hesperelaea palmeri 95 Xanthoceras sorbifolium Chionanthus rupicola Lophophytum mirabile Schisandra sphenanthera Olea europaea Spirodela polyrhiza 100 Cuscuta australis Cuscuta campestris 81 Utricularia reniformis Cuscuta campestris 92 Cynanchum wilfordii 100 Cuscuta australis Gastrodia elata 79 Asclepias syriaca Rhazya stricta Batis maritima Amborella trichopoda 97 Brassica rapa 61 Citrullus lanatus 100 Cocos nucifera Cucumis sativus Eruca vesicaria 71 Cucurbita pepo Sinapis arvensis Monotropa hypopitys Raphanus sativus Phoenix dactylifera Spondias tuberosa Liriodendron tulipifera Nicotiana tabacum 98 Utricularia reniformis Malus domestica 100 90 62 Eucalyptus grandis Eriobotrya japonica Zea perennis Cannabis sativa 79 64 Diplostephium hartwegii Gastrodia elata 100 76 Cynomorium coccineum Hemiptelea davidii Nymphaea colorata 93 Chrysanthemum boreale Tripsacum dactyloides Haberlea rhodopensis Prunus avium 100 Sophora flavescens 87 Vaccinium macrocarpon Hibiscus cannabinus Sorghum bicolor Ziziphus jujuba Xanthoceras sorbifolium Cuscuta campestris Salvia miltiorrhiza 100 Citrus sinensis Epirixanthes elongata Rhazya stricta 95 100 Saccharum officinarum Ricinus communis Carica papaya Styphnolobium japonicum Vigna radiata Lotus japonicus Phaseolus vulgaris Cuscuta australis Eleusine indica Vitis vinifera Millettia pinnata 100 Nelumbo nucifera Bupleurum falcatum Glycine soja 99 Millettia pinnata Cynodon dactylon Medicago truncatula Phaseolus vulgaris 93 Gastrodia elata Lotus japonicus Vigna radiata 69 88 Bupleurum falcatum Bambusa oldhamii Glycine soja Sophora flavescens 95 Vicia faba Medicago truncatula Ammopiptanthus nanus 86 Leucaena trichandra Lolium perenne Liriodendron tulipifera Cocos nucifera Castanospermum australe Styphnolobium japonicum Ammopiptanthus nanus coriaria 100 88 Hordeum vulgare Leucaena trichandra Lophophytum mirabile Haematoxylum brasiletto Cercis canadensis 0.2 61 0.5 Tamarindus indica Phoenix dactylifera 0.2 Castanospermum australe Triticum timopheevii Acacia ligulata Tamarindus indica 100 tora 0.2 Senna tora Libidibia coriaria Haematoxylum brasiletto Cercis canadensis Aegilops speltoides Acacia ligulata Nelumbo nucifera

rps19 sdh3 sdh4 Cycas taitungensis Ginkgo biloba Cycas taitungensis Liriodendron tulipifera Schisandra sphenanthera Pinus taeda Spirodela polyrhiza 78 Hesperelaea palmeri Ginkgo biloba Cocos nucifera Olea europaea Nymphaea colorata Nymphaea colorata Liriodendron tulipifera 88 Chionanthus rupicola Amborella trichopoda Amborella trichopoda 73 Ligustrum quihoui Nelumbo nucifera 100 Schisandra sphenanthera Nepenthes ventricosa Utricularia reniformis Gastrodia elata 77 82 Sesuvium portulacastrum Erythranthe guttata Fallopia multiflora Phoenix dactylifera Monotropa hypopitys 62 87 Asclepias syriaca 66 Oryza sativa 97 Ipomoea nil 100 Bambusa oldhamii Cynanchum wilfordii Erythranthe guttata Haberlea rhodopensis Eucalyptus grandis Eleusine indica Ligustrum quihoui Bombax ceiba Asclepias syriaca 93 Cocos nucifera 81 98 61 Cynanchum wilfordii Cocos nucifera2 Gossypium trilobum Rhazya stricta Liriodendron tulipifera Cucurbita pepo Lagerstroemia indica 85 Vaccinium macrocarpon Cucumis sativus 66Hyoscyamus niger 77 84 90 Physochlaina orientalis Monotropa hypopitys2 non-angiosperms 97 Citrullus lanatus 61 Capsicum annuum Monotropa hypopitys Capsicum annuum Solanum tuberosum Eucalyptus grandis Rhazya stricta Dorcoceras hygrometricum basal + magnoliids 86 61 Vitis vinifera Cynanchum wilfordii Castilleja paramensis Cynomorium coccineum 83 Vaccinium macrocarpon monocots Asclepias syriaca Camellia sinensis 86 Hesperelaea palmeri Hyoscyamus niger Monotropa hypopitys Chionanthus rupicola basal Capsicum annuum Olea europaea Nepenthes ventricosa 80 62 Physochlaina orientalis Utricularia reniformis Sesuvium portulacastrum Chrysanthemum boreale Solanum tuberosum Diplostephium hartwegii Spondias tuberosa Nicotiana tabacum Platycodon grandiflorus rosids / fabids Batis maritima Boechera stricta Cynomorium coccineum 78 Gossypium trilobum 100 Cuscuta australis Ipomoea nil 74 Hibiscus cannabinus rosids / malvids 68 Cuscuta campestris 75 Bombax ceiba Vitis vinifera Carica papaya Corchorus olitorius Nelumbo nucifera Batis maritima asterids Ziziphus jujuba Ziziphus jujuba Carica papaya Ricinus communis Spondias tuberosa asterids / campanulids Morus notabilis 68 Peganum harmala Hevea brasiliensis Ricinus communis 80 Xanthoceras sorbifolium Manihot esculenta Citrullus lanatus asterids / lamiids Hibiscus cannabinus 69 Cucurbita pepo Haematoxylum brasiletto 86 Lagerstroemia indica 100 Cucumis sativus Hemiptelea davidii Libidibia coriaria Cercis canadensis Ziziphus jujuba Nepenthes ventricosa 100 Cercis canadensis Cannabis sativa Hyoscyamus niger Hemiptelea davidii 100 Cuscuta australis Citrus sinensis Cuscuta campestris Solanum tuberosum 100 Populus tremula Cannabis sativa Nicotiana tabacum Salix suchowensis 77 Manihot esculenta 67 Citrullus lanatus2 Platycodon grandiflorus 63 66 Hevea brasiliensis 78 Citrullus lanatus Physochlaina orientalis Ricinus communis Cucurbita pepo2 Tamarindus indica 98 Vitis vinifera Castanospermum australe Cucurbita pepo 90 Cannabis sativa Ammopiptanthus nanus Batis maritima 100 Eriobotrya japonica 0.1 100 Nelumbo nucifera2 99 Carica papaya Malus domestica Nelumbo nucifera Lophophytum mirabile Haematoxylum brasiletto Amborella trichopoda Lophophytum mirabile2 Libidibia coriaria 0.2 Libidibia coriaria Nymphaea colorata Haematoxylum brasiletto Acacia ligulata Schisandra sphenanthera Leucaena trichandra Leucaena trichandra Ginkgo biloba Acacia ligulata Lophophytum mirabile 0.2 100 Cuscuta campestris Pinus taeda Cuscuta australis Lophophytum mirabile2