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. 2012 Sep 21;110(6):1137–1147. doi: 10.1093/aob/mcs197

TABLE S2.

Sequences used in phylogenetic construction and evolutionary rate analysis

Taxa Species   nuclear mitochondrial
PI AP3 FLO/LFY 18S rDNA matR RPB2/RPB2-d copy
paleoAP3/TM6 euAP3
Basal eudicots                
Buxales
 Buxaceae Pachysandra procumbens AF094533 AF197784
Pachysandra terminalis GU357455 (PAtePI) PAteAP3-1 (GU357454)
Proteales PAteAP3-2 (GU357462)
 Platanaceae Platanus occidentalis PloAP3-1 (AY162881) AF106842 U42794 AF197793
PloAP3-2 (AY162882)
Platanus sp. AY566618
Ranunculales
 Lardizabalaceae Akebia quinata AkqPI (AY162837) AkqAP3-1 (AY162835) L31795 AF197810
AkqAP3-2 (AY162839)
Akebia longeracemosa AY566613
 Papaveraceae Eschscholzia californica AY188789
Sabiales
 Sabiaceae Meliosma dilleniifolia MedMdPI (AY436712) MedMdAP3-1 (AY436709)
MedMdAP3-2 (AY436710)
MedMdAP3-2 (AY436711)
Meliosma squamulata DQ008728 DQ007426
Trochodendrales
 Trochodendraceae Trochodendron aralioides TraPI-1 (EF436259) TraAP3 (DQ453774) AF230078 U42816 AF197792 AY563269
TraPI-2 (EF436260)
Core eudicots                
Apiales
 Apiaceae Apium graveolens AF206852
Daucus carota MADS2 (AJ271148) MADS3 (AJ271149)
Petroselinum crispum AY453081
 Aralidiaceae Hedera helix AJ563601
Aquifoliales
 Aquifoliaceae Ilex aquifolium IxaGLO1 (GQ141105) IxaTM6 (DQ479357) IxaAP3 (DQ479356) AY453090
Ilex meseryeae AJ557240
Ilex opaca AF161010
Asterales
 Asteraceae Chrysanthemum x morifolium AB451217
Gerbera hybrida GGLO1 (GHY9726) GDEF1 (AJ009724) GDEF2 (AJ009725) AF107576
PMADS2 (X69947)
Helianthus annuus Ham31 (AY173069) Ham91 (AY173070) Ham63 (EF612598) AY453114
Brassicales
 Brassicacaeae Arabidopsis thaliana PI (D30807) AP3 (D21125) DQ447103 X16077 NC_001284 z19121
 Caricaceae Carica papaya CpPI (EF562500) CpTM6-1 (EF562498) U42514 AF520141
CpTM6-2 (EF562499)
Caryophyllales
 Amaranthaceae Spinacia oleracea SoPI (AY604515) SoAP3 (AY604514) L24420 AY453110 AF020840
 Caryophyllaceae Silene latifolia SLM2 (X80489) SlAP3A (AB090863) SLM3 (X80490)
SlAP3Y (AB090864)
Silene coeli-rosa AJ311804
 Phytolaccaceae Phytolacca americana PhaTM6-1 (DQ479365) U42793
PhaTM6-2 (DQ479366)
 Polygonaceae Homalocladium platycladum DQ017114
Cornales
 Cornaceae Alangium platanifolium AJ555916
Davidia involucrata AJ557002
 Hydrangeaceae Hydrangea macrophylla HmPI (AF230711) HmTM6 (AF230703) HmAP3 (AF230702) U42781 AY453091
 Nyssaceae Nyssa sylvatica NsGLO1 (GQ141111) NsTM6 (GQ141155) NsDEF (GQ141170) X16603
NsGLO2 (GQ141109)
 Styracaceae Styrax japonicus SjGLO (GQ141121) SjTM6 (GQ141163) SjDEF (GQ141185 ) L49296
Cucurbitales
 Coriariaceae Coriaria sarmentosa DQ017097
 Cucurbitaceae Cucumis sativus CsPI (AF043255) CsMADS1 (AY944060) AF059320 AF206894
Dilleniales
 Dilleniaceae Dillenia indica DiiPI-1 (EF549702) DiiTM6 (EF549705) DiiDEF (EF549703) AF520095
DiiPI-2 (EF549703)
Dillenia alata U38314
Ericales
 Balsaminaceae Impatiens auriculata AF520117
Impatiens alsamina AJ888755
 Clethraceae Clethra tomentosa CtGLO (GQ141143) CtTM6 (GQ141180) CtDEF (GQ141166)
 Ericaceae Rhododendron macrophyllum AY566626
 Diapensiaceae Galax urceolata GuGLO1 (GQ141151) GuTM6 (GQ141164) GuDEF (GQ141187) L49281
 Polemoniaceae Phlox paniculata PpGLO (GQ141129) PpTM6 (GQ141157) PpDEF (GQ141172)
 Theaceae Camellia japonica AY566627
Fagales
 Betulaceae Betula pendula BpPI (AJ488589) AY453121
Juglans nigra AF206943
Juglans regia JrAP3 (AJ313089) GU194836
Fabales
 Fabaceae Lotus corniculatus LcPIa (AY770398) LcTM6 (AY770401) LcAP3 (AY770400) AY770393
LcPIb (AY770399)
Pisum sativum AF035163 U43011 AY453078
Tephrosia purpurea AJ556782
Vicia sativa AJ556176
Gunnerales
 Gunneraceae Gunnera tinctoria GtAP3-1 (AY337753)
GtAP3-2 (AY337754)
GtAP3-3 (AY337755)
GtAP3-4 (AY337756)
GtAP3-5 (AY337757)
Gunnera manicata U43787 AF520163
Lamiales
 Oleaceae Syringa vulgaris SvPI (AF052861) SvAP3 (AF052869)
 Plantaginaceae Antirrhinum majus GLOBOSA (X68831) DEFA (X62810) M55525 AJ236047 AY453102 AJ566619
Malpighiales
 Euphorbiaceae Ricinus communis XM_002519014
 Hypericaceae Hypericum canariense AJ556993
 Salicaceae Populus trichocarpa PtPI (grail3·0002017601) PTD (AF057708)
Populus balsamifera U93196 AY652861
Populus maximowiczii AY674556
Myrtales
 Myrtaceae Callistemon subulatus DQ017092
Eucalyptus grandis EGM2 (AF029976) AY640314
Eucalyptus lehmannii AM235528
Melaleuca quinquenervia MeqPI (EU004206)
Myrtus communis EU281109 AJ556164
Rosales
 Rosaceae Malus x domestica MadMdPI (AJ291490) MadMdTM6 (AB081093) AB162028
MadMADS13 (AJ25116)
Prunus persica - - EU375891 L28749
Taihangia rupestris TrPI (DQ248947) TrTM6 (DQ248946) AF520201
Saxifragales
 Altingiaceae Liquidambar sp. AY566623
 Grossulariaceae Ribes aureum - L28143
Ribes sanguineum RsPI (AY337742) RsAP3-1 (AY337758)
RsAP3-2 (AY337758)
Ribes sp. EF370723
 Hamamelidaceae Corylopsis pauciflora CopTM6-1 (DQ479354) CopAP3 (DQ479353) AF094548
CopTM6-2 (DQ479355)
 Saxifragaceae Astillbe sp. AY566622
Saxifraga careyana SacTM6 (DQ479368) SacAP3 (DQ479367)
Santalales
 Balanophoraceae Balanophora fungosa BafPI (JQ613262) BafTM6 (JQ613231) BafAP3 (JQ613229) JQ613242 JN392868 JQ613244 JQ613269
Balanophora laxiflora BalPI (JQ613261) BalTM6 (JQ613232) BalAP3 (JQ613230) JQ613243 JN392870 JQ613245 JQ613270
 Loranthaceae Loranthus delavayi LodPI (JQ613264) LodTM6 (DQ453773) JQ613220 JQ613248
Loranthus kaoi LokPI (JQ613263) LokTM6 (JQ613241) JQ613221 JQ613249 JQ613272
 Olacaceae Olax imbricata OliPI (JQ613259) OliTM6 (JQ613239) JQ613222 JQ613246 JQ613268
 Opilliaceae Champereia manillana ChmPI (JQ613258) ChmTM6 (JQ613237) JQ613223 JQ613247 JQ613271
 Santalaceae Santalum album SaaPI (JQ613256) SaaTM6 (JQ613238) JQ613224 JQ613250 JQ613266
 Thesiaceae Thesium chinense ThcPI (JQ613257) ThcTM6 (JQ613235) JQ613225 JQ613251 JQ613267
 Schoepfiaceae Schoepfia jasminodora ScjPI (JQ613260) ScjTM6 (JQ613240) JQ613226 JQ613252 JQ613273
 Viscaceae Viscum articulatum ViArPI-1 (JQ613255) ViArTM6-1 (JQ613233) JQ613228
ViArPI-2 (JQ613254) ViArTM6-2 (JQ613234)
Viscum anilformosanae ViAlPI (JQ613253) ViAlTM6 (JQ613236) JQ613227 JQ613265
Solanales
 Solanaceae Petunia hybrida FBP1 (m91190) PhTM6 (AF230704) PhGP (X69946) AF030171 DQ020641
Nicotiana sylvestris AY453113
Lycopersicon esculentum TPI (DQ674531) TDR6 (X60759) LeAP3 (AF052868) X51576 U28403
Vitales
 Vitaceae Vitis vinifera MADS9 (DQ988043) VvTM6 (DQ979341) VvAP3 (EF418603) AF450278 NC_012119
Vitis sp. AF207053

Note: sequences newly identified in this study are shown in bold.