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.