Molecular Genetic Insights into Basal Angiosperms Sangtae Kim · 2011-06-03 · Darwin’s Abominable Mystery: explosive evolution andexplosive evolution and diversification of angiosperms

Molecular Genetic Insights into Molecular Genetic Insights into ggBasal AngiospermsBasal Angiosperms

SangtaeSangtae KimKimSangtaeSangtae KimKim

Evolution of Basal AngiospermsEvolution of Basal Angiospermsg pg p

I.I. BasalBasal--most angiosperm and most angiosperm and the Floral Genome Projectthe Floral Genome Projectthe Floral Genome Projectthe Floral Genome Project

IIII Floral gene expressionsFloral gene expressionsII.II. Floral gene expressions Floral gene expressions in basal angiospermsin basal angiosperms

IIIIII. B. B--class gene proteinclass gene protein--protein interactions protein interactions ( )( )in in AmborellaAmborella( )( )

I.I. BasalBasal--most angiosperm and most angiosperm and the Floral Genome Projectthe Floral Genome Project

…

??

Darwin’s Abominable Mystery: explosive evolution andexplosive evolution and diversification of angiosperms

- Charles DarwinCharles Darwinletter to Joseph Dalton Hooker, 22 July 1879.

“…the rapid rise and early diversification of angiosperms is an abominable mystery…”

*

?

Early branching angiosperm(sister to all other angiosperms):

Ranalian complex?Ranalian complex?Ranalian complex?Ranalian complex?

Amentiferae?Amentiferae?

MagnoliaMagnolia??DrimysDrimys??

CeratophyllumCeratophyllum??yy

Soltis et al 1999 Angiosperm

FagalesCucurbitalesRosalesFabalesZygophyllalesCelastrales

Walnuts, chestnutSquashApples, strawberriesLegumesCreosote plant

EudicotsCore-eudicots

Soltis et al., 1999. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402: 402-404.

OxalidalesMalpighialesSapindalesMalvalesBrassicalesCrossosomatalesMyrtales

Star fruitPassion fruitCitrus, cashewsCotton, cocoaArabidopsis, mustard

Pomegranate

- Selected 500 taxa- Multi-gene analyses:

rbcL+atpB+18S

yGernalialesSaxifragalesLamialesSolanalesGentianalesGarryalesAsteralesDi l

GooseberryAntirrhinum, oliveTomato, green pepperCoffee

SunflowerrbcL+atpB+18S DipsacalesApialesAquifolialesCornalesEricalesBerberidopsidalesSantalalesCaryophyllales

ElderberryDill, fennel

Blueberry, cranberry

B ck heat q inoaCaryophyllalesGunneralesBuxalesTrochodendralesProtealesSabiaceae

Buckwheat, quinoa

Macadamia nut

Ranunculales Poppy

Ceratophyllales

Monocots

MagnolialesLauralesPiperalesWinterales

Chloranthales

Illiciaceae

NutmegAvocadoBlack pepper

Star aniseSchisandraceaeAustrobaileyaceaeNymphaeaceaeAmborellaceae

Gymnosperms

Amborella trichopoda

• Shrub, New Caledonia

U i l ll fl• Unisexual small flowers

• Spiral arrangement

• Moderate number of parts

• Undifferentiated perianth



EudicotsCore-eudicots• End of debates?

Soltis et al., 1999. OxalidalesMalpighialesSapindalesMalvalesBrassicalesCrossosomatalesMyrtales


Pomegranate

Mathews and Donoghue, 1999Qiu et al., 1999Soltis, …, Kim, 2000Savolainen et al 2000



SunflowerSavolainen et al., 2000Barkman et al., 2000Zanis et al., 2002Kuzoff and Gasser, 2000

DipsacalesApialesAquifolialesCornalesEricalesBerberidopsidalesSantalalesCaryophyllales



B ck heat q inoaZanis et al., 2002Borsch et al., 2003Goremykin et al., 2003Hilu et al 2003

CaryophyllalesGunneralesBuxalesTrochodendralesProtealesSabiaceae

Buckwheat, quinoa

Macadamia nut

Ranunculales PoppyHilu et al., 2003Soltis and Soltis, 2004Soltis et al., 2004Kim et al., 2004 Ceratophyllales

Monocots

Martin et al., 2005Leebens-Mack et al., 2005 Goremykin et al., 2006Moore et al 2007


Chloranthales

Illiciaceae


Star aniseMoore et al., 2007Jansen et al., 2007…

SchisandraceaeAustrobaileyaceaeNymphaeaceaeAmborellaceae

Gymnosperms

KIM, et al., (2004)

Phylogeny and diversificationPhylogeny and diversification of B-function MADS-box genes in angiosperms: evolutionary and functionalevolutionary and functional implications of a 260-million-year-old duplication.

American Journal of Botany21: 2102-2118.J lJournal cover

AP3 familyKim et al. (2004)

NTDEF Nicotiana

STDEF.Solanum

NTDEF.Nicotiana

PI family

RfPI 1 Ranunculus

MfPI.Michelia

RfPI.1.Ranunculus

SmAP3.SagittariaEbAP3.1.Eupomatia

MfAP3 Mi h li

CUM26Cucumis

MfAP3.Michelia

*

##

**



Eudicots

Current understanding of angiosperm phylogeny

monocots dicots

OxalidalesMalpighialesSapindalesMalvalesBrassicalesCrossosomatalesMyrtales


Pomegranate

angiosperm phylogeny

Traditional view



Sunflower

75%

Traditional view DipsacalesApialesAquifolialesCornalesEricalesBerberidopsidalesSantalalesCaryophyllales



B ck heat q inoaCaryophyllalesGunneralesBuxalesTrochodendralesProtealesSabiaceae

Buckwheat, quinoa

Macadamia nut

Ranunculales Poppy

monocots

eudicots

Ceratophyllales

Monocots 22%Grains, Palms

Recent view


Chloranthales

Illiciaceae


Star anise3%

Basal Angiosperms

Recent viewSchisandraceaeAustrobaileyaceaeNymphaeaceaeAmborellaceae

Gymnosperms

Summary of Angiosperm Phylogeny

72% 25% 3%

Summary of Angiosperm Phylogeny (Soltis et al., 1999; Qiu et al., 1999; Soltis et al., 2000; Zanis et al., 2002; Hilu et al., 2003…)

ms

eudicots

e

monocots basal angiosperms

72% 25% 3%

Arabidopsis

orel

laph

aeac

eae

obai

leya

les

cots

anth

acea

e

les

olia

les

lale

sal

es

t gym

nosp

erm

eral

esod

endr

acea

e

ceae

alesceae

ncul

ales

alal

es

raga

les

ophy

llale

s

sds orel

laph

aeac

eae

roba

ileya

les

rant

hace

ae

ales

nolia

les

llale

sra

les

ArabidopsisAntirrhinum rice

Am

boN

ymp

Aus

tro

mon

oc

Chl

ora

Laur

aM

agno

Can

elPi

pera

exta

nt

Gun

neTr

och

Buxa

cP

rote

a

Sabi

a

Ran

un

San

ta

Saxi

fr

Car

yo

rosi

ds

aste

rid

Am

boN

ymp

Aus

tr

Chl

or

Laur

aM

agn

Can

ePi

per

http://www.floralgenome.org/

Floral Genome Project: A Solution to Darwin’s Abominable Mystery?

• The Goal of the Floral Genome Project:j- Provide an evolutionary genomic framework

for flowers- Address questions of

. Origin and diversification of flowers. g

. Evolution of plant reproduction.


• Floral Genome Project (FGP) PIs and collaborators:

University of Florida: Doug Soltis and Pam Soltis (molecular systematics)David Oppenheimer (high throughput in situs) + ( )pp ( g g p )

Penn State University: Claude dePamphilis (molecular evolution)Jim Leebens Mack Project Manager

( )Jim Leebens-Mack, Project ManagerJohn Carlson (tree genomics)Hong Ma (flower developmental genetics)Naomi Altman (statistics)( )Webb Miller (bioinformatics)

Cornell University: Steve Tanksley (plant genomics; EST informatics)Steve Tanksley (plant genomics; EST informatics)Jeff Doyle (nuclear gene families)

Collaborators:Mike Frohlich (Mostly Male theory; Natural History Museum, London)Victor Albert (expression + seq. analysis; floral evolution;Univ. of Oslo)Steve Farris (expression + seq. analysis; Swedish Mus. Nat. History)


Floral Genome Approaches

• PHYLO-EVO-DEVOTICS= Phylogenetics + Evolution + Developmental Biology + Genomics + Bioinformatics

• Compare expressed genes from early stages of flower development in diverse angiosperms (15 selected taxa)development in diverse angiosperms (15 selected taxa)

>100,000 ESTs

• Determine expression patterns during floral development in diverse species

RT PCR I it iRT-PCR, In situ, microarrays


• Skim papers:

- Soltis et al. (2002) Missing links: the genetic architectureof flower and floral diversification. TIPS 7: 22-31.

- Albert, … Kim, … et al. (2005). Floral gene resources f b l i f i ifrom basal angiosperms for comparative genomics research. BMC Plant Biology 5: 1-15.

CYCLOIDEA Citerne et al., 2006. PNASCYCLOIDEA Citerne et al., 2006. PNAS

Lupinus

Cadia

soc1 and ful : annual to perrenialSiegbert et al. Nnature Genet. 2008

II.II. Floral gene expressions Floral gene expressions in basal angiospermsin basal angiosperms

Flowers are central identifying structure for angiosperms

ABC model (Coen and Meyeorowitz, 1991): Genetic Control of Floral Organ Identity in Model Plants

Our understanding of floral developmental genetics in “model” systems

Genetic Control of Floral Organ Identity in Model Plants

B

A C

A A+B B+C CASepal

A+BPetal

B+CStamen

CCarpel

CarpelPetal

Stamen

S lSepal




B

A CA C

ArabidopsisAP3/PI

AP1/AP2 AG

AP3/PI

AP1/AP2 AG

Sepal Petal Stamen Carpel

MADS box gene family:Transcription factorsp

Extended ABC model (Theissen, 2001)

B

A CD

B

CD

A

EE

A B+C+E C+E D+EA+B+ESepal Stamen Carpel

Carpel

OvulePetal

Stamen

CarpelPetal

SepalOvule




ArabidopsisAP3/PI

AP1/AP2 AG


AP1/AP2 AG

Silky1/ZP1

ZAP1

P l L di l St C l

MaizeAmbrose et al.,2000 ZMM2

ZAG1

PaleaLemma

Lodicule Stamen Carpel

Modified ABC model (van Tunen et al., 1993); Sliding border model

BB


A C

Tepal Tepal

TulipKanno et al., 2003

Sepal Petal Stamen CarpelTepal Tepal

Questions in basal angiosperms

1. Are homologs of ABC B

genes found in basal angiosperms?

B

A C

2. Where are ABC homologs expressed?

ASepal

A+BPetal

B+CStamen

CCarpel

C l homologs expressed?

3. If expression implies Petal

Stamen

Carpel

function, does the ABC model hold for basal angiosperms? Sepal

Persea americana

Asiminalongifolia

Eupomatiabennettii

Magnoliagrandiflora

Illiciumfloridanum

Nupharadvena

Amborellatrichopoda“MADS” search of

b l ibasal angiosperms

ms

eudicots monocots basal angiosperms

rella

ceae

haea

ceae

obai

leya

les

cots

anth

acea

e

es olia

les

lale

sal

es gym

nosp

erm

eral

esod

endr

acea

e

ceae

alesceae

ncul

ales

lale

s

agal

es

phyl

lale

s

ds

Am

bor

Nym

phA

ustro

mon

oc

Chl

ora

Laur

alM

agno

Can

ell

Pipe

ra

exta

nt

Gun

neTr

ocho

Buxa

cP

rote

a

Sabi

ac

Ran

un

San

tal

Sax

ifra

Car

yo

rosi

ds

aste

rid

SK MagrAP3 MagnoliaMpMADS7

ltu016ms1e12, 0112ms3g02, 0116ms4a05SK_EubeAP3.1_EupomatiaSK_EubeAP3.2_EupomatiaSK AsloAP3 Asimina

eca015cs1g10, 0113cs3d12eca015cs3e07

SK_Pe.am.AP3_PerseaSK_Il.fl.AP31Jin1_Illicium

SK_Il.fl.AP32Jin3_IlliciumSK_Il.fl.AP33Jin2_Illicium

SK_Nu.va.AP3.1_Nuphar nad033cs2a08SK_Nu.va.AP3.2_Nuphar nad033ca2a08

SK AmtrAP3 2 AmborellaSK AmtrAP3 1 atr026ms2a12

silkyap3 pep37

25

24

26

2015

176

7331410

101

19

1148 14

2217

46

2215

41 2332

43 1619

42 4328

4739 46

DEF(AP3-like)

B class100

Phylogeny of the MADS-box genes ap3 pep

defa pepMpMADS12ggm2 pep

wmi01 9ms3 g01SK_Nu.ad.PI

SK_Nu.va.PI_NupharSK AmtrPI Amborella

SK_Il.fl.PI.Jin_Illiciumeca01 7ms1 d01

SK EubePI EupomatiaSK EulaPI Eupomatia

SK AsloPI AsiminaMpMADS8

pam018ms3h10, 0113ms3h04, 0112ms1b11, 019ms4b10glo peppi pep

osmads2 pepzmm18 pep

zmm17 pepaeap32 pep

118

50

4837 39 46

4251

61 2534

41

23

20

1017

27 32 614

3824

47

910

627 18

2314

38 4341

31 1929

43 29 6135 GGM13

GLO(PI-like)

B-class

8895

MADS box genes

aeap32 pepggm13 pep

ABS pepFBP24 pep

ap1 pepcal pep

squa pepagl8 pepSK EubeAP1MpMADS15

pam011ms3g02, 014ms1b11, 019ms3d08osmads15zap1 pep

atr0129ms1e07atr024ms2a10

SK NuadSQUA nad0320ms4a07ZMM27 Ze may

OsMADS8 Or satzmm6 pep

eca01 25ms1 b01lt 01 6 2 d07

5343 35

5354 71

61

35

3936

2421

33 7778

8281

6520 20

2530

94 1720

108 710

90

26

4723 6

1227

23 634

SQUA(AP1-like)

GGM1347

A-class98

95

56

Dltu01 6ms2 d07MpMADS13

agl9 pepatr02 12ms4 c09

SK AmtrAGL2 atr0123ms1h09, 027ms3b06MpMADS14

aam015ms3g09SK NuadAGL2 038cs2h04nad0330ms4a04agl4 pepagl2 pep

agl3 pepzmm3 pep

osmads1 pepMpMADS4

ltu0113ms4h04MpMADS3

agl13 pepagl6 pep

aam018ms3g07, 011ms4a11, 019ms3f05, 018ms3g04S G 6 022 4 02 029 1 01

110

3934

3228

1518

1221

23 4654

252858

2617

30 1616

7051 26

23

31

31

18 22 3

31

25 47 5430

2520

AGL2

AGL6

91

72

29

D-,E-class

g gSK AmtrAGL6 atr022ms4e02, 029ms1b01

SK NuadAGL6 nad0332msh09, 0332ms4d09osmads6 pep

zag3 pepggm11 pep

wmi014ms4e10ggm9 pep

CyAGggm3 pep

MpMADS11atr0213ms4b02

SK_Il.fl.AG_JinMpMADS2

SK atr0119ms1a12 AGeca0112ms1b11pam0112ms2d12

agl1 pepagl5 pep

ag pepnad0312ms2g12

70

45

31 11 2031

25 1321

36 28 3219

62

44

37

36

4026

416

40 2033

1825

11 2014

21

2644 9

746 15

1936 32

6339

AGL6

AG C-class

72

gagl11 pep

ZMM25 Ze mayzag1 pep

osmads3 peposmads13 pep

zmm1 pepOsmads26

MpMADS5agl12 pep

ggm10 pepZMM21 Ze may

bm1 pepAGL24

svp pepJOINTLESS

MpMADS1pam0111ms1g02

atr021ms4b09stmads11 pep

ggm12komplett pep1 1

29

49

38

44 39 3947

53 4525

49 2241

6251 26 44

3546

60

35

5945

3318

1125

31 32 5646

5822 37

3728

2051

5548

18

STMADS11

100

8866 gg p p p

agl151 bn pepagl152 bn pep

agl15 pepAGL18ZmMADS2CAD40993

AGL16agl17 pep

agl21 pepanr1 pep

AGL31At5g65060

MAF1 Ar thaFCL2 Ar thalflc1 Ar tha

flc peptm3 pep

soc1MpMADS9

MpMADS6

108

39 59

35

6561 24 18

2922

68

5532

23 36 2625

5129 35

2045

6220

11 1925

818

19 2624

35

3119

36 3214

23 2433

30

FLC

AGL17AGL15

RED: Homologs from

66100

100MpMADS6

At5g51870At5g51860

AGL42FDRMADS8

zmm5 pepAGL19agl14 pep

ggm1 pepwmi019ms3b07

tm8 pepERAF17MpMADS10

pam019ms3c05atr025ms3c01

wmi016ms1a12nad0314ms3a10, 0330ms4g02, 035cs4f08

ltu017ms1e07

50 changes

38

54

41

25 4043 30

4740

34 4538

38 2427

54 1521

6423

30 3534

25 3718

4454 54

5380

TM3

TM8Type I (outgroup)

RED: Homologs from basal angiosperms

79100




B

A C

yes.A

SepalA+BPetal

B+CStamen

CCarpel

C l 1. Where are ABC homologs expressed?

PetalStamen

Carpel

3. If expression implies function does the ABCfunction, does the ABC model hold for basal angiosperms?

Sepal

angiosperms?




B

A C


ASepal

A+BPetal

B+CStamen

CCarpel



Stamen

Carpel


Expression Studies Relative Quantitative RT-PCR Real-time PCR In situ Hybridization

Relative-quantitative-RT PCR Control: organs from Antirrhinum majusorgans from Antirrhinum majus

Whorl 1 2 3 4 n ol

B

A C

peta

lst

amen

carp

elea

f

root

-con

tro

sepa

l

Organs Sepal Petal Stamen Carpel

p s c l r -s

18SDEF(AP3)

18SGLO(PI)

Expression as expected from B-class genes of the ABC model.

• B-class genes expressed throughout all floral organs in Amborella

STAMEN1. 21.2

STAMENRQ RT-PCR

female

0 . 6

0 . 8

1

0.6

0.8

1

TEPAL0 . 2

0 . 4

0.2

0.4

male0

1 2 3 4 50

1 2 3 4 5

male

TEPALCARPELTE STST CA LEAF TE ST LEAFSD CASDSD

18S

PIAP3

B

A C

Whorl 1 2 3 4

STAMINODE

A C

Organs Sepal Petal Stamen Carpel female

• B-class genes expressed throughout all floral organs in Amborella

In situ hybridization

PIAP3

Amborella trichopoda (Amborellaceae)

• Broad expression of B-class genes

female

Tepals Stamens Carpels Leaves

B-classAm.tr.GLO +++ +++ +++ +Am tr DEF 1 +++ +++ ++

1st 2nd 3rd 4th

Am.tr.DEF.1 +++ +++ ++ -Am.tr.DEF.2 +++ +++ - -

C-classAm.tr.AG - +++ +++ -

E-class

BB

E-classAm.tr.AGL2 +++ +++ +++ -

BA C

E

BA C

E

N h d (N h )

• A-class gene expression in carpels and leaves rather than perianth

Nuphar advena (Nympheaceae)

Tepals Stamens Carpels Leaves

A-classNu.ad.SQUA - - - +++ +++

1st 2nd 3rd 4th

B-classNu.ad.GLO +++ +++ +++ +++ -Nu.ad.DEF +++ +++ +++ +++ -

C-classNu ad AG - - +++ +++ -

B

Nu.ad.AG - - +++ +++ -

E-classNu.ad.AGL2 +++ +++ +++ +++ -

BBA C

E

BA C

E

Molecular studies in Arabidopsis and AntirrhinumMolecular studies in Arabidopsis and Antirrhinumdemonstrate that function of floral MADS-box genes is highly correlated with expressiongenes is highly correlated with expression patterns (Ma and dePamphilis, 2000).

Possible A-function gene in basal angiosperms:

AGL6-like gene?showed tepal specific expression

epal

s

tam

ens

Car

pels

eeds

eave

s

cont

rol

path

aceo

usra

cts

- showed tepal-specific expression

18SMa.gr.AGL6

T S C S L e -S br

Outer tepal Inner tepal Stamen Carpel LeavesOuter tepal Inner tepal Stamen Carpel LeavesMa.gr.AGL6 (Magnolia) +++ +++ - - -Li.tu.AGL6 (Liriodendron) +++ +++ - + -Pe.am.AGL6 (Persea) +++ +++ - + -Am tr AGL6 (Amborella) +++ +++ ++ ++Am.tr.AGL6 (Amborella) +++ +++ ++ ++ -

BC

E

DB? C

E

D

Antirrhinum m AmSEP3bAmSEP3B100Antirrhinum m DEFH200AmSEP3A9562DEFH72AmSEP3C81Antirrhinum m DEFH7293

100

Syringa v SvSEP3SvSEP310091

Petunia h FBP2PhSEP386Lycopersicon e LeMADS5LeSEP38455

Nicotiana s NsMADS378

TDR599

92

Chrysanthemum m CDM44

63

Populus t PTM6Betula p MADS148Vitis v VvMADS4

124

Pisum s MTF1MTF1100Gossypium h GhMADS1

3224

Arabidopsis t AGL9SEP3100Sinapis a SaMADSd

10043

Silene l SlSEP346

Chrysanthemum m CDM77Helianthus a HAM13796Gerbera h GRCD1

10049

Ma.gr.AGL2.1Magnolia p MpMADS13100Chl th C SEP3

542740

DNA MIKCML t Magnolia p MpMADS13Chloranthus s CsSEP3Eu.be.AGL2Ltu01 06ms2 d0710027

Pe.am.AGL2.2Pe.am.AGL2.110062

Eca01 25ms1 b11PapnSEP394Akebia t AktSEP3 1

7639

Houttuynia c HcSEP160

40

Lolium p LpMADS8Triticum a TaMADS70Dendrocalamus l MADS5

62Oryza s OsMADS8OsMADS810040

Zea m M27100

Hordeum v HvAGL9Lolium p LpMADS5100Zea m M6

56Oryza s OsMADS7

100100

Asparagus o AOM4Asparagus o AOM110020

Lilium l LMADS3Aranda d OM145

13

TvSEP323

Dendrobium g OTG741

44

Malus d MdMADS1Malus d MdMADS9100Fragaria a RIN

97Cucumis s CAGL2CAGL210030

Vitis v MADS2VvMADS2100Heuchera a HeaSEP1HeaSEP110072

18

Arabidopsis t AGL2SEP1100Brassica o SEP1a

100Arabidopsis t AGL4SEP2100100

Populus t MAGL440

67

Silene l SlSEP1

60

Lycopersicon e TM29LeSEP1100Petunia h PMADS12

91Petunia h FBP5100100

5279

1

67

AG

L2

ML tree326 genesPHYML program

96Petunia h FBP5PhSEP1100Antirrhinum m DEFH49

52SvSEP1

64Gerbera hybrida GRCD2

80Eca01 05cs3 b03

1

Capsicum a MADS1Lycopersicon e LeMADS1100Petunia h FBP23

100Petunia h FBP9Nicotiana t NtMADS4100100

Malus d MADS7MdMADS3100Malus d MADS6

100Eucalyptus g EGM3EGM310096

90

Lycopersicon e MADS RINPetunia h FBP488Capsicum a PepMADS

100Brassica o AGL3aArabidopsis t AGL310068

Dianthus c CMB113

Daucus c MADS547

14

Pachysandra t PatSEP1PatSEP1100Malus d MdMADS4

16

14

34

Houttuynia c HcSEP3Houttuynia c HcSEP2100Ma.gr.AGL2.2

41Nad03 08cs2 h04Am.tr.AGL2.141

Am.tr.AGL2.265

5

Ac.am.AGL239

10

Dendrobium g DOMADS3

32

Chasmanthium latifolium LHS1Danthonia spicata LHS125Aristida longiseta LHS1

14Eleusine coracana LHS1

35Panicum miliaceum LHS1Setaria italica LHS173

Pennisetum glaucum LHS198

47

Sorghum bicolor LHS1Zea m ZMM14100Zea m ZMM8

9072

Lithachne humilis LHS1Dendrocalamus l MADS139649

17

96

A 96

90 AG

L2 E-classDendrocalamus l MADS13Leersia virginica LHS1Oryza s OsMADS1100

Ehrharta erecta LHS1100

Hordeum v BM7Avena sativa LHS197Lolium p LpMADS9

98100

Dendrocalamus l MADS16Zea m ZMM342Lolium p LpMADS6

56Oryza s OsMADS5

100

100

Zea m M31Zea m M24100Oryza s RMADS217

62Triticum a AGLG1Lolium p LpMADS7100100

63

Lilium l LMADS4

75

L6.Li.tu.AGL6.ltu0113ms4h04L6.MpMADS4.Magnolia.AB050646100L6.MfAGL6B.Michelia.AY306158

100L6.Il.pa.AGL6.IlliciumL6.Pe.am.AGL6.2.Persea2562

L6.Ma.gr.AGL6.MagnoliaL6.MfAGL6A.Michelia.AY306157100L6.MpMADS3.Magnolia.AB050645100

57

L6.Pe.am.AGL6.1.Persea65

L6.Es.ca.AGL6.EschscholziaL6.RbAGL6.Ranunculus.AY3061846636

L6.HcAGL6.Houttuynia.AB08916036

L6.Am.tr.AGL6.Amborella27

L6.Nu.ad.AGL6.Nuphar32

L6.HoAGL6.Hyacinthus.AY591333L6.AOM3.Asparagus.AY38355951L6.ApMADS3.Agapanthus.AB079261

99L6.NADS2.Musa.AY941799

9822

L6.Ac.am.AGL6.Acorus50

L6.VvMADS3.Vitis.AF373602Poptr.AGL6.Populus62L6.Ri.sa.AGL6.Ribes

66L6.MdMADS11.Malus.AJ000763

62L6.SvAGL6.Syringa.AY306188L6.pMADS4.Petunia.AB0310357433

L6.grcd3.Gerbera.AJ784157L6.CDM104.Chrysan.AY17306210027

L6 BoAGL6a Brassica AJ508055L6 B AGL6b B i AJ50840910010043

76

53

90

L6

99

AG

L6

L6.BoAGL6a.Brassica.AJ508055L6.BoAGL6b.Brassica.AJ508409100L6.AGL6.Arabidopsis.M55554

100L6.AGL13.Arabidopsis.U20183

100L6.Cu.sa.AGL6.Cucumis.csa013msL6.PaMADS1.Poa.AF372840L6.LpMADS4.Lolium.AY19832978

L6.HvAGL6.Hordeum.AY541067L6.TaMADS12.Triticum.AB007505100100L6.MADS18.Dendro.AY599755

98L6.ZAG3.Zea.L46397L6.ZAG5.Zea.L46398100

48

L6.OsMADS6.Oryza.U7878299

L6.TaeMADS12.Triticum.AJ57737576

L6.OsMADS17.Oryza.AF109153L6.nmads3.Oryza.AF095646100100

93

L6.PrMADS1.Pinus.Y09611PrMADS1100L6.PrMADS2.Pinus.U42400PradMADS2100100

L6.We.mi.AGL6.Welwitschia59

L6.GbMADS8.Ginkgo.AB02947065

L6.GGM11.Gnetum.AJ132217GGM1110072

L6.PrMADS3.Pinus.U76726PrADMADS3100L6.DAL1.Picea.X80902DAL1100100

L6.GbMADS1.Ginkgo.AB029463100

L6.GpMADS3.Gnetum.AB022665GpMADS398L6.GGM9.Gnetum.AJ132215100

82

100

99

FBP26PhFUL100CaMADS6LeFUL24766

NsMADS1NAP1.110097

SCM1POTM1.153LeFUL1

100PFG

8947

AmFUL67

TDR490

SLM5PaFUL91

49

5012

AG

L

98

100 SQU

A

A-classPaFULMdMADS2BpMADS550

HeaFULCsFUL5763

PisFUL42

EAP1AP2L8114

12

PhFLCcFL100HeaFL

100BpMADS4

57PaFL2PaFL110087

RbFL3PapnFL2100RbFL4

100PapsFL2PapnFL1100

CmFL291

9152

PapsFL1CmFL19920

PatFL2PatFL17621

RbFL2RbFL1100RaFL1

10029

7

NsMADS2NAP1.2100NtMADS5

100LeMADS MCLeAP1100100

SQUA SvAP199PeaM4.f

198

PsMDS2CsAP177HeaAP1

92PtMADSBpMADS33925MdMADS5

20

41

DcMADS1

54

SaMADSCBoAP137AP1

100BrCAL100100

48

47

6

26

100

QU

A

100 STM

3

BrCALBoCAL100CAL

100AsAP1 WgAsAP1 As100

HaM75100

GSQUA175

47

SLM4PaAP198

71

DEFH2820

SaMADSBFUL100Ma.gr.SQUAMfFL63

MpMADS15100

Eu.be.SQUA100

Pe.am.SQUA92

Nu.ad.SQUA13

PcFL2PcFL13120

18

ZmMADS3ZAP1100LtMADS2HvMADS810070

OsMADS15100

SbMADS281

TaMADS11HvMADS5100LtMADS1

100OsMADS14

100100

TvFL2TvFL195TvFL3

100DoMADS2

6026

OsMADS28OsMADS18100HvMADS3

100TvFL4

61

25

6

AlFL

25

AtFL

98

TM3.0.1714.FBP27.PetuniaTM3.0.1714.TOBMADS1.Nicotiana64TM3.0.1714.FBP20.Petunia

99TM3.0.1714.TDR3.Lycoper

96TM3 0 1615 PTM5 PopulTM3 0 1615 P t AGL20 P l10026

2589

SQ

T

0.1

TM3.0.1615.PTM5.PopulTM3.0.1615.Poptr.AGL20.Popul100TM3.0.1721.MADS1.Pimpinella

26TM3.0.1713.DEFH68.Antirrhinum

89

TM3.0.1103.MpMADS9.MagnoliaTM3.0.1103.MpMADS6.Magnolia9748

TM3.0.1621.CfAGL20.CardamineTM3.0.1621.AGL20.Arabidop99TM3.0.1621.SaMADSA.Sinapis

10067

TM3.0.1621.AGL19.ArabidopTM3.0.1621.AGL14.Arabidop100TM3.0.1615.Poptr.AGL19.PopulTM3.0.1615.Poptr.AGL14.Popul10072

42

TM3.0.1303.RAGL20.OryzaTM3.0.1303.FDRMADS8.Oryza100

TM3.0.1603.ETL.Eucalyptus43

14

TM3.0.1621.AGL72.ArabidopTM3.0.1621.AGL71.Arabidop100TM3.0.1621.AGL42.Arabidop

7091

TM3.0.0000.PrMADS6.PinusTM3.0.0000.PrMADS8.Pinus91TM3.0.0000.PrMADS7.Pinus

63TM3.0.0000.PrMADS4.Pinus

96TM3.0.0000.DAL3.Picea



100TM3.0.0000.We.mi.TM3.WelwitscTM3.0.0000.GGM1.Gnetum

10089 TM3

Kim et al., in prep.

Questions in basal angiosperms1. Are homologs of ABC

genes found in basalB genes found in basal angiosperms?

B

A C

2 Where are ABC homologsASepal

A+BPetal

B+CStamen

CCarpel

C l


PetalStamen

CarpelBroader “B” expressionDifferent “A” expression

3. If expression implies function does the ABC

Sepalfunction, does the ABC model hold for basal angiosperms?angiosperms?




B

A C


ASepal

A+BPetal

B+CStamen

CCarpel



Stamen

Carpel


Questions in basal angiosperms1. Are homologs of ABC

genes found in basalB genes found in basal angiosperms?

B

A C

2 Where are ABC homologsASepal

A+BPetal

B+CStamen

CCarpel

C l


PetalStamen

Carpel3. If expression implies

function does the ABCfunction, does the ABC model hold for basal angiosperms?

Sepalangiosperms? Not entirely.

• Address evolutionary origin of novel organ

Eupomatia bennettii (Eupomatiaceae)

Calyptra

Perianth? Bract ?

Kim, Sangtae et al. (2005)

Sequence and expression studies of A-, B-, and E-class MADS-box genes in Eupomatiag p(Eupomatiaceae): support for the bracteate origin of the calyptra.calyptra.

International Journal of Plant Sciences (2005) 166: 185-198Sciences (2005) 166: 185-198.

Journal Cover

B class gene expression in EupomatiaB-class gene expression in Eupomatia

B

A C

Evolutionary origin of calyptra:

B+CStamen

CCarpelPerianth

Staminode

Calyptra

?

Carpel

Calyptra

pStaminode

BractStamen

Bract

AsAP1AsAP1

HaM75GSQUA1

DcMADS1SvAP1SQUA

BoAP1SaMADSCAP1 1

A-classBA C

DE

Taxa Gene Name Sepals Petals Stamens Carpels Other(Tepals)

1st 2nd 3rd 4th

euAP1 genes

AP1BoCAL

BrCALCALPeaM4

NAP1.2NsMADS2

NtMADS5LeAP1

LeMADSPaAP1

SLM4CsAP1HeaAP1PsMDS2BpMADS3

MdMADS5PtMADSf

AtFL

euA

P1E

1st 2nd 3rd 4th OV

Arabidopsis AP1 +++ +++ - -Arabidopsis CAL + + - -Antirrhinum SQUA +++ +++ - + BractPisum PEAM4 +++ +++ - -Silene SLM4 +++ +++ - - Infl., Bract

PaFL1PaFL2DEFH28

CcFLPhFL

HeaFLBpMADS4PapnFL1

PapsFL2CmFL2

PapnFL2RbFL3RbFL4

RbFL1RbFL2RaFL1

PatFL2PatFL1

CmFL1 Eudi

cots

euFUL genesArabidopsis FUL - - - +++ Inf.Antirrhinum DEFH28 - - - +++ Inf., BractSilene SLM5 ++ ++ - +++ Inf., Bract

Monocots

CmFL1PapsFL1

LeFUL2CaMADS6

PhFULFBP26

NAP1.1NsMADS1

LeFUL1TDR4

POTM1.1SCM1

PFGFULSaMADSB

PisFULPaFULSLM5

AmFULCsFUL

H FUL

euFU

LMonocotsOryza RAP1a Lemma, palea - - lodiculesLolium LtMADS1 Glume, lemma ++ ++ Veg. meri.Lolium LtMADS2 Glume, lemma - - Veg. meri.

Basal angiosperm genes

Cs UHeaFULAP2L

BpMADS5EAP1

MdMADS2MfFL

MpMADS15Ma.gr.SQUAEu.be.SQUAPe.am.SQUA

PcFL1PcFL2

HvMADS8LtMADS2OsMADS15

SbMADS2ZmMADS3ZAP1

HvMADS5T MADS11 gi

ospe

rms

cots

Persea Pe.am.SQUA +++ ++ - Leaves +++Eupomatia Eu.be.SQUA + +++ Leaves +++Magnolia Ma.gr.SQUA + ++ ++ Leaves +++ Nuphar Nu.ad.SQUA - - +++ Leaves +++

TaMADS11LtMADS1OsMADS14

TvFL1TvFL2

TvFL3DoMADS2

AlFLOsMADS18OsMADS28

HvMADS3TvFL4Nu.ad.SQUA

AmSEP3CDEFH72AmSEP3B

AmSEP3ASvSEP3

LeSEP3PhSEP3

Bas

al a

ng

Mon

o

AGL2 and AGL6(outgroup)

PhSEP3TDR5

MTF1SEP3

PapnSEP3TvSEP3

OsMADS8LeSEP1PhSEP1

SvSEP1HeaSEP1

SEP1SEP2

CAGL2VvMADS2

EGM3MdMADS3

PatSEP1DAL1

P ADMADS3 (outgroup)PrADMADS3GpMADS3

GGM11PradMADS2PrMADS1

AGL6SvAGL6

RbAGL6MpMADS4

MfAGL6BMfAGL6A

10 changes

T G N S l P t l St C l Oth

B-class (DEF-lineage)32.LeAP3.Lycopersicon

32.STDEF.Solanum32.NTDEF.Nicotiana

32.PMADS1.Petunia32 SvAP3 Syringia 3

BA C

DE Taxa Gene Name Sepals Petals Stamens Carpels Other

(Tepals)1st 2nd 3rd 4th

Core eudicots: EuAP3 genesArabidopsis AP3 - +++ +++ -

32.SvAP3.Syringia32.DEF.1.Antirrhinum

31.RsAP3.1.Ribes31.RsAP3.2.Ribes31.NMH7.Medicago

32.HmAP3.Hydrangea31.AP3.Arabidopsis

31.BobAP3.Brassica31.Boi1AP3.Brassica31.Boi2AP3.Brassica

32.HPDEF1.Hieracium32.HPDEF2.Hieracium

32 GDEF2 G b

euA

P3E

1st 2nd 3rd 4th OV

pAntirrhinum DEF - +++ +++ -Petunia PMADS1 - +++ +++ -Nicotiana NTDEF - +++ +++ -Silene SLM3 - +++ +++ -Gerbera GDEF2 - +++ +++ - leaves, bracts

32.GDEF2.Gerbera30.RAD1.Rumex

30.RAD2.Rumex30.SLM3.Silene

31.JrAP3.Juglans32.DcMADS3.Daucus

32.TM6.Lycopersicon32.PhTM6.Petunia

32.HmTM6.Hydrangea32.GDEF1.Gerbera

31.MdTM6.Malus31.MdMADS13.Malus TM

3

Eudi

cots

Core eudicots: TM6 genesLycopersicon TM6 - +++ +++ +++Polulus PTD - +++ +++ -Gerbera GDEF1 - + + -Dianthus CMB2 - +++ - -

31.MASAKO.B3.Rosa30.CMB2.Dianthus

31.PTD.Populus30.GtAP3.3.Gunnera30.GtAP3.5.Gunnera

30.GtAP3.2.Gunnera30.GtAP3.1.Gunnera30.GtAP3.4.Gunnera

03.PhAP3.Peperomia20.PcAP3.Papaver

20.PnAP3.1.Papaver20.RbAP3.1.Ranunculus

T

Basal eudicotsDicentra DeAP3 - - +++ -Papaver PnAP3-2 - - +++ -

Monocots

20.RfAP3.1.Ranunculus20.RbAP3.2.Ranunculus

20.RfAP3.2.Ranunculus20.PnAP3.2.Papaver

20.ScAP3.Sanguinaria20.DeAP3.Dicentra

20.PtAP3.1.Pachysandra20.PtAP3.2.Pachysandra

02.MpMADS7.Magnolia02.MfAP3.Michelia

MgAP3.Magnolia02 LtAP3 Liriodendron s

Zea SILKY Lodicules +++ -Oryza OsMADS16 Lodicules +++ -

Basal angiospermsPersea Pe.am.DEF +++ + -Magnolia Ma gr DEF +++ +++

02.LtAP3.LiriodendronAlAP3.Asimina

EbAP3.1.EupomatiaEbAP3.2.Eupomatia

01.CfAP3.2.CalycanthusPaAP3.Persea

01.CfAP3.1.Calycanthus11.OSMADS16.Oryza11.SILKY1.Zea11.TaMADS51.Triticum

10.LRDEF.Lilium10.LMADS1.Lilium

10 SmAP3 Sagittaria angi

ospe

rms

Mon

ocot

s

Magnolia Ma.gr.DEF +++ +++ -Eupomatia Eu.be.DEF +++ +++Asimina As.lo.DEF - +++ +++ -Illicium Il.fl.DEF.1 - +++ +++ -Illicium Il.fl.DEF.2 + +++ ++ -Illicium Il.fl.DEF.3 - +++ - -

10.SmAP3.Sagittaria10.HhMADS1.Hemerocallis10.TcAP3.Tacca

00.CsAP3.Chloranthus03.AeAP3.1.Asarum

Nu.ad.DEF_nad03_19m_e2400.NvAP3.2.Nuphar

00.NvAP3.1.Nuphar00 AtAP3 Amborella

00.IlAP3.IlliciumIl.fl.AP3-1----Jin1

Il.fl.AP3-2----Jin3Il.fl.AP3-3----Jin2

Bas

al a M

Nuphar Nu.ad.DEF +++ +++ +++Amborella Am.tr.AP3-1 +++ +++ ++Amborella Am.tr.AP3-2 +++ +++ +++

00.AtAP3.AmborellaAm.tr.AP3-2

00.NvPI.NupharNu.ad.GLO.2_nad03_27m_o16

00.NaPI.NupharNu.ad.GLO.1_nad03_30ms2_a10

Il.fl.PI.Jin00.AtPI.Amborella

10 changes

GLO-like(outgroup)

ots

31.RsPI.Ribes31.CUM26Cucumis

31.MdPI.Malus31.MASAKO.BP.Rosa

32.HmPI.Hydrangea32.SvPI.Syringia ot

s

B-class (GLO-lineage)BA C

DE

Taxa Gene Name Sepals Petals Stamens Carpels Other(Tepals)

1st 2nd 3rd 4th

Core eudicotsCor

e eu

dico32.GLO.Antirrhinum

32.NTGLO.Nicotiana32.FBP1.Petunia

32.PMADS2.Petunia31.EGM2.Eucalyptus

31.PI.Arabidopsis30.SLM2.Silene

03.PhPI.Peperomia03.PmPI.1.Piper

Eudi

coE

1st 2nd 3rd 4th OV

Arabidopsis PI - +++ +++ -Antirrhinum GLO - +++ +++ -Petunia FBP1 - +++ +++ -Gerbera GGLO1 - +++ +++ -Nicotiana NTGLO - +++ +++ -Silene SLM2 - +++ +++ -oc

ots

p03.PmPI.2.Piper

32.GGLO1.Gerbera11.OSMADS2.Oryza

11.nmads1.Oryza11.ZMM16.Zea

11.ZMM18.Zea11.ZMM29.Zea

11.OSMADS4.Oryza10.LRGLOA.Lilium Silene SLM2 - +++ +++ -

Basal eudicotsDicentra DePI - - +++ -Papaver PnPI-1 - - +++ -

Mon

ots

10.LRGLOA.Lilium10.LRGLOB.Lilium

10.TcPI.Tacca10.OrcPI.Orchis10.HPI1.Hyacinthus10.HPI2.Hyacinthus10.SmPI.Sagittaria

20.CpPI.Caltha20.RbPI.1.Ranunculus20 RfPI 1 Ranunculus Monocots

Oryza OsMADS2 Lodicules +++ -

Basal angiospermsPersea Pe.am.GLO.1 +++ +++ +Persea Pe.am.GLO.2 +++ +++ -s

Eudi

co20.RfPI.1.Ranunculus20.RbPI.2.Ranunculus20.RfPI.2.Ranunculus

20.DaPI.Delphinium20.PnPI.1.Papaver

20.PnPI.2.Papaver20.ScPI.Sanguinaria

20.DePI.DicentraEbPI.Eupomatia02 ElPI E ti

Magnolia Ma.gr.GLO +++ +++ -Eupomatia Eu.be.GLO +++ ++Asimina As.lo.GLO - +++ +++ -Illicium Il.fl.GLO ++ +++ ++ -Nuphar Nu.ad.GLO +++ +++ +++Amborella Am tr GLO +++ +++ +++an

gios

perm

s02.ElPI.EupomatiaAlPI.Asimina

MpMADS8.Magnolia02.MfPI.Michelia

02.LtPI.Liriodendron03.AePI.Asarum

00.CsPI.Chloranthus01.CfPI.1.Calycanthus

PaPI.PerseaCf C Amborella Am.tr.GLO +++ +++ +++

Bas

al a01.CfPI.2.Calycanthus

Il.fl.PI.Jin00.NvPI.Nuphar

00.NaPI.NupharNu.ad.GLO.1_nad03_30ms2_a10Nu.ad.GLO.2_nad03_27m_o16

00.AtPI.Amborella00.AtAP3.Amborella

Am.tr.AP3-2

DEF-like(outgroup)

Nu.ad.DEF_nad03_19m_e2400.NvAP3.1.Nuphar

00.IlAP3.IlliciumIl.fl.AP3-1----Jin1

Il.fl.AP3-2----Jin3Il.fl.AP3-3----Jin2

10 changes

HAM45CDM37

GAGA1GAGA2

SLM1PhaAG1

RAP1TAG1

NAG1pMADS3Farinelli

GAG2 G

C-classBA C

DE Taxa Gene Name Sepals Petals Stamens Carpels

1st 2nd 3rd 4th

euAG genesArabidopsis AG +++ +++

DcMADS4AG

SxcAG1CaMADS1

BpMADS6JrAG

STAGMASAKOC1

MdMADS15PTAG1PTAG2

AY083173CAG2

euAGE

1st 2nd 3rd 4th OV

Arabidopsis AG - - +++ +++Antirrhinum FAR - - +++ +++Nicotiana NAG1 - - +++ +++Petunia PMADS3 - - +++ +++

PLE genes

CAG3AGL1

BnSHP1AGL5

LAGVvMADS1

FBP6NTPLE36

PLEMASAKOD1

MdMADS14HoAG1a

HoAG1bRfAG1

PLE

Antirrhinum PLE - - +++ +++Arabidopsis SHP1 - - - +++Arabidopsis SHP2 - - - +++Petunia FBP6 - - +++ +++

Basal eudicots

RfAG1AqaAG1

ThdAG1CiAG1

AqaAG2ThdAG2

RfAG2CiAG2

EST_Es.ca.AGScAG

BgAGAkqAG

MdAG1ZMM2 ot

s

eudi

cots

neag

e

Basal eudicotsEschscholzia Es.ca.AG

Monocot genesZea AGL1 - - +++ +++Oryza OSMADS3 - - +++ +++

ZMM2ZMM23

OSMADS3AHvAG2WAG

ZAG1HvAG1

PeMADS1HAG1

aam0118ms1e03 AGNymAG2

SK_Nu.ad.AGNymAG1

HtcAG

mon

oco

rms

C-li

Basal angiospermsMagnolia Ma.gr.AG.1 - +++ +++Persea Pe.am.AG ++ ++ +++Illicium Il.f..AG - +++ +++ +Nuphar Nu.ad.AG - +++ +++

HtcAGSK_Pe.am.1AG

EST_Pe.am.2AGSK_Il.fl.AG_Jin

MpMADS2SrhAGCsAG1

SK_Am.tr.AGMcAGCAG1

GHMADS2AGL11

MdMADS10FBP11 ag

e

asal

ang

iosp

e

pAmborella Am.tr.AG.1 - +++ +++

FBP11TAG11

FBP7PhaAG2

VvMADS5SxcAG2

ZAG2ZMM1

OsMADS13Kr4_P0408G07.14ZMM25

CsAG2ApMADS2

MdAG2

D-li

neaBa

MpMADS11NymAG3

atr0213ms4b02 AGSAG1DAL2AF023615

GGM3CyAG

GBM5

10 changes

Gymnosperms(outgroup)

SlSEP1Fragaria

MdMADS9MdMADS8

CAGL2MAGL4AGL2/SEP2

SEP1aAGL4/SEP4

MADS2TAGL2TM29

BA C

DE TM29

FBP5PMADS12

DEFH49LeMADS1MADS1

FBP23NtMADS4

FBP9MdMADS3MADS7

MADS6EGM3

Eca01 05cs3 b03MADS RIN

PepMADSE-class

E

1st 2nd 3rd 4th OV

Taxa Gene Name Sepals Petals Stamens Carpels Leaves(Tepals)

1st 2nd 3rd 4th

PepMADSFBP4

MADS5AGL3AGL3a

MdMADS4PatSEP1

HcSEP3HcSEP2

Ma.gr.AGL2.2Am.tr.AGL2

Nad03 08cs2 h04ZMM14

ZMM8MADS1

L MADS9

inea

ge

1 2 3 4

SEP1,2 lineageArabidopsis SEP2 - +++ +++ +++ -Arabidopsis SEP3 - +++ +++ +++ -Magnolia Ma.gr.AGL2.2 +++ +++ +++ ++

LpMADS9BM7

MADS13Dendrocalamus l MADS16

LpMADS6OsMADS5

ZMM3LMADS4

BAA81882RMADS217

LpMADS7AGLG1

ZmM24ZmM31

DOMADS3

SE

P1,

2 l

Nuphar Nu.ad.AGL2 +++ +++ +++ -Amborella Am.tr.AGL2 +++ +++ +++ -

SEP3 lineage Arabidopsis SEP1 - +++ +++ +++Magnolia Ma gr AGL2 1 +++ +++ +++

DEFH72AmSEP3b

DEFH200SvSEP3

CDM44NsMADS3FBP2LeMADS5

SaMADSdAGL9/SEP3

MTF1GhMADS1

PTM6MADS1

VvMADS4 age

Magnolia Ma.gr.AGL2.1 - +++ +++ +++ -Eupomatia Eu.be.AGL2 +++ +++ -

VvMADS4HAM137

GRCD1CDM77

Eca01 25ms1 b11MpMADS13Ma.gr.AGL2.1

Ltu01 06ms2 d07Eu.be.AGL2Pe.am.AGL2.1

Pe.am.AGL2.2OsMADS7FDRMADS1

OsMADS45LpMADS5

BM9

SE

P3

linea

BM9ZmM6

DMADS5TaMADS

OsMADS8ZmM27

AOM1DOM1

LMADS3AdOM1

CsSEP3HcHcSEP1

nes

AG

L6-li

ke g

en(o

utgr

oup)

r

m a na olia

ncul

us

core eudicots

eudicots

aria

m

magnoliids

dops

is

hinu

m

a rarella r

monocots

agus

Nup

har

Illic

ium

Per

sea

Asi

min

Mag

no

Ran

un

Sag

itta

Tulip

a

Ory

za

Zea

Asa

rum

Sile

ne

Ara

bid

Ant

irrh

Pet

unia

Ger

ber

Am

bor

Nup

har

PI

AP1

Asp

ara

AP3

AG

• Evolution of gene expression patterns of floral• Evolution of gene expression patterns of floral MADS-box genes in angiosperms.

Color-filled floral part: strongly expressedAP1 A p g y pEmpty floral part: not expressed/weakly expressedDashed organs: equivocal or uncertainAP3

PI

AG

B

C

ConclusionsCo c us o s

In basal angiospermsIn basal angiosperms,• A-class genes are primarily expressed in carpels and

vegetative organs rather than perianth.g g ppossible A-class candidate is AGL6.

• B-class genes are more broadly expressed than in eudicots

Thi b d tt f i i “ t l”This broader pattern of expression is “ancestral”; the localized patterns in Arabidopsis and other eudicots is derivedeudicots is derived

III. BIII. B--class gene proteinclass gene protein--protein protein i t ti ii t ti i A b llA b llinteractions in interactions in AmborellaAmborella

Extended ABC model: ABCDE model (Theissen, 2001)

BBB

A CD

B

CD

A

EE

A+ES l

A+B+EP t l

B+C+ESt

C+EC l

D+EO lSepal Petal Stamen Carpel

Carpel

Ovule

PetalStamen

S lSepalOvule

The ‘quartet model” of floral organ specification in Arabidopsis (modified from Theissen, 2001)

B

A C

AP3, PI

AP1 AP2 AGA C

E

D

AP1, AP2 AG

SEP1/SEP2/SEP3/SEP4

STK/SHP1/SHP2Stamens

AP3 PI

Petals

AP3 PI

AG SEP

AP1 SEPCarpels

SEP AG

SepalsAG SEP

AP1 SEP

SEP AP1Ovules

SEP STK

SEP SHP

Major evolutionary lineages of B-class genes and the evolution of their protein interactions

Angiosperms Gymnosperms

Arabidopsis Antirrhinum Lilium Gnetum

AP3-like genesPI likPI-like genesGGM2-like genes

Modified from Winter et al., 2002; Kaufmann 2005

Conserved aa residues in angiosperm PI- and AP3-homologues in K-domain except Amborella

PI PI

9798

102

AP3-2PI

PI AP3-1

…PI.Arabidopsis EIDRIKKENDSLQLELRHLLtPI.Liriodendron EVERIKKENDSMQIKLRHLCsPI.Chloranthus ELDRIKKENDSMQIELRHL

2ENENENgu

es

AP3-1 AP3-1

AP3-1 PI

CfPI.1.Calycanthus EVERIKKENDSMQIKLRHLPe.am.PI.Persea EVERIKKENDSMLIKLRHLIl.pa.PI.Illicium EVDRVRKENESMQIELKHLNu.ad.PI.Nuphar ELDRIRKENENMQIELRHF

ENENENEN-h

omol

og

AP3-2AP3-1

AP3-1 AP3-1

p QNu.ve.PI.Nuphar ELDRIRKENENMQIELRHFAm.tr.PI.Amborella EVDRMKKDNEQMRIELRHL

Am.tr.AP3-1.Amborella DLGNLKEESNRLRKLIRQK

ENN

E

N R

R

PI-

AP3-2 AP3-1

AP3-2 PI

Am.tr.AP3 1.Amborella DLGNLKEESNRLRKLIRQKAm.tr.AP3-2.Amborella ELSSLKEENNRLQKLIRQKNu.ve.AP3.1.Nuphar EFNKLKEKNERLRRSIRQRNu.ve.AP3.2.Nuphar EFNKLKEKNERLRKSIRQRIl.pa.AP3.Illicium ELNKLKEENNKLR-KIRQR

ENNN RN RN Rlo

gues AP3-2AP3-2

Il.pa.AP3.Illicium ELNKLKEENNKLR KIRQRCsAP3.Chloranthus YFEKLKETNNKLRKEIRQRCfAP3.1.Calycanthus HLSKLTEDNNRLRREIRQRPe.am.AP3.Persea HLNKLKDDNNKLRREIRQREbAP3 1 Eupomatia HLNKLKEDNNNLRREIRQR

N RN RN RN RN RP

3-ho

mo

EbAP3.1.Eupomatia HLNKLKEDNNNLRREIRQRAP3.Arabidopsis TKRKLLETNRNLRTQIKQR…

N RN RA

P

GGM2.Gnetum ELIKERRENEKLRSKLRYMGymnosperm

Similar C-domain sequences between Amborella AP3 and PIY X

AP3 PI

YX

K-domain C-domain

exon 5 exon 6 exon 7exon 4PI.Arabidopsis ...HQMEILI----SKRRNEKMMAEEQRQLTFQL--QQQEMAIASNA-RGMMMR--DH-------DG--Q-----------------FGYRV-QPI----QPN-L-QE...

PI/PI derived motif

Y XYXgu

es

pFBP1.Petunia ...KQNEVLR----MMRKKTQSMEEEQDQLNCQL-RV-LEIATM--N-RNMGEIGEVFQQRENH-DY--Q---NHM----------PFAFRV-QPM----QPN-L-QE...GLO.Antirrhinum ...KQMEFVR----MMRKHNEMVEEENQSLQFKL-RQMHLDP-MNDN-VMESQAVYDHHHHQNIADYEAQ-----M----------PFAFRV-QPM----QPN-L-QE...MASAKO.BP.Rosa ...RMSKYMD----AVRENNRALEDENKRLAYQL-HK-MMKSE-E-NLRDM--------------NYNNNT---QI----------PFALRV-QPN----QPN-L-HD...SLM2.Silene ...KQMEMYK----LHKKNHKMLEDENNQLAYMLHKQ--EMDG---NMREMEAGVCSNPSD--RRDYHYQ---NPI---------PPYGFRV-QPM----QPN-L-QD...CpPI.Caltha ...KQMEIYR----MMKRNDRKLEEDNKRLVLKLQHQQ--QLM-NGNGRE-----YP----S------------QM---------PPFTFQL-HPS----QPN-L-QE...OrcPI.Orchis ...KQMDFLK----MLKKNERMLEEENKRLKYLLQHQQ--LAI-EGSMRELE-ISYHQK-DP---EY-AD----QM----------PMTFRV-QPF----QPN-L-HG...SmPI.Sagittaria ...KQMEIFK----KKAKNQKALEEENKQLAYIL-HQQ-SLAM-NGNLREMP-QDYHQK-D--RRDF-TA----PV----------PFGFRV-QPM----QPN-L-QE...

PI-h

omol

og

gAePI.Asarum ...KQAELLK----TLKKNGRALEDENKRLAYILHHQQ--IAM-DENKREMD-NGYHKREE-----Y-PS----QM----------PFAFCV-QPM----QPN-L-HQ...MfPI.Michelia ...RQMQCLK----MLKKNERSLEEENKRLSYILQHQQQ-LAM-DVNVREMD-HGYHQR-E--RREYHP-----QM----------PFTFRV-QPI----QPN-L-HQ...EbPI.Eupomatia ...KQMDYLK----MLKKNERVLEEENKRLSYIL-HQQQ-LAM-EGNVRELE-HGYHQR-E--RREG-PP----QM----------PFAFRV-QPI----QPN-L-HQ...Pe.am.PI.Persea ...RQMEFLR----ALKKNERNLEDENKRLSYIL-HQQQ-ISM-GGNVREVDHHGYHQK--G-RRDY-PS----QI----------PFAFRV-QPI----QPN-L-HQ...CfPI.1.Calycanthus ...RQMECLR----IYKKNERTLEDENKRLTYIL-HQQQQMAM-DGNVREVD-HGYHHK--I-R-DY-SN----QM----------PFAFRI-QPI----QPN-L-HQ...CsPI.Chloranthus ...KQMDFLK----MLKKNERTLEDENKRLSYILHHQQ--LAL-DGNMRDLD-NGFHPK-E--R-DY-SS----QM----------PFIFRV-QPI----QPN-L-QQ...Iillicium PI* ...KQMELLN----MLKKSERDLEDENKRLNSILHHQQ--LAM-DGNVRELD-PGYHQR--G-R-DF-TS----QM----------PFAFRV-HPI----QPN-L-QG...Nu.va.PI.Nuphar ...KQTECLNNDIQILKKNERILEEENRQMKYIL-HQQ-EQMA-GEL-KDIL--GSNNK--G---KY-PSQSG-Q-----------PFGCCV-QPI----QPN-L-QP...Nu.ad.PI.Nuphar ...KQTECLNNDIQILKKNERILEEENRQLKYIL-HQQ-EAIALPEL-RDID-PGRNKK--G---KGIPSTSGVQ-----------PFGFRV-QPI----QPN-L-QR...Am.tr.PI.Amborella ...KQMEHIRTRTEMLKNNERILEDQNKQLKYIM-HQI-EGG--DEAER-----RYQNQQNG-R-DY-P-----QQAL---------TAFRV-QPI----QPN-L-QQ...

Am.tr.AP3.Amborella ...KKNHLVTNQTETCKKRIKNLEEQNKMMRHMM-E---E----DEAER-----GLED--DG---DYE-S----QLALGVRNTH-L-FAYRM-RPA----EGN-I-HD...Nu.va.AP3-1.Nuphar ...ALDNKIKRQIDTYRKKIKAADSIRNIGFMEL--Q--------ELN-----CSF-DGSEE---NYE-S------MLVMRNGNAQPFPISV-QPN----HPN-L-HE...Nu.va.AP3-2.Nuphar ...VLDSKIKRQIDTYKKKIRSAESNRNKVFRDA--Q--E-----ELN-----CTFEE-SEE---DYE-S------MLVMRNGNPQLFPIRV-QPT----HPN-L-HE...

-hom

olog

ues Il.pa.AP3.Illicium ...RKYHVINNESETFRKKIRNLEERHKELLSAMEG-----------NPPS--YLFEDN--GA--EST-G------DLGSRN-SSLMFAFRV-QPS----QPN-L-HD...

CsAP3.Chloranthus ...RKYHVIKTQTETYGKKLKHRQEEHEKLLHRLEGI-------DM-NQG---YDMLDR-EG---DYE-T------AFGLANGGGHVFAFRL-QPI----QPN-L-HD...CfAP3.1.Calycanthus ...RKYHVINTQTETYKKKLRSLHEIHTNLIHTLEGR-------EV-NGH---FGFSGND--AP-HYG-A------VINLAHGG-----------N----H-D-L-HE...Pe.am.AP3.Persea ...RKYHVINTQTETYKKKLRSLHESHANLVRALEGK-------DD-NGD---CALGDN--GGP-DYE-T------ALGWANGGSQMFAFCI-QPC----QPN-L-QE...Eu.be.AP3-1.Eupomatia ...RKYHVIATQTETYKKKLRNLHEAHARLVRALEGQ-------AE-NGG---YGLVDD--GGP-DYE-S------ALALANGGAHHH--------------S-L-HD...MfAP3.Michelia ...RKYHVIQTQTETYKKKLRSLNDEQAKLIRVLEGQ-------AE-NGA---YGLVDN--GGP-DYE-S------ALVLANGGAHI-----------------L-HD...AeAP3.1.Asarum ...KKYQVISSQTETKKKKVKNLEQTHKNLGCALAGK-------DA-ICA---YGIAYN-E-T-LDYK-S------VLGLANDASHIFAFRI-QPC----QPN-L-HN...

AP

3- TcAP3.Tacca ...RKYHVITTQTDTYKKKLKNSHEAHRNLMRELEMR-------DE-HPV---YGFVDN-DPT--NYD-S------ALALANAGSHVYAYRV-QPS----QPN-L-HG...ScAP3.Sanguinaria ...RKYHVITTQTDTTRKKIRSLTETHHNLLREFEGR-------DE-DPH---YALANQ-E---EDYE-A------VLELANGGPNIFAFRL-QPS----QPN-L-HD...HmTM6.Hydrangea ...RKYHVLKTQTETCRKKVRNLEERYGNLFLDWEGK-------CE-DPQ---YGLVEN-DG---EYD-S------AVAFANRVPNSYAFGL-QPS----HPN-LHHG...AP3.Arabidopsis ...RKFKSLGNQIETTKKKNKSQQDIQKNLIHELELR-------AE-DPH---YGLVD--NG--GDYD-S------VLGYQIEGSRAYALRFHQNHHHYYPNHGLHAP...HPDEF1.Hieracium ...RKLKVIGNKLETSKKKVRSAQDVYKKLMHEFGIR-------GE-DPQ---FGMIE--DG---EYD-A------VYGYPPQMSAPRILTF-RLH----PNN-L-HA...DEF.Antirrhinum ...RKYKVISNQIDTSKKKVRNVEEIHRNLVLEFDAR-------RE-DPH---FGLVD--NE--GDYNS-------VLGFPNGGPRIIALRLPTNHH-----PTLHSG...

“DEAER” motif in Amborella

X Y X X Y Y

AP3-2 AP3-2 AP3-2AP3-2 AP3-2 AP3-2

AP3-1

X Y

AP3-1

X X

AP3-1

Y Y

X Y X X Y Y

AP3-1 AP3-1 AP3-1

AP3-2 AP3-1

X Y

AP3-2 AP3-1

X X

AP3-2 AP3-1

Y Y

X Y X X Y Y

AP3-2 AP3-1

Y X

Purpose of this study:test MADS box proteinX Y X X Y Y

X Y X X Y Y

PI PI PIAP3-2 AP3-2 AP3-2

Y X

Y X

PIAP3-2

test MADS-box protein-protein interactions in Amborella using Y2H.

AP3-1

X X

AP3-1

Y Y

X Y X X Y Y

PI PI

Y X

AP3-1

Y X

PI AP3

X Y

PI

g

X X Y YY X

PI PI

X Y

PI PI

X X

PI PI

Y Y

X Y

X Y X X Y Y

eudicots

1 4 21Amborella

monocots, maybe most of basal angiosperms1: 4: 21

Yeast two-hybridization system

Bait Prey

BD DNA-binding ActivationAD

Yeast

BD gdomain plasmidTRP1

domain plasmid

AD

LEU2

Medium:-Trp/-Leu

ADADBD

ADE2, HIS3, lacZ, MEL1

Yeast two-hybridization system

Bait PreyBaitX

PreyY

Yeast

BD DNA-binding ActivationAD

X Y

DNA bi diBD

X

A ti tiAD

Y

Medium:-Trp/-Leu

BD gdomain plasmidTRP1

domain plasmid

AD

LEU2

DNA-binding domain plasmid

BD Activationdomain plasmid

AD/-His/-Ade

TRP1 LEU2

RNAX

TranscriptionADYInteraction

RNApolymeraseBD

Transcription

ADE2, HIS3, lacZ, MEL1

AD

Confirm presence of bait and prey plasmids: -L/-T

PI/AP3 2

PI/PI

Nodata

PI/AP3-1PI/AP3-2

AP3-1/PIAP3-2/PI

AP3-1/AP3-1AP3-2/AP3-2

AP3 1/AP3 2AP3 2/AP3 1 AP3-1/AP3-2AP3-2/AP3-1

Low stringent medium: -L/-T/-H + 0.5 mM 3AT

PI/AP3 2

PI/PI

Nodata

PI/AP3-1PI/AP3-2

AP3-1/PIAP3-2/PI

AP3-1/AP3-1AP3-2/AP3-2


Medium stringent medium: -L/-T/-H + 3 mM 3AT

PI/AP3 2

PI/PI

Nodata

PI/AP3-1PI/AP3-2

AP3-1/PIAP3-2/PI

AP3-1/AP3-1AP3-2/AP3-2


High stringent medium: -L/-T/-H/-A + 3 mM 3AT

PI/AP3 2

PI/PI

Nodata

PI/AP3-1PI/AP3-2

AP3-1/PIAP3-2/PI

AP3-1/AP3-1AP3-2/AP3-2


A i G



Arabidopsis Antirrhinum Lilium GnetumArabidopsis Antirrhinum Lilium GnetumAmborella

?

AP3-like genesPI lik

AP3-like genesPI-like genesPI-like genes

GGM2-like genes

PI like genesGGM2-like genes

Conclusions:Conclusions:

• In Amborella, PI/AP3-1(AP3-1/PI) and PI/AP3-2 (AP3-2/PI) interactions are ( )confirmed.

• B-class protein interaction demonstrated inB class protein interaction demonstrated in Arabidopsis likely dates to common ancestor of angiosperms and is not a recent innovationof angiosperms and is not a recent innovation in eudicot models.

General take home message

The “Abominable mystery” is far from solved, butis far from solved, but progress is being made!

Charles DarwinCharles DarwinBritish Naturalist

1809 -1882

Ongoing projects:Ongoing projects:

-- Proteomics:Proteomics: ProteinProtein--protein interaction of MADSprotein interaction of MADS--box box genes ingenes in Amborella trichopodaAmborella trichopodagenes in genes in Amborella trichopodaAmborella trichopoda..

-- Genetics:Genetics: Phenotype recovery experiments usingPhenotype recovery experiments usingGenetics:Genetics: Phenotype recovery experiments using Phenotype recovery experiments using Arabidopsis Arabidopsis mutants to address functional homologies of mutants to address functional homologies of floral genes between floral genes between ArabidopsisArabidopsis and and AmborellaAmborella by by introducing introducing AmborellaAmborella genes into genes into ArabidopsisArabidopsis ABC ABC mutants. mutants.

-- Phylogenetics:Phylogenetics: Phylogenetic analyses of MADSPhylogenetic analyses of MADS--box genes box genes (about 3000 sequences)(about 3000 sequences)(about 3000 sequences) (about 3000 sequences)

-- Genomics:Genomics: AmborellaAmborella transcriptome sequencing using transcriptome sequencing using 454 system454 system

http://www.flmnh.ufl.edu/soltislab/http://www.flmnh.ufl.edu/soltislab/Many thanks to:Many thanks to:

Douglas SoltisS

pp

-- Postdoc advisorsPostdoc advisorsDouglas SoltisPamela SoltisDouglas SoltisDouglas Soltis

Pamela SoltisPamela Soltis

-- Colleagues in Soltis labColleagues in Soltis labAndre ChanderbaliAndre ChanderbaliAndre ChanderbaliAndre ChanderbaliMatyas BuzgoMatyas BuzgoMatt GitzendannerMatt GitzendannerMatt GitzendannerMatt Gitzendanner……

-- The Floral Genome Project groupThe Floral Genome Project group

National Institute of Biological Resources, KoreaNIBR

Documents

Molecular Genetic Insights into Basal Angiosperms Sangtae Kim · 2011-06-03 · Darwin’s Abominable Mystery: explosive evolution andexplosive evolution and diversification of angiosperms