Molecular Genetic Insights intoMolecular Genetic Insights intoMolecular Genetic Insights into Molecular Genetic Insights into Basal Basal Angiosperms:Angiosperms:g pg p
Focused on Focused on AmborellaAmborella and and M liM liMagnoliaMagnolia
SangtaeSangtae 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. . EvoEvo--devodevo in in MagnoliaceaeMagnoliaceae
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
FagalesCucurbitalesRosalesFabalesZygophyllalesCelastrales
Walnuts, chestnutSquashApples, strawberriesLegumesCreosote plant
EudicotsCore-eudicots• End of debates?
Soltis et al., 1999. OxalidalesMalpighialesSapindalesMalvalesBrassicalesCrossosomatalesMyrtales
Star fruitPassion fruitCitrus, cashewsCotton, cocoaArabidopsis, mustard
Pomegranate
Mathews and Donoghue, 1999Qiu et al., 1999Soltis, …, Kim, 2000Savolainen et al 2000
yGernalialesSaxifragalesLamialesSolanalesGentianalesGarryalesAsteralesDi l
GooseberryAntirrhinum, oliveTomato, green pepperCoffee
SunflowerSavolainen et al., 2000Barkman et al., 2000Zanis et al., 2002Kuzoff and Gasser, 2000
DipsacalesApialesAquifolialesCornalesEricalesBerberidopsidalesSantalalesCaryophyllales
ElderberryDill, fennel
Blueberry, cranberry
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
MagnolialesLauralesPiperalesWinterales
Chloranthales
Illiciaceae
NutmegAvocadoBlack pepper
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
*
##
**
FagalesCucurbitalesRosalesFabalesZygophyllalesCelastrales
Walnuts, chestnutSquashApples, strawberriesLegumesCreosote plant
Eudicots
Current understanding of angiosperm phylogeny
monocots dicots
OxalidalesMalpighialesSapindalesMalvalesBrassicalesCrossosomatalesMyrtales
Star fruitPassion fruitCitrus, cashewsCotton, cocoaArabidopsis, mustard
Pomegranate
angiosperm phylogeny
Traditional view
yGernalialesSaxifragalesLamialesSolanalesGentianalesGarryalesAsteralesDi l
GooseberryAntirrhinum, oliveTomato, green pepperCoffee
Sunflower
75%
Traditional view DipsacalesApialesAquifolialesCornalesEricalesBerberidopsidalesSantalalesCaryophyllales
ElderberryDill, fennel
Blueberry, cranberry
B ck heat q inoaCaryophyllalesGunneralesBuxalesTrochodendralesProtealesSabiaceae
Buckwheat, quinoa
Macadamia nut
Ranunculales Poppy
monocots
eudicots
Ceratophyllales
Monocots 22%Grains, Palms
Recent view
MagnolialesLauralesPiperalesWinterales
Chloranthales
Illiciaceae
NutmegAvocadoBlack pepper
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:- Provide an evolutionary genomic framework y g
for flowers- Address questions of q
. Origin and diversification of flowers.
. Evolution of plant reproduction. p p
• 2001~ 2007
http://www.floralgenome.org/
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
http://www.floralgenome.org/
Ski• Skim papers:
- Soltis et al (2002) Missing links: the genetic architecture- 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 from basal angiosperms for comparative genomics
h BMC Pl t Bi l 5 1 15research. BMC Plant Biology 5: 1-15.
CYCLOIDEA Citerne et al., 2006. PNASCYCLOIDEA Citerne et al., 2006. PNAS
Lupinus
Cadia
soc1 and ful : annual to perennial Siegbert et al. Nature Genet. 2008
http://amborella.org
FGP II:FGP project is continued as the Amborella Genome Project
Next Generation Sequencing (NGS) TechnologiesNext Generation Sequencing (NGS) Technologies
SolexaSolexa; Illumina
GSGS‐‐TitaniumTitanium; Roche 454
SOLiDSOLiD; ABI
SMRTSMRT; Pacific Bioscience HelicosHelicos; Helicos Bioscience
‐ Next (or Current) generation sequencing technologies have accelerated the speed
of genome sequencing projects and have broaden application range of genomeof genome sequencing projects and have broaden application range of genome
sequences.
13 Published Higher Plant Genomes from 10 Species13 Published Higher Plant Genomes from 10 Species
Species name Journal Method Size (Mb) # of contigs # of transcripts
Arabidopsis thaliana Nature, 2000 BAC +α 119.19 5 32,615
Data from Dr. Jongsun Park
Oryza sativa japonicaScience, 2002Nature, 2005
BAC +α 372.08 12 66,710
Oryza sativa indicaScience, 2002PL S Bi l 2005
WGS 426.32 10,267 49,710yPLoS Biology, 2005
, ,
Oryza sativa japonica (syngenta)
PLoS Biology, 2005 WGS 391.14 7,777 45,824
Populus trichocarpa Science, 2006 WGS 485.51 22,012 45,555opu us t c oca pa Sc e ce, 006 GS 85 5 ,0 5,555
Vitis vinifera Nature, 2007WGS, Complete
497.51 35 30,434
Carica papaya Nature, 2008 WGS 369.69 17,677 28,589
Lotus japonicus DNA Research, 2008 WGS 323.24 110,945 26,700
Sorghum bicolor Nature, 2009 WGS 738.54 3,304 36,338
Zea mays Science, 2009 BAC, WGS 2,061.02 11 53,764
Cucumis sativusNature genetics, 2009
WGS 243.57 47,488 26,682
Glycine max Nature 2010 WGS 996 90 4 262 62 199Glycine max Nature, 2010 WGS 996.90 4,262 62,199
Brachypodiumdistachyon
Nature, 2010 WGS 273.27 197 32,255
Unpublished 8 Higher Plant GenomesUnpublished 8 Higher Plant Genomes
Species name Method Size (Mb) # of contigs # of transcripts
Data from Dr. Jongsun Park
Arabidopsis lyrata WGS 206.67 695 32,670
Medicago truncatula BAC, WGS 278.69 9 38,334
Selaginella moellendorffii WGS 212.76 768 22,285
Lycopersicon esculentum WGS, BAC 794.60 7,409 49,389
Solanum phureja WGS 702.58 57,681 110,512
Ricinus communis WGS 362.47 28,518 38,613
Mimulus guttatus WGS 416.66 11,243 47,442
Manihot esculenta WGS 321.73 2,216 27,501
7 Unicellular Plants Genomes7 Unicellular Plants Genomes
Species name Journal MethodSize (Mb)
# of ti
# of transcripts
Data from Dr. Jongsun Park
p(Mb) contigs
p
Chlamydomonas reinhardtii Science, 2007 WGS 112.31 88 16,709
Micromonas pusilla CCMP1545 Science, 2009 WGS 22.04 27 10,547
Micromonas sp. RCC299 Science, 2009 WGS 20.99 17 10,108
Ostreococcus lucimarinus CCE9901 PNAS 2007 WGS 13 2 21 7 488Ostreococcus lucimarinus CCE9901 PNAS, 2007 WGS 13.2 21 7,488
Ostreococcus sp. RCC809 Not published yet WGS 13.41 22 7,492
Ostreococcus tauri PNAS, 2007 WGS 12.58 118 7,725
Coccomyxa sp C169 Not published yet WGS 48 95 45 9 629Coccomyxa sp. C169 Not published yet WGS 48.95 45 9,629
Distribution of 21 Plant Genome SizeDistribution of 21 Plant Genome Size
2500MbMb
Data from Dr. Jongsun Park
2000
2,061.02
1000
1500
794 6
996.9
500212.76 243.57
323.24 321.73369.69
497.51
273.27
119.19206.67
738.54
278.69362.47
485.51391.14 416.66
794.6
426.32372.08
702.58
0
119.19
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
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 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
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
ArabidopsisAP3/PI
AP1/AP2 AG
Sepal Petal Stamen Carpel
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
Sepal Petal Stamen Carpel
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
Questions in basal angiosperms
1. Are homologs of ABC B
genes found in basal angiosperms?
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?
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
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
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
48TM3.0.0000.PrMADS9.Pinus
39TM3.0.0000.PrMADS5.Pinus
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
2. Where are ABC homologs expressed?
PetalStamen
CarpelBroader “B” expressionDifferent “A” expression
3. If expression implies function does the ABC
Sepalfunction, does the ABC model hold for basal angiosperms?angiosperms?
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
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
2. Where are ABC homologs expressed?
PetalStamen
Carpel3. If expression implies
function does the ABCfunction, does the ABC model hold for basal angiosperms?
Sepalangiosperms? Not entirely.
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. III. EvoEvo--devodevo in in MagnoliaceaeMagnoliaceae
FagalesCucurbitalesRosalesFabalesZygophyllalesCelastrales
Walnuts, chestnutSquashApples, strawberriesLegumesCreosote plant
Current understanding of Current understanding of angiosperm angiosperm relationships relationships
OxalidalesMalpighialesSapindalesMalvalesBrassicalesCrossosomatalesMyrtales
Star fruitPassion fruitCitrus, cashewsCotton, cocoaArabidopsis, mustard
Pomegranate
g pg p pp(Moore et al., 2007; (Moore et al., 2007; SoltisSoltis et al., 2004)et al., 2004)
yGernalialesSaxifragalesLamialesSolanalesGentianalesGarryalesAsteralesDi l
GooseberryAntirrhinum, oliveTomato, green pepperCoffee
Sunflower eudicotsDipsacalesApialesAquifolialesCornalesEricalesBerberidopsidalesSantalalesCaryophyllales
ElderberryDill, fennel
Blueberry, cranberry
B ck heat q inoa
eudicots
Ceratophyllales
CaryophyllalesGunneralesBuxalesTrochodendralesProtealesSabiaceae
Buckwheat, quinoa
Macadamia nut
Ranunculales PoppyCeratophyllales
Magnoliales
Monocots
li t li t
Grains, Palms MonocotsMagnolialesLauralesPiperalesWinteralesChloranthalesIlliciaceae
magnolia, tulip treeAvocadoBlack pepper
Star anise BasalSchisandraceaeAustrobaileyaceaeNymphaeaceaeAmborellaceae
Gymnosperms
Basalangiosperms
OneOne of wellof well--recognized characters in magnolia: recognized characters in magnolia: tepalstepals(undifferentiated(undifferentiated perianthperianth))(undifferentiated (undifferentiated perianthperianth))
Magnolia grandiflora
SepaloidSepaloid--tepalstepals are only found in the are only found in the YulaniaYulania cladeclade in the in the MagnoliaceaeMagnoliaceae
Magnolia salicifolia
Sepal or sepal-like structure is evolved multiple times in the evolutionary history of angiospermsy y g p
?
Magnolia stellata
Magnolia lilliflora
Magnolia biondii
Phylogeny ofPhylogeny of Magnoliaceae:11 subgroups are recognized in the family(Kim et al., 2001)
Phylogeny of Magnoliaceaebased on 10 chloroplast
Michelia cavalerieiM. pealiana
Michelia bailloniiMichelia champ
Michelia odoraMichelia figo
1.00
1.00
1.00
1.00 1.00
79
89
64
9398MICHELIA
Mi
MicheliaElmerrillia
sect. Maingolasect Alcimandra
pregions (Kim et al., in prep.)
Michelia figoE.ovalis
Michelia cathcartiiM. elegans
M. biondiiM. kobus
M. dawsoniana
1.000.98
1.00
1 001 00
8277
100
0 70
Al
Ar
Bu
Bu
Yu
sect. Alcimandrasect. Aromadendron
M. campbelliiM. denudataM. cylindrica
M. acuminataM. sinica
Pachylarnax praecalva
1.00
1.00
1.001.00
1.00
1.00
100100
9797
700.70
80
YULANIA
GYNOPODIUM
Yu
Yu
Cy
Tu
Mt
subgen. Yulania
sect. ManglietiastrumPachylarnax
Posterior probability
Bootsrtapvalue
M. nitidaM. panamensis
M. virginianaM. tamaulipanaM. grandiflora
M. guatemalensisK i d
1.00
1 00
1.00
0.99
100
60
10063
Gy
THEORHODON
Th
Ma
Th
Th
Th
sect. Gynopodium
sect. Theorhodon s.s.sect. Magnolia
Kmeria duperreanaKmeria septentrionalis
Manglietia grandManglietia aroma
Manglietia coniferaManglietia glauca
M officinalis
1.00
1.001.00
100
86
100
KMERIA
MANGLIETIA
R
Manglietia
Kmeria
M. officinalisM. tripetala
M. sieboldiiM. wilsonii
M. fraseri var. fraseriM. fraseri var. pyramidata
M macrophylla
1.00
1.001.00
1.00
1 00
100
9298
100 FRASERIRy
Ry
Ry
RYTIDOSPERMUM
Ry
Ry
Oy
Oy
sect. Rytidospermum s.s.sect. Oyama
M macrophyllaM. fraseri
M. macrophyllaM. dealbata
M. cocoM. gigantifolia
M. henryiM. pterocarpaM. liliifera
1.00
1.00
1.00
0.99100
100
75
85
1001.00
MACROPHYLLA
GWILLIMIA
Gw
Bl
Gw
Li
Bl
Ry
Ry
M. macrophyllaM. dealbata
sect. Gwillimiasect. Lirianthesect. Blumiana
M. splendensM. mexicana
M. dodecapetalaLiriodendron chinense
Liriodendron tulipifera0.001 substitutions/site
1.001.00100
100
Bl
TALAUMASp
Ta
Ta
sect. Talaumasect. Splendentes
Mich. cvcalerieiMich. forveolataMich. ingrataMich. macclureiMich. maudiaeMich. chapensisMich. martiniiM. pealiana
1
1
1
59 d1Phylogeny of MagnoliaceaeBased on ndhF sequences M. pealiana
Mich. balanse
Mich. champacaMich. lacei
Mich. masticata
Mich. montanaMich. velutina
Mich. baillonii
Mich. shiluensisMich. odora
Mich. wilsoniiMich figo
1
11
1
2
42
11
11
1
57 d1
61 d1
57 d161 d1
42 d1
64 d1
Based on ndhF sequences(Kim et al., 2001)
Mich. figoMich. doltsopaMich. hypolampra
Mich. floribundaE. ovalis
M. cathcartiiM. amoena
M. zenii
M. biondiiM. kobus
M. stellataM dawsoniana
21
22
14
1
522
1
67 d2
61 d1
41 d1
61 d1
M. dawsonianaM. sargentianaM. campbelliiM. sprengeri
M. denudataM. cylindricaM. lilliflora
M. salicifoliaM. acuminata var. acuminata
M. acuminata var. subcordataP. praecalvaM sinica
2
2
1 61
11
1
27 1
1
57 d1
67 d1
77 d1 100 d6
100 d6
62 d1
64 d1
Yulania clade
M. sinicaM. nitida var. lotungensis
M. nitidaMang. duclouxii
Mang. szechuanicaMang. grandisMang. hebecarpa
Mang. aromaticaMang. conifera
Mang. insignisMang. dolichogyna
Mang fordiana
61
4
1
1
1 1
1
2
21
99 d6
58 d1
49 d1
58 d1
161 d1
73 d1
Mang. fordianaMang. glauca
Mang. megaphylla
Mang. motoM. championii
M. cocoM. henryi
M. pterocarpaM. lilliferaAromadendron sp.
M d l i
1
11
3
1
2 1
52
111
5
33 d1
93 d4
71 d2
46 d1
78 d2M. albosericea
pM. delavayi
M. obovataM. officinalis
M. tripetalaM. rostrata
M. sieboldii var. sinensisM. sieboldii var. sieboldii
M. wilsoniiM. globosa
M. virginianaM t l i
M. sharpii
32
5
2
11
2 11
1
23
43
1
11
63 d2
60 d165 d1
90 d2
72 d2100 >d6 92 d4
M. guatemalensisp
M. tamaulipanaM. grandiflora
K. duperreanaK. septentrionalis
M. fraseri var. pyramidataM. macrophylla var. macrophylla
M. macrophylla var. asheiM. dealvata
L. chinensisL. tulipifera
1
73
56
71
1
88
68 d164 d1
90 d5
100 d668 d1
M amoena5 M. amoena
M. biondiiM. kobus
M. stellata
12
261 d1
M. zenii
M. dawsonianaM. sargentiana
1 6
1
162 d1
M. campbelliiM. sprengeri
M. denudata
1 6 1
1
1
77 d1 100 d6
M. cylindricaM. lilliflora
M. salicifoliaM acuminata var acuminata
2 1
267 d1 64 d1
M. acuminata var. acuminata
M. acuminata var. subcordata7
1100 d6
Thi t i ld 15 Y l i t t f b t 30- This tree incldes 15 Yulania taxa out of about 30. - Sepaloid-tepal is not a synapomorphy in some clade.- It seems that sepaloid-tepals are evolved several times in the evolution of Yulania group
For some representatives Magnoliasalicifolia
Magnoliastellata
pof magnolia having sepaloid-tepals,
We
(1) isolated homologues of A-, B-, C-, and E-class genes
(2) examined the expression patterns of these floral genes in each floral organin each floral organ
(3) compared their expression patterns with those of ( ) p p pMagnolia grandiflora, which is previously studied taxon having tepals.
Magnoliagrandiflora
ZMM27OsMADS8
ZMM6AGL9
Ma.gr.AGL2.2 (M. grandiflora)Eu.be.AGL9
Am.tr.AGL2
Ma.gr.AGL2.1 (M. grandiflora)AGL4
AGL2E
clas
9899
82
10093Ma.st.AGL2.1 (M. stellata)
Ma.sa.AGL2.1 (M. salicifolia)MpMADS14 (M. kobus)
100
Ma.st.AGL2.2 (M. stellata)Ma.sa.AGL2.2 (M. salicifolia)
MpMADS13 (M. kobus)
100
99100100Identification of new sequences
- Selective representatives of each major clade of MADS-box genes AGL4
AGL2Nu.ad.AGL2
AGL3ZMM3
OsMADS1AP1
CALSQUA
AGL8
Ma.gr.AP1 (M. grandiflora)Eu.be.AP1Pe.am.AP1
OsMADS15ZAP1Nu ad AP1
SQUA (AP1)
A classss100516893
100
98 67
70
5888 99
8287 MpMADS15 (M. kobus)
Ma.sa.AP1 (M. salicifolia)Ma.st.AP1 (M. stellata)100
9999
g(sequences from Becker and Theissen (2003)
+ sequences from basal angiosperms (Kim et al., 2005)+ new sequences from M. salicifolia and M. stellata (red)
- Strict consensus tree of amino acid MP analysisNu.ad.AP1
OsMADS6ZAG3
Ma.gr.AGL6Am.tr.AGL6
AGL13AGL6
GGM11GGM9
Pe.am.AG
AGL6
AG
s
100
54
100
62
70
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
Ma.sa.AG.1 (M. salicifolia)MpMADS11 (M. kobus)
100
Ma.st.AG.2 (M. stellata)Ma.sa.AG.2 (M. salicifolia)
MpMADS2 (M. kobus)100
98
100
C (and
Nu.ad.AGIl.fl.AG
Am.tr.AGZAG1
OsMADS3AGAGL1AGL5
AGL11ZMM25
OsMADS13ZMM1
OsMADS26AGL12
TM8ERAF17
GGM10OsMADS2
AGL12TM8
100100
100
100
100
97
Ma.gr.AG.2 (M. grandiflora) D)class
OsMADS2ZMM18
GLOPI
Pe.am.PI.2Eu.be.PI
Eu.la.PIAs.lo.PI
Pe.am.PI.1Il.fl.PI
Am.tr.PINu.ad.PI
GLO (PI) B clas
100
71
98 52
72
70
99 Ma.gr.PI (M. grandiflora)
MpMADS8 (M. kobus)Ma.sa.PI (M. salicifolia)
Ma.st.PI (M. stellata)100100
100
Ma.sa.AG.1 (M. salicifolia)MpMADS7 (M. kobus)
100
As.lo.AP3Eu.be.AP3
Pe.am.AP3Il.fl.AP3.1
AP3DEFA
SILKYIl.fl.AP3.2
Il.fl.AP3.3Nu.ad.AP3.2
Nu.ad.AP3.1Am.tr.AP3GGM2
ABSFBP24
ZMM17AeAP3.2
GGM13
DEF (AP3)
GGM13
ss
72
100
100
100 94
59
95 91
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
( )98
70
GGM13ZmMADS2CAD40993
AGL16AGL17
AGL21ANR1
At5g51870At5g51860
AGL42FDRMADS8
ZMM5AGL19AGL14
TM3SOC1
GGM1AGL151
AGL152AGL15
AGL18
TM3
AGL17
AGL15
98 50
100 98
100 96
98
100 7678 75
100 51
62AGL18
AGL31At5g65060
MAF1FCL2
FCL1FLC
ZMM21BM1
SVPJOINTLESS
StMADS11AGL24
GGM12
50 changes
FLC
AGL15
STMADS11
100 89
91 96
86
8691
83
ZMM27OsMADS8
ZMM6AGL9
Ma.gr.AGL2.2 (M. grandiflora)Eu.be.AGL9
Am.tr.AGL2
Ma.gr.AGL2.1 (M. grandiflora)AGL4
AGL2E
clas
9899
82
10093Ma.st.AGL2.1 (M. stellata)
Ma.sa.AGL2.1 (M. salicifolia)MpMADS14 (M. kobus)
100
Ma.st.AGL2.2 (M. stellata)Ma.sa.AGL2.2 (M. salicifolia)
MpMADS13 (M. kobus)
100
99100100Identification of new sequences
- Selective representatives of each major clade of MADS-box genes AGL4
AGL2Nu.ad.AGL2
AGL3ZMM3
OsMADS1AP1
CALSQUA
AGL8
Ma.gr.AP1 (M. grandiflora)Eu.be.AP1Pe.am.AP1
OsMADS15ZAP1Nu ad AP1
SQUA (AP1)
A classss100516893
100
98 67
70
5888 99
8287 MpMADS15 (M. kobus)
Ma.sa.AP1 (M. salicifolia)Ma.st.AP1 (M. stellata)100
9999
g(sequences from Becker and Theissen (2003)
+ sequences from basal angiosperms (Kim et al., 2005)+ new sequences from M. salicifolia and M. stellata (red)
- Strict consensus tree of amino acid MP analysisNu.ad.AP1
OsMADS6ZAG3
Ma.gr.AGL6Am.tr.AGL6
AGL13AGL6
GGM11GGM9
Pe.am.AG
AGL6
AG
s
100
54
100
62
70
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
Ma.sa.AG.1 (M. salicifolia)MpMADS11 (M. kobus)
100
Ma.st.AG.2 (M. stellata)Ma.sa.AG.2 (M. salicifolia)
MpMADS2 (M. kobus)100
98
100
C (and
Nu.ad.AGIl.fl.AG
Am.tr.AGZAG1
OsMADS3AGAGL1AGL5
AGL11ZMM25
OsMADS13ZMM1
OsMADS26AGL12
TM8ERAF17
GGM10OsMADS2
AGL12TM8
100100
100
100
100
97
Ma.gr.AG.2 (M. grandiflora) D)class
E classOsMADS2
ZMM18GLO
PIPe.am.PI.2
Eu.be.PIEu.la.PI
As.lo.PI
Pe.am.PI.1Il.fl.PI
Am.tr.PINu.ad.PI
GLO (PI) B clas
100
71
98 52
72
70
99 Ma.gr.PI (M. grandiflora)
MpMADS8 (M. kobus)Ma.sa.PI (M. salicifolia)
Ma.st.PI (M. stellata)100100
100
Ma.sa.AG.1 (M. salicifolia)MpMADS7 (M. kobus)
100
As.lo.AP3Eu.be.AP3
Pe.am.AP3Il.fl.AP3.1
AP3DEFA
SILKYIl.fl.AP3.2
Il.fl.AP3.3Nu.ad.AP3.2
Nu.ad.AP3.1Am.tr.AP3GGM2
ABSFBP24
ZMM17AeAP3.2
GGM13
DEF (AP3)
GGM13
ss
72
100
100
100 94
59
95 91
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
( )98
GGM13ZmMADS2CAD40993
AGL16AGL17
AGL21ANR1
At5g51870At5g51860
AGL42FDRMADS8
ZMM5AGL19AGL14
TM3SOC1
GGM1AGL151
AGL152AGL15
AGL18
TM3
AGL17
AGL15
98 50
100 98
100 96
98
100 7678 75
100 51
62AGL18
AGL31At5g65060
MAF1FCL2
FCL1FLC
ZMM21BM1
SVPJOINTLESS
StMADS11AGL24
GGM12
50 changes
FLC
AGL15
STMADS11
100 89
91 96
86
8691
83
ZMM27OsMADS8
ZMM6AGL9
Ma.gr.AGL2.2 (M. grandiflora)Eu.be.AGL9
Am.tr.AGL2
Ma.gr.AGL2.1 (M. grandiflora)AGL4
AGL2E
clas
9899
82
10093Ma.st.AGL2.1 (M. stellata)
Ma.sa.AGL2.1 (M. salicifolia)MpMADS14 (M. kobus)
100
Ma.st.AGL2.2 (M. stellata)Ma.sa.AGL2.2 (M. salicifolia)
MpMADS13 (M. kobus)
100
99100100Identification of new sequences
- Selective representatives of each major clade of MADS-box genes AGL4
AGL2Nu.ad.AGL2
AGL3ZMM3
OsMADS1AP1
CALSQUA
AGL8
Ma.gr.AP1 (M. grandiflora)Eu.be.AP1Pe.am.AP1
OsMADS15ZAP1Nu ad AP1
SQUA (AP1)
A classss100516893
100
98 67
70
5888 99
8287 MpMADS15 (M. kobus)
Ma.sa.AP1 (M. salicifolia)Ma.st.AP1 (M. stellata)100
9999
g(sequences from Becker and Theissen (2003)
+ sequences from basal angiosperms (Kim et al., 2005)+ new sequences from M. salicifolia and M. stellata (red)
- Strict consensus tree of amino acid MP analysisNu.ad.AP1
OsMADS6ZAG3
Ma.gr.AGL6Am.tr.AGL6
AGL13AGL6
GGM11GGM9
Pe.am.AG
AGL6
AG
s
100
54
100
62
70
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
Ma.sa.AG.1 (M. salicifolia)MpMADS11 (M. kobus)
100
Ma.st.AG.2 (M. stellata)Ma.sa.AG.2 (M. salicifolia)
MpMADS2 (M. kobus)100
98
100
C (and
Nu.ad.AGIl.fl.AG
Am.tr.AGZAG1
OsMADS3AGAGL1AGL5
AGL11ZMM25
OsMADS13ZMM1
OsMADS26AGL12
TM8ERAF17
GGM10OsMADS2
AGL12TM8
100100
100
100
100
97
Ma.gr.AG.2 (M. grandiflora) D)class
A l OsMADS2ZMM18
GLOPI
Pe.am.PI.2Eu.be.PI
Eu.la.PIAs.lo.PI
Pe.am.PI.1Il.fl.PI
Am.tr.PINu.ad.PI
GLO (PI) B clas
100
71
98 52
72
70
99 Ma.gr.PI (M. grandiflora)
MpMADS8 (M. kobus)Ma.sa.PI (M. salicifolia)
Ma.st.PI (M. stellata)100100
100
Ma.sa.AG.1 (M. salicifolia)MpMADS7 (M. kobus)
100
A classAs.lo.AP3
Eu.be.AP3Pe.am.AP3
Il.fl.AP3.1AP3
DEFASILKY
Il.fl.AP3.2Il.fl.AP3.3
Nu.ad.AP3.2Nu.ad.AP3.1
Am.tr.AP3GGM2ABS
FBP24ZMM17
AeAP3.2GGM13
DEF (AP3)
GGM13
ss
72
100
100
100 94
59
95 91
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
( )98
GGM13ZmMADS2CAD40993
AGL16AGL17
AGL21ANR1
At5g51870At5g51860
AGL42FDRMADS8
ZMM5AGL19AGL14
TM3SOC1
GGM1AGL151
AGL152AGL15
AGL18
TM3
AGL17
AGL15
98 50
100 98
100 96
98
100 7678 75
100 51
62AGL18
AGL31At5g65060
MAF1FCL2
FCL1FLC
ZMM21BM1
SVPJOINTLESS
StMADS11AGL24
GGM12
50 changes
FLC
AGL15
STMADS11
100 89
91 96
86
8691
83
ZMM27OsMADS8
ZMM6AGL9
Ma.gr.AGL2.2 (M. grandiflora)Eu.be.AGL9
Am.tr.AGL2
Ma.gr.AGL2.1 (M. grandiflora)AGL4
AGL2E
clas
9899
82
10093Ma.st.AGL2.1 (M. stellata)
Ma.sa.AGL2.1 (M. salicifolia)MpMADS14 (M. kobus)
100
Ma.st.AGL2.2 (M. stellata)Ma.sa.AGL2.2 (M. salicifolia)
MpMADS13 (M. kobus)
100
99100100Identification of new sequences
- Selective representatives of each major clade of MADS-box genes AGL4
AGL2Nu.ad.AGL2
AGL3ZMM3
OsMADS1AP1
CALSQUA
AGL8
Ma.gr.AP1 (M. grandiflora)Eu.be.AP1Pe.am.AP1
OsMADS15ZAP1Nu ad AP1
SQUA (AP1)
A classss100516893
100
98 67
70
5888 99
8287 MpMADS15 (M. kobus)
Ma.sa.AP1 (M. salicifolia)Ma.st.AP1 (M. stellata)100
9999
g(sequences from Becker and Theissen (2003)
+ sequences from basal angiosperms (Kim et al., 2005)+ new sequences from M. salicifolia and M. stellata (red)
- Strict consensus tree of amino acid MP analysisNu.ad.AP1
OsMADS6ZAG3
Ma.gr.AGL6Am.tr.AGL6
AGL13AGL6
GGM11GGM9
Pe.am.AG
AGL6
AG
s
100
54
100
62
70
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
Ma.sa.AG.1 (M. salicifolia)MpMADS11 (M. kobus)
100
Ma.st.AG.2 (M. stellata)Ma.sa.AG.2 (M. salicifolia)
MpMADS2 (M. kobus)100
98
100
C (and
Nu.ad.AGIl.fl.AG
Am.tr.AGZAG1
OsMADS3AGAGL1AGL5
AGL11ZMM25
OsMADS13ZMM1
OsMADS26AGL12
TM8ERAF17
GGM10OsMADS2
AGL12TM8
100100
100
100
100
97
Ma.gr.AG.2 (M. grandiflora) D)class
OsMADS2ZMM18
GLOPI
Pe.am.PI.2Eu.be.PI
Eu.la.PIAs.lo.PI
Pe.am.PI.1Il.fl.PI
Am.tr.PINu.ad.PI
GLO (PI) B clas
100
71
98 52
72
70
99 Ma.gr.PI (M. grandiflora)
MpMADS8 (M. kobus)Ma.sa.PI (M. salicifolia)
Ma.st.PI (M. stellata)100100
100
Ma.sa.AG.1 (M. salicifolia)MpMADS7 (M. kobus)
100
As.lo.AP3Eu.be.AP3
Pe.am.AP3Il.fl.AP3.1
AP3DEFA
SILKYIl.fl.AP3.2
Il.fl.AP3.3Nu.ad.AP3.2
Nu.ad.AP3.1Am.tr.AP3GGM2
ABSFBP24
ZMM17AeAP3.2
GGM13
DEF (AP3)
GGM13
ss
72
100
100
100 94
59
95 91
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
( )98
C (and D) classGGM13
ZmMADS2CAD40993
AGL16AGL17
AGL21ANR1
At5g51870At5g51860
AGL42FDRMADS8
ZMM5AGL19AGL14
TM3SOC1
GGM1AGL151
AGL152AGL15
AGL18
TM3
AGL17
AGL15
98 50
100 98
100 96
98
100 7678 75
100 51
62AGL18
AGL31At5g65060
MAF1FCL2
FCL1FLC
ZMM21BM1
SVPJOINTLESS
StMADS11AGL24
GGM12
50 changes
FLC
AGL15
STMADS11
100 89
91 96
86
8691
83
Identification of new sequences- Selective representatives of each major clade of MADS-
box genes
ZMM27OsMADS8
ZMM6AGL9
Ma.gr.AGL2.2 (M. grandiflora)Eu.be.AGL9
Am.tr.AGL2
Ma.gr.AGL2.1 (M. grandiflora)AGL4
AGL2E
clas
9899
82
10093Ma.st.AGL2.1 (M. stellata)
Ma.sa.AGL2.1 (M. salicifolia)MpMADS14 (M. kobus)
100
Ma.st.AGL2.2 (M. stellata)Ma.sa.AGL2.2 (M. salicifolia)
MpMADS13 (M. kobus)
100
99100100
B class (PI)g(sequences from Becker and Theissen (2003)
+ sequences from basal angiosperms (Kim et al., 2005)+ new sequences from M. salicifolia and M. stellata (red)
- Strict consensus tree of amino acid MP analysis
AGL4AGL2
Nu.ad.AGL2AGL3
ZMM3OsMADS1
AP1CAL
SQUAAGL8
Ma.gr.AP1 (M. grandiflora)Eu.be.AP1Pe.am.AP1
OsMADS15ZAP1Nu ad AP1
SQUA (AP1)
A classss100516893
100
98 67
70
5888 99
8287 MpMADS15 (M. kobus)
Ma.sa.AP1 (M. salicifolia)Ma.st.AP1 (M. stellata)100
9999
( )
Nu.ad.AP1OsMADS6
ZAG3Ma.gr.AGL6Am.tr.AGL6
AGL13AGL6
GGM11GGM9
Pe.am.AG
AGL6
AG
s
100
54
100
62
70
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
Ma.sa.AG.1 (M. salicifolia)MpMADS11 (M. kobus)
100
Ma.st.AG.2 (M. stellata)Ma.sa.AG.2 (M. salicifolia)
MpMADS2 (M. kobus)100
98
100
C (and
Nu.ad.AGIl.fl.AG
Am.tr.AGZAG1
OsMADS3AGAGL1AGL5
AGL11ZMM25
OsMADS13ZMM1
OsMADS26AGL12
TM8ERAF17
GGM10OsMADS2
AGL12TM8
100100
100
100
100
97
Ma.gr.AG.2 (M. grandiflora) D)class
OsMADS2ZMM18
GLOPI
Pe.am.PI.2Eu.be.PI
Eu.la.PIAs.lo.PI
Pe.am.PI.1Il.fl.PI
Am.tr.PINu.ad.PI
GLO (PI) B clas
100
71
98 52
72
70
99 Ma.gr.PI (M. grandiflora)
MpMADS8 (M. kobus)Ma.sa.PI (M. salicifolia)
Ma.st.PI (M. stellata)100100
100
Ma.sa.AG.1 (M. salicifolia)MpMADS7 (M. kobus)
100
As.lo.AP3Eu.be.AP3
Pe.am.AP3Il.fl.AP3.1
AP3DEFA
SILKYIl.fl.AP3.2
Il.fl.AP3.3Nu.ad.AP3.2
Nu.ad.AP3.1Am.tr.AP3GGM2
ABSFBP24
ZMM17AeAP3.2
GGM13
DEF (AP3)
GGM13
ss
72
100
100
100 94
59
95 91
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
( )98
70
GGM13ZmMADS2CAD40993
AGL16AGL17
AGL21ANR1
At5g51870At5g51860
AGL42FDRMADS8
ZMM5AGL19AGL14
TM3SOC1
GGM1AGL151
AGL152AGL15
AGL18
TM3
AGL17
AGL15
98 50
100 98
100 96
98
100 7678 75
100 51
62AGL18
AGL31At5g65060
MAF1FCL2
FCL1FLC
ZMM21BM1
SVPJOINTLESS
StMADS11AGL24
GGM12
50 changes
FLC
AGL15
STMADS11
100 89
91 96
86
8691
83
Identification of new sequences- Selective representatives of each major clade of MADS-
box genes
ZMM27OsMADS8
ZMM6AGL9
Ma.gr.AGL2.2 (M. grandiflora)Eu.be.AGL9
Am.tr.AGL2
Ma.gr.AGL2.1 (M. grandiflora)AGL4
AGL2E
clas
9899
82
10093Ma.st.AGL2.1 (M. stellata)
Ma.sa.AGL2.1 (M. salicifolia)MpMADS14 (M. kobus)
100
Ma.st.AGL2.2 (M. stellata)Ma.sa.AGL2.2 (M. salicifolia)
MpMADS13 (M. kobus)
100
99100100
B class (AP3)g(sequences from Becker and Theissen (2003)
+ sequences from basal angiosperms (Kim et al., 2005)+ new sequences from M. salicifolia and M. stellata (red)
- Strict consensus tree of amino acid MP analysis
AGL4AGL2
Nu.ad.AGL2AGL3
ZMM3OsMADS1
AP1CAL
SQUAAGL8
Ma.gr.AP1 (M. grandiflora)Eu.be.AP1Pe.am.AP1
OsMADS15ZAP1Nu ad AP1
SQUA (AP1)
A classss100516893
100
98 67
70
5888 99
8287 MpMADS15 (M. kobus)
Ma.sa.AP1 (M. salicifolia)Ma.st.AP1 (M. stellata)100
9999
B class (AP3)
Nu.ad.AP1OsMADS6
ZAG3Ma.gr.AGL6Am.tr.AGL6
AGL13AGL6
GGM11GGM9
Pe.am.AG
AGL6
AG
s
100
54
100
62
70
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
Ma.sa.AG.1 (M. salicifolia)MpMADS11 (M. kobus)
100
Ma.st.AG.2 (M. stellata)Ma.sa.AG.2 (M. salicifolia)
MpMADS2 (M. kobus)100
98
100
C (and
Nu.ad.AGIl.fl.AG
Am.tr.AGZAG1
OsMADS3AGAGL1AGL5
AGL11ZMM25
OsMADS13ZMM1
OsMADS26AGL12
TM8ERAF17
GGM10OsMADS2
AGL12TM8
100100
100
100
100
97
Ma.gr.AG.2 (M. grandiflora) D)class
OsMADS2ZMM18
GLOPI
Pe.am.PI.2Eu.be.PI
Eu.la.PIAs.lo.PI
Pe.am.PI.1Il.fl.PI
Am.tr.PINu.ad.PI
GLO (PI) B clas
100
71
98 52
72
70
99 Ma.gr.PI (M. grandiflora)
MpMADS8 (M. kobus)Ma.sa.PI (M. salicifolia)
Ma.st.PI (M. stellata)100100
100
Ma.sa.AG.1 (M. salicifolia)MpMADS7 (M. kobus)
100
As.lo.AP3Eu.be.AP3
Pe.am.AP3Il.fl.AP3.1
AP3DEFA
SILKYIl.fl.AP3.2
Il.fl.AP3.3Nu.ad.AP3.2
Nu.ad.AP3.1Am.tr.AP3GGM2
ABSFBP24
ZMM17AeAP3.2
GGM13
DEF (AP3)
GGM13
ss
72
100
100
100 94
59
95 91
Ma.gr.AG.1 (M. grandiflora)Ma.st.AG.1 (M. stellata)
( )98
70
GGM13ZmMADS2CAD40993
AGL16AGL17
AGL21ANR1
At5g51870At5g51860
AGL42FDRMADS8
ZMM5AGL19AGL14
TM3SOC1
GGM1AGL151
AGL152AGL15
AGL18
TM3
AGL17
AGL15
98 50
100 98
100 96
98
100 7678 75
100 51
62AGL18
AGL31At5g65060
MAF1FCL2
FCL1FLC
ZMM21BM1
SVPJOINTLESS
StMADS11AGL24
GGM12
50 changes
FLC
AGL15
STMADS11
100 89
91 96
86
8691
83
MADS-box gene expression in M. grandiflora (Kim et al., 2005a, b)
T1 T2T1 T2
T2T3
T3
T1T2 T3
T3T3
Spathaceous Tepals Stamens Carpels Leaves
T1
T2
T lSpathaceous Tepals Stamens Carpels Leavesbract (T1, T2, T3)
A-classMa.gr.AP1 +++ + ++ ++ +++
B-classMa gr PI - +++ +++ - -
Tepals(T1, T2, T3)1st 2nd 3rd 4th
Ma.gr.PI - +++ +++ - -Ma.gr.AP3 + +++ +++ - -
C-classMa.gr.AG.1 - - +++ +++ -
D-classD classMa.gr.AG.2 - - - +++ -
E-classMa.gr.AGL2.1 - +++ +++ +++ -Ma.gr.AGL2.2 +++ +++ +++ +++ ++
BA C
E
DBA C
E
DB
E
Relative-quantitative RT-PCR
Ma.sa.AP1
PER STE TE STN CAR
A class
qin M. salicifolia
Ma.sa.PI
Ma.sa.AP3
B classMa.sa.PI
Ma.sa.AG.1C class
Ma sa AGL2 1
Ma.sa.AG.2
C c ass
Ma.sa.AGL2.1
Ma.sa.AGL2.2
E class
ACTINE
Real-time PCR in M. salicifolia
Ma.sa.AP1 Ma.sa.PIMa.sa.AP3
0 35
0.40
0.45
0.50
0 35
0.40
0.45
0.50
0 35
0.40
0.45
0.50
0.25
0.30
0.35
0 R E E N R
0.25
0.30
0.35
0 R E E N R
0.25
0.30
0.35
0 R E E N R
0.05
0.100.150
PER
STE
TE STN
CAR
0.05
0.100.150
PER
STE
TE STN
CAR
0.05
0.100.150
PER
STE
TE STN
CAR
0.50 0.50 0.50 0.50Ma.sa.AGL2.1 Ma.sa.AGL2.2Ma.sa.AG.1 Ma.sa.AG.2
0.30
0.35
0.40
0.45
0.30
0.35
0.40
0.45
0.30
0.35
0.40
0.45
0.30
0.35
0.40
0.45
0 05
0.100.15
0.25
0
PER
STE TE STN
CA
R
0 05
0.100.15
0.25
0
PER
STE TE STN
CA
R
0 05
0.100.15
0.25
0
PER
STE TE STN
CA
R0 05
0.100.15
0.25
0
PER
STE TE STN
CA
R
0.05 0.05 0.05 0.05
Relative-quantitative RT-PCR
Ma.sa.AP1
PE STE TE ST CA
A class
qin M. salicifolia
Ma.sa.PI
Ma.sa.AP3
B classMa.sa.PI
Ma.sa.AG.1C class
Ma sa AGL2 1
Ma.sa.AG.2
C c ass
Ma.sa.AGL2.1
Ma.sa.AGL2.2
E class
ACTINE
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 SEPPI AP3
?
AP1 SEPCarpels
SEP AG
AGL2.1 AGL2.2
SepalsAG SEP ?
AP1 SEP
SEP AP1Ovules
SEP STK
? AP3
AGL2.2?SEP SHP
?
ConclusionThi t d t l t th t th• This study strongly suggests that the genetic control of sepal (sepaloid-tepal) and petal (tepal) identities in Magnolia are different from those in eudocots.different from those in eudocots.
• Candidate genes of sepaloid-tepal and t l id tit d li t d B ltepal identity are duplicated B class genes (PI and AP3) and E class genes (AGL2.1and AGL2.2) in Magnolia.
Further researchFurther research
• Dimer and tetramer formation of proteins of these genes using Y2H.g g
• Gene silencing experiments using VIGS systemsystem.
Ongoing projectsOngoing projects::
-- Proteomics:Proteomics: ProteinProtein--protein interaction of MADSprotein interaction of MADS--box box genes in genes in Amborella trichopodaAmborella trichopoda..gg pp
-- Genetics:Genetics: Phenotype recovery experiments using Phenotype recovery experiments using A bid iA bid i t t t dd f ti l h l i ft t t dd f ti l h l i fArabidopsis 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 introducingintroducing AmborellaAmborella genes intogenes into ArabidopsisArabidopsis ABCABCintroducing introducing AmborellaAmborella genes into genes into ArabidopsisArabidopsis ABC ABC mutants. mutants.
-- PhylogeneticsPhylogenetics:: Phylogenetic analyses of MADSPhylogenetic analyses of MADS--box genes box genes (about 3000 sequences) (about 3000 sequences)
-- Genomics:Genomics: AmborellaAmborella Genome project (genome + Genome project (genome + transcriptometranscriptome sequencing usingsequencing using NGS)NGS) MagnoliaMagnolia GenomeGenometranscriptometranscriptome sequencing using sequencing using NGS), NGS), MagnoliaMagnolia GenomeGenomeprojectproject
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
Many thanks to:Many thanks to:
Douglas SoltisS
-- 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 The Floral Genome Project Floral Genome Project groupgroupS hiS hi U i itU i it-- SungshinSungshin UniversityUniversity
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