EvoDevo
(2022) 13:5
Tong et al. EvoDevo
https://doi.org/10.1186/s13227-021-00189-8
Open Access
RESEARCH
Duplication and expression patterns
of CYCLOIDEA‑like genes in Campanulaceae
Jingjing Tong1, Eric B. Knox2, Clifford W. Morden3, Nico Cellinese4, Fatima Mossolem1, Aarij S. Zubair1 and
Dianella G. Howarth1*
Abstract
Background: CYCLOIDEA (CYC)-like transcription factors pattern floral symmetry in most angiosperms. In core eudicots, two duplications led to three clades of CYC-like genes: CYC1, CYC2, and CYC3, with orthologs of the CYC2 clade
restricting expression dorsally in bilaterally symmetrical flowers. Limited data from CYC3 suggest that they also play a
role in flower symmetry in some asterids. We examine the evolution of these genes in Campanulaceae, a group that
contains broad transitions between radial and bilateral floral symmetry and 180° resupination (turning upside-down
by twisting pedicle).
Results: We identify here all three paralogous CYC-like clades across Campanulaceae. Similar to other core eudicots,
we show that CamCYC2 duplicated near the time of the divergence of the bilaterally symmetrical and resupinate
Lobelioideae. However, in non-resupinate, bilaterally symmetrical Cyphioideae, CamCYC2 appears to have been lost
and CamCYC3 duplicated, suggesting a novel genetic basis for bilateral symmetry in Cyphioideae. We additionally,
utilized qRT-PCR to examine the correlation between CYC-like gene expression and shifts in flower morphology in
four species of Lobelioideae. As expected, CamCYC2 gene expression was dorsoventrally restricted in bilateral symmetrical flowers. However, because Lobelioideae have resupinate flowers, both CamCYC2A and CamCYC2B are highly
expressed in the finally positioned ventral petal lobes, corresponding to the adaxial side of the flower relative to
meristem orientation.
Conclusions: Our sequences across Campanulaceae of all three of these paralogous groups suggests that radially
symmetrical Campanuloideae duplicated CYC1, Lobelioideae duplicated CYC2 and lost CYC3 early in their divergence,
and that Cyphioideae lost CYC2 and duplicated CYC3. This suggests a dynamic pattern of duplication and loss of major
floral patterning genes in this group and highlights the first case of a loss of CYC2 in a bilaterally symmetrical group.
We illustrate here that CYC expression is conserved along the dorsoventral axis of the flower even as it turns upsidedown, suggesting that at least late CYC expression is not regulated by extrinsic factors such as gravity. We additionally show that while the pattern of dorsoventral expression of each paralog remains the same, CamCYC2A is more
dominant in species with shorter relative finally positioned dorsal lobes, and CamCYC2B is more dominant in species
with long dorsal lobes.
Keywords: Campanulaceae, CYCLOIDEA, Flower symmetry, Gene expression, Gene duplication, Lobelioideae,
Cyphioideae, Campanuloideae
Background
*Correspondence: howarthd@stjohns.edu
1
Department of Biological Sciences, St. John’s University, Jamaica, NY,
USA
Full list of author information is available at the end of the article
Campanulaceae diversity
Campanulaceae, the bellflower family, are a large core
eudicot group that encompasses roughly 2400 species
in 84 genera [1]. They are found on six continents and
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Tong et al. EvoDevo
(2022) 13:5
many oceanic islands and are distributed from the tropics
to the subarctic zones. There are at least three putative
synapomorphic characters shared in Campanulaceae:
laticifers, stamens attached to the disc of the ovary, and
epigynous flowers [1]. The group is also recognized for its
diversity in floral symmetry, resupination, and its pollination presentation mechanism.
The Campanulaceae are divided into five monophyletic subfamilies: Campanuloideae, Cyphioideae, Lobelioideae, Cyphocarpoideae, and Nemacladoideae [1].
Related groups to Campanulaceae are largely radially
symmetrical, including the entirely radially symmetrical
Rousseaceae. Campanuloideae have radially symmetrical flowers, while the other four clades have bilaterally
symmetrical flowers [1, 2]. Campanuloideae includes
approximately 1050 species in 50 genera. They are distributed worldwide, especially in temperate areas of the
Old World, with the major centers of diversity in the
Mediterranean Basin and the Middle East [1–3]. The
Lobelioideae encompass about 1200 species in 29 genera [1]. They are also distributed nearly worldwide, with
an origin in southern Africa [4], and a center of diversity
in the New World tropics with a predominantly South
American clade, “CBS (named for Centropogon, Burmeistera, and Siphocampylus),” containing roughly half
the extant species [1, 5, 6]. Most species in Lobelioideae
have resupinate (rotated 180° on the dorsoventral axis),
bilaterally symmetrical flowers, connate (fused) stamens
that form a staminal column tipped with an anther tube
that releases pollen to the interior, and styles with brush
hairs. The Lobelioideae exhibit a large diversification in
growth-form, from small, herbaceous plants, to shrubs,
to woody-rosette giant lobelias [7–10]. The Cyphioideae
include 64 + species that are restricted to tropical and
southern Africa. Cyphioideae and Campanuloideae are
sister-groups [11], and share a simple pollen deposition mechanism [2]. The other three subfamilies (Lobelioideae, Cyphocarpoideae, and Nemacladoideae) weakly
group together as a separate clade [2, 7, 11–13] The two
smallest subfamilies, Cyphocarpoideae and Nemacladoideae, with smaller ranges and 3 and 25 species respectively [1], were not sampled in this study.
Flower architecture and morphology
The symmetry of flowers is associated with their pollination, speciation, and diversification [14–16]. Floral
symmetry can be classified into two main types: radially
symmetrical (actinomorphic; polysymmetric), in which
the flower has two or more central axes of symmetry;
and bilaterally symmetrical (zygomorphic, monosymmetric), which have a flower with only one central axis
of symmetry [14, 17]. Most asterid species have an additional complexity of partial corolla fusion, forming a
Page 2 of 22
sympetalous corolla tube proximally, and distinct petal
lobes distally. Generally, bilaterally symmetrical flowers
have floral organs of three different sizes or shapes (especially in the corolla lobes): dorsal (adaxial), lateral, and
ventral (abaxial). In core eudicots, bilaterally symmetrical flowers most frequently have a corolla lobe arrangement of 2 dorsal lobes, 2 lateral lobes, and 1 ventral lobe
(2 + 3 form). Other common forms include (4 + 1) and
(0 + 5), with all of these types including a central ventral
lobe pointed downward while the other four lobes shift in
location [17].
The ancestral flower symmetry of Campanulaceae
remains equivocal given that Campanulaceae is divided
into a bilaterally symmetrical clade (Lobelioideae,
Cyphocarpoideae, and Nemacladoideae) and a clade
with both bilaterally (Cyphoideae) and radially (Campanuloideae) symmetric lineages. Ancestral state reconstruction suggests the ancestor may have had bilaterally
symmetrical flowers, with a reversal to radially symmetrical flowers in the Campanuloideae (Fig. 1A–D), [2],
but related outgroups are nearly all radially symmetrical
and the independent evolution of zygomorphy is equally
plausible. In the other major clade, Lobelioideae, almost
all species have resupinate flowers with (2 + 3) or (0 + 5)
final floral displays (Figs. 1E–I, 2), except in Monopsis
and two species of Downingia, in which flowers are not
resupinate (with reversal to resupination in M. decipiens)
[1, 18]. The remaining three subfamilies have non-resupinated flowers, with Cyphioideae (Fig. 1J, K) and Nemacladoideae having a (3 + 2) form, and Cyphocarpoideae
having a (1 + 4) form [1, 2]. The shift in this family in
both symmetry and resupination provide novel variation
to examine how genes affect plant organ orientation and
twisting of structures (Fig. 2).
Resupination in Lobelioideae occurs via the twisting
of the pedicle after floral buds have formed [19]. Here
we follow the terminology of Bukhari et al. [20] and use
adaxial/abaxial to refer to the floral meristem orientation
of the floral bud at developmental initiation, relative to
the stem and subtending bract. We use dorsal/ventral to
refer to the orientation of the final floral display (Fig. 2).
Therefore, in resupinate Lobelioideae species, their abaxial region is in the dorsal position at anthesis.
Genetic basis of floral symmetry
CYCLOIDEA (CYC) was the first characterized member
of the floral symmetry gene regulatory network with a
strong dorsal phenotypic effect, especially in the corolla
and androecium [21–26]. In Antirrhinum majus (snapdragon), CYC-like genes are necessary to establish the
dorsoventral axis in bilaterally symmetrical flowers [21].
CYC genes are members of the TCP gene family which
exhibit high levels of sequence conservation in their
Tong et al. EvoDevo
(2022) 13:5
Page 3 of 22
Fig. 1 Campanulaceae species. A–D Campanuloideae species, have radially symmetrical flowers. E–I Nearly all Lobelioideae species, have different
forms of resupinate, bilaterally symmetrical flowers. J and K Cyphioideae species, have bilaterally symmetrical flowers that are not resupinate. A
Campanula carpatica, B Asyneuma prenanthoides*, C Platycodon grandiflorus, D Campanula portenschlagiana, E Lobelia anceps, F Lithotoma axillaris,
G Lobelia siphilitica, H Lobelia erinus, I Lobelia polyphylla, J Cyphia longifolia**, K Cyphia longipetala**. *Photo right reserved to Marlin Harm. **Photo
right reserved to Eric Knox. Other photos taken by Jingjing Tong
TCP and R domains [27]. CYC, together with its paralog
DICHOTOMA (DICH), co-express in the dorsal domain
of the floral meristem from initiation and cause a reduction in growth of the corolla and stamens [28]. Cyc-dich
double mutants in A. majus form radially symmetrical,
ventralized flowers. Evidence from numerous comparative studies across flowering plants has shown that the
duplication of CYC-like genes is highly correlative with
the development of floral morphology in bilaterally symmetrical flowers [29–38]. Duplications or changes in the
location or level of gene expression of CYC-like genes is
highly associated with evolutionary shifts between radially symmetrical and bilaterally symmetrical flowers [39,
40].
Previous research has shown that two duplication
events near the time of the diversification of the core
eudicots produced three clades of CYC-like genes: CYC1,
CYC2 and CYC3 [41]. Originally characterized CYC and
DICH from A. majus are members of the CYC2 clade
and is widely involved in controlling bilateral symmetry across core eudicots [39, 41]. There are two or more
paralogs of CYC2 genes in nearly all characterized bilaterally symmetrical clades of core eudicots. In Asteraceae
and Dipsacaceae, some clades have capitate inflorescences, which contain both radially and bilaterally symmetrical flowers. In these groups, there are multiple
copies of CYC2 genes, and they appear to be differentially
expressed across the flowers of the inflorescence [29, 31–
38, 40]. Additionally, the dorsoventral gradient of CYC2
expression positively correlates with the level of bilateral
symmetry [40]. In Asteraceae, the over-expression of
CYC2 genes can result in radially symmetrical disc flowers shifting to be more bilaterally symmetric [37].
The two additional paralogs of CYC-like genes have
received less attention, although evidence indicates
that they are also involved in inflorescence and/or floral patterning. The CYC1 genes have not been shown
to be directly involved in floral development, but CYC1
genes may be responsible for plant or inflorescence
branching architecture in Arabidopsis, Populus, and
Asteraceae [37, 42–44]. The function of CYC3 genes are
still unclear in floral development [44]; however, based
Tong et al. EvoDevo
(2022) 13:5
Page 4 of 22
Fig. 2 Lobelioideae flowers. A Lobelia erinus flower, B L. erinus floral buds in different stages. C Lobelia polyphylla large flower bud at the late
development stage with removed bract. Asterisk marks location of latex exuding from removal of abaxial bract. Lobelioideae have resupinate
flowers with the entire bud turning 180-degrees during development, resulting in the adaxial floral meristem region being the ventral region, and
the abaxial floral meristem region being the dorsal region when the flower is mature. During floral bud growth, pedicels turn around at a relatively
early stage of bud development and are completely turned 180-degrees upside-down by later stages of bud development. White dots show the
location of the twist in the pedicels. Photos taken by Jingjing Tong
on gene expression data from Dipsacales and Asterales,
CYC3 genes may play a role in symmetry, at least in the
campanulid (asterid II) clade [40, 45].
Given the resupinate flowers of the Lobelioideae, as
well as the shifts in symmetry in the Campanulaceae
sensu lato, we aimed to examine the evolutionary history of the Campanulaceae CYC-like (CamCYC-like)
genes. We sampled CamCYC from Campanuloideae,
Lobelioideae, and Cyphioideae species (Table 1) and
compared them to molecular phylogenetic results for
Campanulaceae [3, 7, 46]. The main aims in this study
were to pinpoint the duplication events of CamCYC
-like genes across Campanulaceae and use qRT-PCR to
investigate the expression of CamCYC2 genes in Lobelioideae species with resupinate, bilaterally symmetrical flowers. We examined expression in four species
with different forms of bilateral symmetry and relative
lobe lengths. CamCYC2A and CamCYC2B are highly
expressed in the finally positioned ventral lobes (the
adaxial side of the flower), suggesting conservation of
dorsal identity in upside-down flowers. Additionally,
individual copies of CamCYC2 genes show different
expression levels in different lobes, suggesting possible
subfunctionalization between these copies.
Results
CamCYC1, CamCYC2, and CamCYC3 from Campanulaceae
Sequencing the TCP through R domains, we isolated
CamCYC1 from 83 Lobelioideae species, eight Campanuloideae species, and seven Cyphioideae species;
CamCYC2 from 90 Lobelioideae species and four Campanuloideae species; and CamCYC3 from five Lobelioideae species, three Campanuloideae species, and eight
Cyphioideae species. There were no CamCYC2 gene
sequences isolated from Cyphioideae. The tree topologies
across the CamCYC1, CamCYC2, and CamCYC3 clades
were generally congruent with the estimated species phylogenies in these groups, especially in the best-sampled
Lobelioideae. All three subfamilies were monophyletic and were consistent with a sister group relationship
between Campanuloideae and Cyphioideae (Figs. 3, 4,
and 5).
The CamCYC1 sequence matrix was 492 bps long
with 140 sequences, which included 12 sequences from
Campanuloideae and nine sequences from Cyphioideae.
Using midpoint rooting, Campanuloideae and Cyphioideae grouped in one clade, sister to the remaining
119 sequences, all isolated from 83 Lobelioideae species
(Fig. 3). Our data support a duplication in CamCYC1
Tong et al. EvoDevo
(2022) 13:5
Page 5 of 22
Table 1 Campanulaceae species used in this study, including Genbank numbers for each sequenced gene/allele in each CYC gene
clade
Clade
Label
Genus
Species
CYC1
CYC2B
Campanuloideae
JC002(JT)
Campanula
carpatica
OM262907
OM263037
Campanuloideae
JC008(JT)
Campanula
cochleariifolia
OM262908
OM262909
Campanuloideae
3195(NC)
Campanula
drabifolia
Campanuloideae
JC006(JT)
Campanula
glomerata
CYC2A
CYC3
OM263196
OM263198
OM262910
OM263038
OM263039
Campanuloideae
CP011(JT)
Platycodon
grandiflorus
OM262918
Campanuloideae
CJ009(JT)
Jasione
montana
OM262915
Campanuloideae
CJ001(JT)
Campanula
persicifolia
OM262911
OM262912
Campanuloideae
JC007(JT)
Campanula
portenschlagiana
OM262913
OM262914
Campanuloideae
CP012(JT)
Phyteuma
scheuchzeri
OM262916
OM262917
Cyphioideae
K4686
Cyphia
comptonii
OM262919
OM263203
OM263209
Cyphioideae
P5532
Cyphia
digitata
OM262920
OM263199
OM263200
Cyphioideae
K4725
Cyphia
eckloniana
OM262921
OM263207
Cyphioideae
K2340
Cyphia
lasiandra
OM262922
OM263210
Cyphioideae
K4734
Cyphia
longipetala
OM262924
OM263201
OM263204
Cyphioideae
P5461
Cyphia
rogersii
OM262925
OM263208
Cyphioideae
K4831
Cyphia
smutsii
Cyphioideae
P5555
Cyphia
sp. nov
OM262923
OM263202
OM263205
Cyphioideae
K4726
Cyphia
volubilis
OM262926
OM263212
Cyphioideae
K4675
Cyphia
zeyheriana
OM262927
OM263206
Genistoid E
K4216
Lobelia
baumannii
OM262958
Genistoid E
K4942
Lobelia
comptonii
OM262965
Genistoid E
K4773
Lobelia
dasyphylla
OM262969
Genistoid E
K4314
Lobelia
goetzei
OM262973
OM263154
OM263066
Genistoid E
K3316
Lobelia
hartlaubii
OM262976
OM263114
OM263067
Genistoid E
K4814
Lobelia
malowensis
OM262987
OM263159
OM263070
Genistoid E
K4609
Lobelia
patula
OM262991
OM263075
OM263076
Genistoid E
P5475
Lobelia
pteropoda
OM262992
Genistoid E
K4634
Lobelia
tomentosa
OM263010
Genistoid E
K4654
Lobelia
vanreenensis
OM263014
Impares F
K5251
Lobelia
cleistogamoides
OM262962
OM262963
OM263215
Impares F
K5245A
Lobelia
heterophylla
OM262964
OM263213
OM263214
Impares F
K5210
Colensoa
physaloides
OM262935
OM262936
OM263218
Impares F
K5242
Lobelia
rarifolia
OM262994
OM262995
OM263080
Impares F
K5259
Lobelia
rhombifolia
OM262996
OM262997
OM263081
Impares F
K5253
Lobelia
rhytidosperma
OM262998
Impares F
K5279
Lobelia
simplicicaulis
OM263000
OM263002
Impares F
K5234
Lobelia
tenuior
OM263007
OM263197
OM263036
OM263211
Lobelioideae
OM263140
OM263055
OM263061
OM263063
OM263079
OM263177
OM263094
OM263084
OM263172
OM263087
OM263216
Tong et al. EvoDevo
(2022) 13:5
Page 6 of 22
Table 1 (continued)
Clade
Label
Genus
Species
CYC1
Impares F
A10185
Lobelia
trigonocaulis
OM263011
Impares F
K5252
Lobelia
winifrediae
Monopsis G
K4628
Monopsis
alba
OM263023
Monopsis G
K4790
Monopsis
debilis
OM263025
Monopsis G
K4646
Monopsis
decipiens
OM263024
Monopsis G
K5116
Monopsis
flava
OM263026
Monopsis G
K4402
Monopsis
stellarioides
OM263027
Monopsis G
P5246
Monopsis
unidentata
OM263028
Broom H
P5621
Lobelia
lasiantha
OM262978
Broom H
K4599
Lobelia
linearis
OM262980
Grammatotheca I
K4642
Lobelia
thermalis
Erinoid L
K4951
Lobelia
boivinii
Erinoid L
K3475
Lobelia
cymbalarioides
OM262968
Erinoid L
JL002(JT)
Lobelia
erinus
OM262970
Erinoid L
K4964
Lobelia
inconspicua
Erinoid L
K3401
Lobelia
minutula
OM262988
Erinoid L
K4841
Lobelia
wilmsiana
OM263017
Wimmerella M
K5276
Lobelia
anceps
CYC2B
CYC2A
CYC3
OM263091
OM263217
OM263082
OM263083
OM263108
OM263107
OM263104
OM263109
OM263105
OM263106
OM263089
OM263057
OM263062
OM263152
OM263065
OM263068
OM263073
OM263090
OM263137
Wimmerella M
K4685
Wimmerella
bifida
OM263035
OM263192
Wimmerella M
K4594
Wimmerella
hederacea
OM263033
OM263193
OM263097
Wimmerella M
K4545
Wimmerella
pygmaea
OM263034
OM263194
OM263101
Wimmerella M
K5104
Wimmerella
secunda
OM263195
OM263102
Mezlerioid3 N
K5182
Lobelia
jasionoides
OM262977
OM263155
Mezlerioid3 N
K4566
Lobelia
laurentioides
OM262979
OM263157
Mezlerioid3 N
K4589
Lobelia
muscoides
OM262989
OM263161
Solenopsis O
Gr04/1
Lobelia
urens
W North America P
K4663
Downingia
bicornuta
OM262948
W North America P
UCBG770105
Palmerella
debilis
OM262946
W North America P
K4667
Porterella
carnosula
OM262947
Diastatea Q
Wo8295
Diastatea
E North America R
Jl007(JT)
E North America R
K5282
OM263180
OM263092
OM263098
OM263115
OM263099
micrantha
OM263110
OM263111
OM263050
Lobelia
cardinalis
OM263146
OM263060
Lobelia
dortmanna
OM263151
E North America R
K2408
Lobelia
fenestralis
E North America R
K5092
Lobelia
puberula
OM262949
OM263112
E North America R
JL003(JT)
Lobelia
siphilitica
South America S
Ra s.n.2
Burmeistera
crispiloba
OM262930
OM262931
South America S
Lu15078
Centropogon
comosus
OM262932
OM262933
OM263119
OM263043
South America S
JL005(JT)
Lobelia
bridgesii
OM262960
OM262961
OM263143
OM263058
South America S
JL006(JT)
Lobelia
polyphylla
OM263164
OM263165
OM263078
South America S
JL004(JT)
Lobelia
tupa
OM263113
OM263173
OM263012
OM263013
OM263088
OM263042
OM263178
OM263179
Australasia T
RBGK2368
Hypsela
Reniformis
OM262942
OM263129
Australasia T
A9820
Isotoma
gulliveri
OM262944
OM262945
OM263132
Australasia T
K5237
Isotoma
hypocrateriformis
OM262943
OM263133
OM263134
Tong et al. EvoDevo
(2022) 13:5
Page 7 of 22
Table 1 (continued)
Clade
Label
Genus
Species
CYC1
CYC2B
CYC2A
Australasia T
LI010(JT)
Lithotoma
axillaris
Australasia T
W5440
Lithotoma
petraea
OM262954
OM263130
OM263051
OM263131
Australasia T
K5024A
Lobelia
macrodon
OM263052
OM262985
OM263072
Australasia T
Ck2245
Lobelia
OM263071
pratioides
OM262993
OM263166
Australasia T
K5027
OM263077
Lobelia
roughii
OM262999
OM263167
Australasia T
K2369
OM263085
Pratia
arenaria
OM262950
OM262951
OM263187
Australasia T
W5265
Pratia
gelida
OM262952
OM263188
Australasia T
A5357
Pratia
pedunculata
OM262953
OM263189
Giants U
NTBG970260
Apetahia
longistigmata
OM262928
OM262929
OM263116
OM263117
Giants U
4561(CM)
Brighamia
insignis
OM262905
OM262906
OM263118
OM263040
OM263041
Giants U
6799(CM)
Clermontia
micrantha
OM263120
OM263044
Giants U
7011 (CM)
Clermontia
persicifolia
OM262934
OM263121
OM263045
Giants U
1754(CM)
Cyanea
acuminata
OM262937
OM262938
OM263122
OM263046
Giants U
K2375
Cyanea
leptostegia
OM262939
OM262940
Giants U
2452(CM)
Cyanea
superba
OM262941
OM263123
OM263124
Giants U
5416(CM)
Delissea
rhytidosperma
OM262896
OM262897
OM262903
OM262904
OM263125
OM263126
OM263047
OM263048
Giants U
3835(CM)
Delissea
subcordata
OM262901
OM262902
OM263127
OM263128
OM263049
Giants U
K706
Lobelia
aberdarica
OM262955
OM262956
OM263135
OM263136
OM263053
Giants U
K731
Lobelia
bambuseti
OM263138
OM263139
OM263054
Giants U
K220
Lobelia
bequaertii
OM263141
OM263142
OM263056
Giants U
K802
Lobelia
burttii
OM263144
OM263145
OM263059
Giants U
M2085
Lobelia
columnaris
OM262966
OM262967
OM263147
OM263148
Giants U
K2353
Lobelia
doniana
OM262900
OM263149
OM263150
Giants U
K118
Lobelia
giberroa
OM262971
OM262972
OM263153
Giants U
K698
Lobelia
gregoriana
OM262974
OM262975
Giants U
K2381
Lobelia
kauaensis
OM262898
OM262899
Giants U
K3522
Lobelia
longisepala
OM262981
Giants U
K623
Lobelia
lukwangulensis
OM262982
OM262983
OM262984
OM262957
OM262959
Giants U
K426
Lobelia
mildbraedii
Giants U
K619
Lobelia
morogoroensis
OM262986
Giants U
NTBG910521
Lobelia
niihauensis
OM262990
Giants U
7162(CM)
Lobelia
oahuensis
OM263100
OM263064
OM263156
OM263069
OM263096
OM263158
OM263093
OM263160
OM263074
OM263162
OM263163
CYC3
Tong et al. EvoDevo
(2022) 13:5
Page 8 of 22
Table 1 (continued)
Clade
Label
Genus
Species
CYC1
CYC2B
CYC2A
Giants U
K610
Lobelia
sancta
OM263001
OM263168
OM263169
OM263086
Giants U
RBGK5627
Lobelia
sessilifolia
Giants U
K120
Lobelia
stuhlmannii
OM263003
OM263004
Giants U
K689
Lobelia
telekii
OM263005
OM263006
Giants U
K876
Lobelia
thuliniana
OM263008
OM263009
OM263175
OM263176
Giants U
4097(CM)
Lobelia
villosa
OM263015
OM263015
OM263022
OM263181
OM263182
Giants U
K262
Lobelia
wollastonii
OM263018
OM263019
OM263183
OM263184
Giants U
K2379
Lobelia
yuccoides
OM263020
OM263021
OM263185
OM263186
Giants U
4887(CM)
Trematolobelia
kauaiensis
OM263029
OM263031
Giants U
4764(CM)
Trematolobelia
macrostachys
OM263030
OM263032
CYC3
OM263170
OM263171
OM263174
OM263190
OM263191
OM263095
OM263103
Included a total of 132 DNA samples, from 128 species, including 9 Cyphioideae species, 9 Campanuloideae species, and 110 Lobelioideae species
(JT = Jingjing Tong, NC = Nico Cellinese, CM = Clifford Morden, all other samples provided by Eric Knox) [75, 76]
within the Campanuloideae that is not shared with the
other subfamilies (ML bootstrap = 100), with Campanula cochlearifolia, C. persicifolia, C. portenschlagiana,
and Phyteuma scheuchzeri occurring in both clades.
Cyphioideae CamCYC1 sequences form a single clade,
although multiple CamCYC1 gene sequences were isolated from most Cyphioideae samples, likely due to allelic
diversity.
Lobelioideae CamCYC1 formed a single clade with no
broad duplication detected across Lobelioideae. Species
distribution in Lobelioideae CamCYC1 subclades are
congruent with previously published Lobelioideae phylogenetic relationships [7, 10, 46, 47]. Clade names and
letter designations used are from [7, 10, 46, 47] and Knox
(unpublished data), with Genistoid (E) and Impares (F)
subclades forming a clade sister to the remaining samples. The Impares (F) subclade appears to have duplicated
CamCYC1 (ML bootstrap = 92) with 5 out of 10 sampled species (Lobelia cleistogamoides, L. simplicicaulis,
L. rhombifolia, L. rarifolia, and Colensoa physaloides)
yielding two highly differentiated copies. The U subclade, often called the giant lobelias, in some cases yield
three highly differentiated sequence copies. The duplicated copies in the U2-A and U2-B subclades are possibly a result of this group being ancient tetraploids [48,
49]. There is no obvious explanation for the copies that
comprise the U1 subclade, which is weakly embedded in
a clade with members of the P, R, S, and T subclades.
The CamCYC2 matrix was 363 bps long with 160
sequences, which included 156 sequences from Lobelioideae and only four sequences isolated from Campanuloideae (Fig. 4). No CamCYC2 sequences were obtained
from any Cyphioideae species despite targeted amplification. In the CamCYC2 gene tree (Fig. 4), sequences
from Lobelioideae species formed two clades, both of
which were broadly congruent with the hypothesized
species relationships: CamCYC2A (ML bootstrap = 92)
and CamCYC2B (ML bootstrap = 90). Species relationships in both Lobelioideae CamCYC2 clades shared a
similar pattern and also corresponded with the CamCYC1 tree. In the CamCYC2 tree, sequences from 43
Lobelioideae species were found in both CamCYC2A
and CamCYC2B clades. There were separate duplications
into two U subclades in each of the CamCYC2 paralogs.
Our data indicate that CamCYC2 genes have duplicated
in the Lobelioideae, a duplication that does not appear
to be shared with the CamCYC2-like genes isolated from
Campanuloideae.
The CamCYC3 gene tree included species from all
three sampled subfamilies (Fig. 5). The CamCYC3
matrix was 329 bps long with 23 sequences, including
three sequences from Campanuloideae, 14 sequences
from Cyphioideae, and six sequences from Lobelioideae.
Fewer CamCYC3 sequences were recovered compared
to the other CamCYC genes. The three Campanuloideae
sequences formed a clade. Sequences from Cyphioideae
Tong et al. EvoDevo
(2022) 13:5
Page 9 of 22
Fig. 3 CamCYC1 RAxML phylogenetic tree. Campanuloideae and Cyphioideae group into one clade, sister to Lobelioideae. The CamCYC1 gene
duplicated broadly within Campanuloideae, which is not shared with the other two subfamilies. Lobelioideae CamCYC1 sequences are congruent
with previously published Lobelioideae phylogenies [7, 10, 46, 47], with letter designations provided by Knox (unpublished). ML bootstrap values
provided. Closed circles indicate hypothesized duplication
(See figure on next page.)
Fig. 4 CamCYC2 RAxML phylogenetic tree. The CamCYC2 tree only includes sequences isolated from Lobelioideae and Campanuloideae,
with no CamCYC2 genes found in Cyphioideae. In Lobelioideae there is a clear duplication across the entire clade, which is not shared with
Campanuloideae. The species relationship patterns are congruent between the two Lobelioideae subclades. The U clade includes multiple
duplicate lineages in both CamCYC2 paralogs. ML bootstrap values provided. Closed circles indicate hypothesized duplication
Tong et al. EvoDevo
(2022) 13:5
Fig. 4 (See legend on previous page.)
Page 10 of 22
Tong et al. EvoDevo
(2022) 13:5
Page 11 of 22
Fig. 5 CamCYC3 RAxML phylogenetic tree. ML bootstrap values provided. Closed circles indicate hypothesized duplication. Campanuloideae and
Cyphioideae form a clade sister to Lobelioideae. A duplication is suggested in Cyphioideae. In Lobelioideae, only the F clade was recovered and is
potentially lost from other lineages
grouped into two clades, and sequences from three species (Cyphia longipetala, C. sp. nov., and C. comptonii) in
both clades suggests that CamCYC3 duplicated sometime during the evolution of Cyphia. The very limited
recovery of CamCYC3 sequences from the Lobelioideae
suggests that this gene has been lost in the subfamily
except for the Impares (F) clade.
Expression of CamCYC2 genes in Lobelioideae species
CamCYC2A and CamCYC2B expression levels were
assayed with qRT-PCR across four Lobelioideae species with different floral morphologies, Lobelia erinus
(Africa), Lo. siphilitica (North America), Lithotoma
axillaris (Australia), and Lo. polyphylla (South America). All four species have typical resupinate Lobeliaceae flowers with a final display having a medial
ventral petal lobe (Fig. 6), and all expression patterns
are described using dorsal and ventral position of that
final display. The overall expression patterns were
broadly similar across all four species (Fig. 6A-I, B-I,
C-I, D-I), although, the expression levels between the
two paralogs varied. In all species, CamCYC2A and
CamCYC2B are strongly expressed in flowers and not
leaves, and in most cases the expression levels were
not statistically significant across flower bud stages. In
the dorsal, lateral, and ventral corolla-lobe dissections
across all four species, both CamCYC2A and CamCYC2B were highly expressed in the ventral region
(adaxial initiation), and only minimally expressed in
the dorsal region (abaxial initiation). CamCYC2A was
expressed similarly in lateral and ventral lobes and
significantly reduced in dorsal lobes. CamCYC2B was
expressed in a gradient, with the highest expression in
the ventral lobe, medium expression in lateral lobes,
and lowest expression in dorsal lobes. This pattern was
consistent among all four species, but which paralog
predominated varied among species (Fig. 6A-II, B-II,
C-II, D-II).
Lobelia erinus has resupinate flowers with the smallest size ratio of dorsal to lateral and ventral corolla lobes,
with the lateral and ventral lobes similar in size, and the
dorsal lobes about 15–20% as large (Figs. 2A, 6). CamCYC2 genes are highly expressed in the lateral and ventral lobes (adaxial initiation) and have extremely low
expression in the dorsal lobes (abaxial initiation; Fig. 6AII). CamCYC2A is highly expressed in lateral and ventral
lobes at similar levels (p = 0.762). By contrast, the dorsal lobe expression is significantly lower (dorsal/lateral
p = 0.0017; dorsal/ventral p = 0.0002). CamCYC2B shows
a dorsoventral gradient of expression, being most highly
Tong et al. EvoDevo
(2022) 13:5
A-I
0.12
a
0.11
Page 12 of 22
B-I
C-I
0.05
0.1
a
0.1
a
0.04
0.07
a
0.02
0.05
0.03
0.02
a
a
0.01
a
Large Medium Small Leaf
bud bud
bud
B-II
0.2
0.19
0.18
0.17
0.16
0.15
0.14
0.13
0.12
0.11
0.1
0.09
0.08
0.07
0.06
0.05
0.04
0.03
0.02
0.01
0
0.12
b
b
0.02
Leaf
0.11
b
b
0.08
0.07
0.06
0.05
c
0.04
0.03
b
c
Dorsal Lateral Ventral Leaf
a
0.02
0.01
0
0
b
0.03
a/b
0.02
0.01
Large Medium Small
bud bud
bud
a a
b
Dorsal Lateral Ventral Leaf
CamCYC2A
0.25
0.24
0.23
0.22
0.21
0.2
0.19
0.18
0.17
0.16
0.15
0.14
0.13
0.12
0.11
0.1
0.09
0.08
0.07
0.06
0.05
0.04
0.03
0.02
0.01
0
b
0.04
Leaf
C-II
0.09
a
0.05
0.03
a
a
0.06
a
0.04
Large Medium Small
bud bud
bud
0.1
a
0.07
0.01
A-II
0.08
0.06
a
0.01
0
0.09
a/b
0.05
a
0.04
0
a
0.1
0.07
a
a
0.11
0.08
0.03
0.06
0.12
b
0.09
0.09
0.08
D-I
0
a
b
a
Large Medium Small
bud bud
bud
Leaf
D-II
c
c
0.5
0.4
0.3
b
b
bb
0.2
b
a a
Dorsal Lateral Ventral Leaf
b
0.1
0
a a
Dorsal Lateral Ventral Leaf
CamCYC2B
Fig. 6 Relative expression levels of CamCYC2A (blue) and CamCYC2B (orange) genes in Lobelioideae species. A Lobelia erinus, B Lobelia siphilitica,
C Lithotoma axillaris, D Lobelia polyphylla. A-I, B-I, C-I, D-I show CamCYC2 genes in different floral bud stages, both CamCYC2 genes are expressed
through the whole floral growth stage; A-II, B-II, C-II, D-II show CamCYC2 genes in different corolla lobes from medium buds. CamCYC2A is highly
expressed in the ventral and lateral lobes, exhibiting lower expression in dorsal lobes; CamCYC2B is highly expressed in the ventral lobe, exhibiting
intermediate expression in lateral lobes and low expression in dorsal lobes. Lines of the Y-axis are labeled with the same scale across all diagrams
except (D-II). Y-axis is the relative expression level, normalized to CamACTIN as the reference gene. Levels of expression of a single paralog with
statistically significant differences (p ≤ 0.05) across different tissues are indicated by separate letters, a, b, or c. All species resupinate at maturity
expressed in the ventral lobe, moderately expressed in
the lateral lobes, and only minimally expressed in the
dorsal lobes. The expression of CamCYC2B was significantly different in the three corolla lobe types (dorsal/
lateral p = 0.006; dorsal/ventral p = 0.0008; and lateral/
ventral p = 0.0031). Dorsal lobe expression in both CamCYC2A and CamCYC2B was similar to leaf expression.
Temporally, CamCYC2A and CamCYC2B genes express
in very early stages of flower development, and steadily
express through bud growth stages, with no significant
differences in expression levels in either gene (Fig. 6AI). Comparing the two paralogs, CamCYC2A is much
more highly expressed than CamCYC2B in floral tissue
and flower buds in Lo. erinus. For instance, CamCYC2A
expression is roughly 15 times higher than that of CamCYC2B in the ventral lobe (Fig. 6A-II).
Lobelia siphilitica has resupinate flowers with relatively
large dorsal lobes compared with Lo. erinus, and dorsal
lobes are about 40% the size of lateral and ventral lobes
(Figs. 1G, 6). The expression patterns of CamCYC2A
Tong et al. EvoDevo
(2022) 13:5
and CamCYC2B are similar to that of Lo. erinus. In Lo.
siphilitica, CamCYC2A is highly expressed in a similar
level in lateral and ventral lobes (p = 0.6438), and barely
expressed in dorsal lobes (dorsal/lateral p = 0.0025 and
dorsal/ventral p = 0.0032 (Fig. 6B-II). CamCYC2B is
expressed most highly in the ventral lobe, intermediately
in the lateral lobes, and extremely minimally in the dorsal
lobes (dorsal/lateral p = 0.0009, dorsal/ventral p = 0.0004,
and lateral/ventral p = 0.0029) (Fig. 6B-II). Temporally,
CamCYC2A and CamCYC2B genes express in very
early stages of flower development, and steadily express
through bud growth stages, with no significant differences in expression levels in either gene (Fig. 6B-I). Similar to in Lo. erinus, CamCYC2A is more highly expressed
than CamCYC2B in floral tissue and flower buds in Lo.
siphilitica, but, with less of a differential between the
paralogs. For instance, CamCYC2A expression is only
roughly two times greater in the ventral lobe than that of
CamCYC2B (Fig. 6B-II).
All five corolla lobes of resupinate Lithotoma axillaris flowers have similar size and shape, but the orientation of the staminal column (with filaments adnate to
the fully connate corolla tube, which lacks the dorsal
slit to the base typical of Lobelia) makes these flowers
bilaterally symmetrical (Figs. 1F, 6). CamCYC2A and
CamCYC2B have much higher expression in lateral and
ventral lobes and are barely expressed in dorsal lobes,
with overall expression patterns similar to Lo. erinus and
Lo. siphilitica (Fig. 6C-II). CamCYC2A is significantly
less expressed in dorsal lobes than lateral (p = 0.0163)
and ventral (p = 0.0015) lobes, with similar expression
between dorsal and lateral lobes (p = 0.5634). In CamCYC2B each lobe type has significantly different expression along a gradient as in the other species, with ventral/
lateral (p = 0.0139), ventral/dorsal (p = 0.0012), and lateral/dorsal (p = 0.0016). Temporally, both paralogs are
expressed early and continued to be expressed through
development but with a statistically significant decrease
in expression in large buds (Fig. 6C-I). In CamCYC2A
the difference in expression in large bud versus medium
bud is statistically significant (p = 0.0136), while other
comparisons are not (large bud/small bud p = 0.1508 and
medium bud/small bud p = 0.2016). CamCYC2A is consistently expressed through the bud development, with
only a slight up-regulation in the medium buds. CamCYC2B expression peaks in the medium buds, and then
decreases in large buds (p = 0.0021). A major difference
in expression between Li. axillaris and previously discussed Lobelia species is that CamCYC2B is more highly
expressed overall, compared to CamCYC2A in floral buds
and corolla lobes (more than 7 times greater in ventral
lobes). Therefore, the overall expression patterns among
Page 13 of 22
lobe types are the same across species, but the gene copy
that is the most highly expressed flips.
Lobelia polyphylla has resupinate flowers with dorsal,
lateral, and ventral lobes that are similar in size and shape,
with the dorsal lobes slightly longer than the lateral and
ventral lobes (Figs. 1I; 6). Additionally, all five lobes bend
downward and away from the staminal column (toward
the finally positioned ventral region in these resupinate
flowers). CamCYC2A and CamCYC2B have significantly
higher expression in lateral and ventral lobes and are
barely expressed in dorsal lobes, with expression patterns
similar to Lithotoma axillaris (Fig. 6D-II). CamCYC2A
is expressed significantly less in dorsal lobes than lateral
(p = 0.0079) and ventral (p = 0.0002) lobes, with similar
expression between dorsal and lateral lobes (p = 0.5783).
In CamCYC2B there is a dorsoventral gradient of expression, highest in ventral corolla lobes, with each lobe type
having significantly different expression between dorsal/
lateral (p = 0.0161), dorsal/ventral (p = 0.0011), and lateral/ventral (p = 0.0099) lobes. Temporally, both paralogs are expressed early and continue to be expressed
through development, but with a statistically significant
decrease in expression in large buds in only CamCYC2A
(Fig. 6D-I). In CamCYC2A, expression in large buds is
significantly less than that of small buds (p = 0.0004) or
medium buds (p = 0.0042). In Lo. polyphylla CamCYC2B
is more highly expressed than CamCYC2A, similar to
the pattern observed in Li. axillaris, with CamCYC2B
roughly 3.5 times more highly expressed than CamCYC2A in the ventral lobe.
Discussion
The three subfamilies of Campanulaceae sampled in this
study have distinctly different floral symmetry modifications with radially symmetrical flowers in Campanuloideae, non-resupinate bilaterally symmetric flowers in
Cyphioideae, and bilaterally symmetric flowers that are
predominately 180° resupinate in Lobelioideae [1, 2, 7].
In these three groups, we uncovered broad gene duplications and losses that correlate with these morphological
shifts. We detected all three core eudicot CYC-like genes
from the CYC1, CYC2, and CYC3 clades [41]. CamCYC1 was thoroughly sampled from all three subfamilies, while CamCYC2 was likely lost in Cyphioideae and
CamCYC3 was likely lost from all except the Impares (F)
subclade of Lobelioideae (which along with the Genistoid
(E) subclade is sister to the rest of the subfamily; Knox
2014). Additionally, we found evidence for subfamily
duplications—CamCYC1 duplicated in Campanuloideae,
CamCYC2 duplicated in Lobelioideae, and CamCYC3
duplicated in Cyphioideae (Fig. 7).
Tong et al. EvoDevo
(2022) 13:5
Page 14 of 22
Fig. 7 Summary CYC-like duplication events across Campanulaceae. CamCYC1 duplicated in Campanuloideae and might have narrower
duplications in the F and U clades in Lobelioideae. CamCYC2 showed a clear duplication event specific to Lobelioideae and an apparent loss in
Cyphioideae. CamCYC3 duplicated in Cyphioideae and is apparently lost in all but one clade of Lobelioideae. CamCYC3 might play a key role in
bilateral symmetry instead of CYC2-like genes in Cyphioideae. Blue dots indicate hypothesized location of broadly duplicated clades
CamCYC1 duplicated in the radially symmetric
Campanuloideae
CamCYC2—the Campanulaceae member of CYC2,
which is a clade that has shown functional conservation in patterning floral bilaterally symmetry [28, 30,
41, 50, 51]—was present across the radially symmetrical
Campanuloideae, from four species that span the major
clades of the group (Fig. 3). There was no evidence for
duplications in CamCYC2, which is consistent with
other radially symmetrical groups [39, 41]. Additionally,
Campanuloideae CamCYC2 copies had high sequence
diversity, being on very long branches, and were therefore difficult to align with Lobelioideae species (Fig. 4). In
other lineages with both radially symmetrical and bilaterally symmetrical flowers, such as Fabales, Malpighiales,
and Dipsacales, species with radially symmetrical flowers have CYC2-like genes expressed uniformly across the
whole corolla or have lost floral expression entirely [36,
38, 40, 52–58].
CamCYC3 was also found in Campanuloideae, but only
in the C2 clade [3] and also on a long branch compared to
Cyphioideae and Lobelioideae sequences (Fig. 5). CYC3
has been shown to be involved in axillary bud outgrowth
[44] and in floral symmetry [40], but with variable function in different plant groups.
The Campanuloideae show the most diversification
in CamCYC1 genes, with a duplication possibly shared
across the Campanuloideae clade (Figs. 3, 7). With only
minor differences, these duplicate gene trees agree with
the estimated Campanuloideae species phylogeny [2, 3].
Studies in plant groups across core eudicots suggest that
CYC1 genes are functionally conserved, regulating the
number and position of axillary bud development [42–
44], as well as inflorescence architecture and development [37]. Loss-of-function mutants in Arabidopsis and
Populus lead to a marked increase in bud outgrowth and
plant branching [42–44]. It is possible that the duplication of CamCYC1 set the stage for the variation in plant
and inflorescence architecture in Campanuloideae. Flowers vary from solitary to complex inflorescences such as
capitulate heads [1]. Broad duplications in CYC1 are less
common than in the other CYCclades, although they are
consistently duplicated in lineages known for capitulate
heads such as in the Asteraceae [31, 45], Dipsacaceae
[59], and Actinodium [35].
Cyphioideae have lost CamCYC2 and duplicated CamCYC3
Cyphioideae typically have non-resupinate bilaterally
symmetrical flowers with a 3 + 2 form, with one dorsal lobe, two lateral lobes, and two ventral lobes. In all
other core eudicot bilateral symmetrical lineages studied to date, CYC2 is differentially expressed across the
dorsoventral axis and functions to pattern that bilateral
symmetry [39]. Occasionally, CYC2 genes appear to lose
floral expression or be lost from the genome of certain
species, however, these are always marked by shifts to
radial symmetry [53, 54, 56, 57]. Additionally, in almost
all cases, CYC2 genes are duplicated in bilaterally symmetrical lineages [39, 41]. Here we report the first case
of an apparent loss of CYC2 in a bilaterally symmetrical core eudicot group, Cyphioideae (Fig. 7). Sampling
nine species with multiple primer sets, no CamCYC2
Tong et al. EvoDevo
(2022) 13:5
sequences were found, despite easily recovering them
from Campanuloideae and Lobelioideae.
Along with a likely loss of CYC2 in Cyphioideae, CamCYC3 appears to be duplicated in this lineage (Figs. 5, 7).
This is in stark contrast to Lobelioideae, which appear
to have lost CamCYC3 in all but the Impares (F) clade,
with no evidence of gene duplication. CYC3 is the most
understudied paralog across core eudicots and also
appears to be the most variable in function. CYC3 genes
are duplicated in some groups such as Dipsacales and
Asteraceae [45, 59, 60], but have been likely lost in others such as Leguminosae and Gesneriaceae [61, 62]. In
Arabidopsis (Brassicaceae) and Populus (Salicaceae),
CYC1 (Branched1) and CYC3 (Branched2) orthologs
have redundant function in regulating bud outgrowth
[44, 63] with an increase in branching in loss-of-function mutants. Interestingly, branched1 had the stronger
phenotype in Arabidopsis [44] and branched2 had the
stronger phenotype in Populus [63]. Although CYC3
gene function in floral symmetry has not previously been
shown, studies in Dipsacales and Asteraceae reported
expression patterns that are suggestive of this role, with
dorsoventral expression of KmCYC3B in Knautia macedonica [40] and HaCYC3a expression specific to ray
florets in Helianthus annuus [37]. This evidence suggests
that CYC3 function is highly labile. Additionally, function specific to plant branching appears to be found in
rosids while floral expression has been seen in campanulid asterids. CYC3 could play a role in floral symmetry
in campanulids such as Cyphia, and is possibly filling the
role of the lost CYC2.
Even though Cyphioideae are bilaterally symmetrical,
their genetic signature compared to other core eudicot
species would actually suggest they are radially symmetrical, with an apparent loss of functional CYC2-like
genes. In the latest phylogenetic analyses [2] Cyphioideae
are sister to radially symmetrical Campanuloideae,
which retain CYC2-like genes, however, they are highly
diverged. Additionally, Cyphioideae are not resupinate
as are most species of Lobelioideae. However, unlike the
lobe arrangement of most bilaterally symmetrical core
eudicots, Cyphia flowers (Fig. 1J, K) have 3 dorsal corolla
lobes and 2 ventral lobes. Standard orientation of core
eudicot bilaterally symmetrical flowers have a single ventral corolla lobe, pointed downward, with two lateral and
two dorsal lobes each acting as pairs that can shift along
the dorsoventral axis in tandem [17]. Campanuloideae
and Lobelioideae have medial ventral petal lobes [64], but
the later only after resupination via torsion of the pedicel [65, 66]. The lobe arrangement in Cyphioideae, with a
3 + 2 corolla lobe arrangement, necessitates a shift in that
axis at some point early in development, possibly through
an independent resupination event or differentiation in
Page 15 of 22
the location of primordial initiation. The latter is suggested by Leins and Erbar [67] with initiation of petal
lobe primordia in a 3 + 2 arrangement, however, with
asymmetric early development across the dorsoventral
axis. Therefore, these data support the hypothesis that
the ancestral Campanulaceae was radially symmetrical and that the genetic programming of bilateral symmetry likely evolved independently in Cyphioideae and
Lobelioideae.
In Lobelioideae, CamCYC1 duplicated within two subclades
while CamCYC3 appears to be lost in all but the Impares
clade
In Lobelioideae, CamCYC1 is broadly congruent with the
hypothesized species phylogeny with no obvious subfamily-wide duplications (Figs. 3, 7) [7–10, 46, 47]. There are
multiple sequences in a few species; however, these are
likely alleles or more recent isolated duplications. CamCYC1 has not been implicated in bilateral symmetry in
any groups, instead being involved in plant and inflorescence branching in several lineages [44, 63, 68]. CamCYC1, in keeping with the general paucity of CYC1 gene
duplications found in other groups, lacks the broad duplication pattern commonly seen in CYC2 and CYC3 genes
correlating with a shift to bilateral symmetry [45, 60, 62].
However, there are duplications found in the Impares (F)
clade as well as the giant lobelioids (U), likely due to independent ancient genome duplications [48, 49, 69].
The Impares clade, appearing to have duplicated CamCYC1 early in its diversification (Fig. 3), is notable for
having a diversity of chromosome numbers, varying
among 8, 9, 10, and 11 [69], while most of Lobeliaceae
have multiples of 7 chromosomes. This suggests that a
genome duplication occurred early in the diversification
of the Impares clade, followed by subsequent frequent
chromosome losses. The duplication in CYC1 likely correlates with that genome duplication; however, we have
no hypothesis for why these genes were maintained in
this lineage. The Impares clade also appears to be the
only group to have retained CamCYC3 genes (Figs. 5,
7). This means that this lineage maintains both an extra
CYC1 and an extra CYC3 gene compared to most other
Lobelioideae clades. The Impares corolla shape does differ from other groups in having large, broad ventral and
lateral corolla lobes and greatly reduced, nearly scale-like
dorsal lobes [70]. However, there are no data that tie this
morphology with extra CYC1 and CYC3 gene copies to
date.
The giant lobelias (U clade) primarily grow in tropical
montane habitats around the globe and have synapomorphies of a tree-like habit, often with lignification, and are
tetraploid with a chromosome number of n = 14 [7, 10,
71]. In the U clade, there are 3 subclades of CamCYC1,
Tong et al. EvoDevo
(2022) 13:5
with the U1 clade grouping with other Neotropical, Australia, and South American Lobelioideae species sister
to a clade including U2A and U2B. The current topology suggests separate duplications in Pacific Basin species (Fig. 3, green) and non-Pacific Basin species (Fig. 3,
yellow); however, there was no bootstrap support for
the relationships of these clades, so a single duplication
could be shared across all the giant lobelias. These groups
were difficult to tease apart because sequence divergence
is minimal and they were amplified and cloned together,
which resulted in some mixing of sequences among copies. Nevertheless, CYC1 duplicates are maintained in the
giant lobelias, and better sampling could shed light on
the precise ancestor(s) of this clade. For instance, in the
U1 clade, Lobelia doniana is sister to the rest, supporting the East Asian origin hypothesis of giant lobelias [46],
although they are nested within a grade of North American species.
Duplication of CamCYC2 in Campanulaceae is highly
associated with bilateral symmetry in Lobelioideae
CamCYC2 genes are the orthologs of CYCLOIDEA, a
gene which has been shown repeatedly to exhibit dorsally
restricted expression in bilaterally symmetrical groups
(see Hileman [39]). Additionally, the evolution of bilateral
symmetry has been correlated with duplications in CYC2
genes [39, 60]. These genes are of interest in bilaterally
symmetrical species of Campanulaceae, where we expect
gene expression to be restricted to one side of the flower
and that duplications will likely be frequent. CamCYC2
in Lobelioideae was well-sampled and, as expected, had
a clear duplication across the entire clade (Figs. 4, 7). The
CamCYC2 duplication very likely occurred in the Lobelioideae ancestral lineage after it diverged from Campanulaceae sensu stricto. Both Lobelioideae CamCYC2 gene
clades share a similar pattern and are broadly congruent
both with previous research [8, 10, 46, 47] and with the
Lobelioideae CamCYC1 gene clade. As in CamCYC1,
we also detected duplications in the U subclade in both
CamCYC2 paralogs, likely due to tetraploidy. Flowers of Lobelioideae are resupinate, twisting their pedicel
(Fig. 2A, C). However, since mature flowers, after turning, end up having a flower that looks right side up (i.e., a
standard core eudicot 2 + 3 lobe arrangement); this suggests there is a developmentally earlier change in orientation to create an initial 3 up, 2 down lobe arrangement.
Taxa such as species in Monopsis (G) do not twist their
pedicel and end up with mature 3 + 2 flowers, reverting
to the hypothesized ancestral Lobelioideae flower orientation. That said, Monopsis species did not lose their
CamCYC2 copies like Cyphioideae, which similarly does
not undergo resupination. There are currently no known
genes involved in twisting of plant tissues, for instance,
Page 16 of 22
to present the flower upside down, allowing us to potentially uncover novel gene functions of CYC-like genes
with further studies of these groups.
Within both of the CamCYC2A and CamCYC2B
clades, the U subclade (giant lobelias) occur in two duplicate locations in the phylogeny, likely due to their tetraploid ancestry [48, 49]. This means that there are four
separate clades of CYC2 in giant lobelias. One of the U
clades in each of CamCYC2A and CamCYC2B have no
clear sister group; however, the other clade in each is
most-closely related to Lobelia urens. This relationship
to Lo. urens is not well-supported in either clade, and
Lo. urens is clearly part of a Mediterranean clade likely
derived by amphitropical dispersal from what is now
the Western Cape of South Africa [46]. Two species in
the Tupa group of South America have evolved woody
growth independently from the giant lobelias [5, 10, 46].
The hexaploid Tupa group [19] appears to have independently duplicated in CamCYC2B, similar to the giant
lobelia (U) group.
Gene expression of CamCYC2 in Lobelioideae species
is conserved following resupination and paralog
dominance is correlated with dorsal petal size
In Lobelioideae species, we isolated two copies of CamCYC2 genes and utilized qRT-PCR to examine their
temporal and spatial expression patterns. As previous
researchers have shown, CYC2-like genes are dorsally
restricted, limited to the adaxial region of flower tissues.
In most examined bilaterally symmetrical species, CYC2like paralogs are diverged in their expression, with one
copy being more restricted dorsally than the other [36,
39]. Lobelioideae have resupinate flowers and we hypothesized that CamCYC2 expression would, like other bilaterally symmetrical flowers, be adaxial, corresponding
to finally positioned ventral in these resupinate flowers.
Using four Lobelioideae species, Lobelia erinus, Lo. siphilitica, Lo. polyphylla, and Lithotoma axillaris, we found
that (1) the paralogs varied in how restricted they were
on the dorsoventral axis, (2) that resupinate flowers led
to the highest expression in finally positioned ventral
regions, and (3) the overall patterns of expression among
lobes was similar across species; however, which paralog
exhibited greater expression varied (Figs. 6, 8).
The temporal expression patterns of CamCYC2 genes
were relatively uniform through development, which is
similar to that observed in other groups [21]. The spatial
expression patterns of CamCYC2A and CamCYC2B are
relatively concordant among the four species (Figs. 6AII, B-II, C-II, D-II, 8). CamCYC2A is expressed similarly in lateral and ventral lobes, or the whole ventral
region of the flower (the adaxial region) and has very low
Tong et al. EvoDevo
(2022) 13:5
expression in the dorsal lobes (abaxial initiation). CamCYC2B is always highly expressed in the ventral lobe
(adaxial initiation), has an intermediate expression level
in lateral lobes, and is barely expressed in dorsal lobes
(abaxial initiation). Both CamCYC2A and CamCYC2B
have little to no expression in the dorsal lobes, similar to
leaf expression. A similar phenomenon is seen in Malpighiaceae, with a shift in the axis of the early flower primordia resulting in a rearrangement of floral petals in the
New World Malpighiaceae species, which have 1 dorsal
petal, 2 lateral petals, and 2 ventral petals. The expression
CYC2-like genes in Malpighiaceae, however, remains in
the dorsal regions of the corolla [56–58].
Previous work in Dipsacales has shown that even subtle
differences in the dorsoventral gradient of CYC2 expression is correlated with significantly different growth patterns of the lobes [40]. In Lobelia erinus, flowers with
small dorsal lobes, CamCYC2A is significantly more
expressed than CamCYC2B (Fig. 6A-II). In Lo. siphilitica,
flowers with relatively larger dorsal lobes than Lo. erinus,
the pattern is the same, but the distinction between the
level of expression is not as great, especially in the ventral lobe where the CamCYC2B gene expression level
is almost 50% of the CamCYC2A gene expression level
(Fig. 6B-II). In Lithotoma axillaris and Lo. polyphylla,
there is no distinct difference in shape or size between
Page 17 of 22
dorsal, lateral, and ventral lobes. In an opposite pattern,
the CamCYC2B gene is more highly expressed than the
CamCYC2A gene (Fig. 6C-II, and D-II). This is effectively
an increase in expression of the gene with the broader
zone of expression, which has been shown to be correlated with a more radialized flower [36]. In flower primordia, CYCgenes repress cell growth and control organ
number, and in later stages, A. majus CYC2 paralogs can
also upregulate cell division [26, 28]. In this case, Lobelioideae species have relatively larger lateral and ventral
lobes (the genetically adaxial region), likely due to the
high CamCYC2 gene expression. However, it does not
easily explain how Li. axillaris and Lo. polyphylla flowers
have lobes with almost the same size and shape. Nonetheless, this change in the expression ratio among paralogs sets up an intriguing system to study not just CYC
function and evolution, but also how morphology can be
substantially altered by shifts in expression dominance
among gene paralogs.
Conclusions
Campanulaceae are a large core eudicot clade that exhibits a variety of floral symmetries, including varying types
of resupination and pollination syndromes. The family occurs nearly world-wide and has become a model
Fig. 8 CamCYC2A and CamCYC2B expression pattern in Lobelioideae species. A–D CamCYC2A expression pattern, E–F CamCYC2B expression
pattern. A, E Lobelia erinus, B, F Lobelia siphilitica, C, G Lithotoma axillaris, D, H Lobelia polyphylla. Low saturation of color represents minor expression,
high saturation of color represents high expression in flower buds. CamCYC2A is more highly expressed in species with relatively small dorsal corolla
lobes, (A, B) while CamCYC2B is the more highly expressed in species with relatively large dorsal corolla lobes (G, H). CamCYC2A is weakly expressed
in the dorsal corolla lobes (the true ventral domain) and is highly expressed in the ventral domain (the true dorsal domain). CamCYC2B has weak
expression in the dorsal corolla lobes (the true ventral corolla lobes), medium expression in lateral corolla lobes, and high expression in the ventral
corolla lobe (the true dorsal corolla lobe)
Tong et al. EvoDevo
(2022) 13:5
for studying adaptive radiations in many locations. We
sequenced all three core eudicot paralogs of CamCYC
genes, CamCYC1, CamCYC2, and CamCYC3 (Fig. 7).
The CamCYC1 genes duplicated in radially symmetrical
Campanuloideae, but not in other bilaterally symmetrical
flower subfamilies. As expected, CamCYC2 genes duplicated in the Lobelioideae clade with bilaterally symmetrical flowers. However, we show for the first time a loss of
CYC2-like genes in a bilaterally symmetrical group, with
no sequences found in Cyphioideae. Instead of CamCYC2, we found a potential duplication of CamCYC3
in this group. It is possible that, in Cyphioideae, CamCYC3 genes may have taken on the role of CYC2-like
genes. Future studies examining floral RNA expression
in Cyphia should be highly informative. Nonetheless, the
genetic programming of floral symmetry appears to be
independently derived in Cyphioideae and Lobelioideae,
supporting the hypothesis that ancestral Campanulaceae
were radially symmetrical.
In Lobelioideae, expression patterns of CamCYC2
genes were similar to previous studies across core eudicots species, with CamCYC2A and CamCYC2B both
highly expressed in the adaxial side of flower related to
meristem orientation (Fig. 8), despite resupination resulting in a ventral presentation in the flower, suggesting conservation of dorsal identity in these upside-down flowers.
In addition, the CamCYC2A and CamCYC2B show distinctly different expression patterns in species with a different dorsal lobe size ratio. CamCYC2A is the dominant
CamCYC2 gene in species with smaller dorsal lobes, like
Lobelia erinus, and Lo. siphilitica. CamCYC2B is the
dominant CamCYC2 gene in species with bigger dorsal
lobes, in which the dorsal lobes are almost the same size
as the lateral and ventral lobes, like Lithotoma axillaris
and Lo. polyphylla. We illustrate here for the first time
that CYC expression is conserved along the dorsoventral
axis of the flower even as it turns upside-down, suggesting that at least later CYC expression is not regulated by
extrinsic factors such as gravity. Additionally, the shift in
expression dominance among paralogs provides intriguing data that differences in ratios of expression in CYC
could lead to shifts in morphological growth ratios in the
flower.
Materials and methods
Sampling and plant materials
We examined a total of 132 DNA samples from 128 species, including nine Cyphioideae species, nine Campanuloideae species, and 110 Lobelioideae species. Table 1
provides DNA source information for previously prepared samples. An additional eight Campanuloideae
and eight Lobelioideae species were from live plants
growing in the greenhouse at St. John’s University.
Page 18 of 22
Table 2 Primers for different CYC paralogs in Campanulaceae
Locus
Primer
Primer sequences (5′-3′)
CYCLOIDEA1
Astl CYC1Fa
CGRAGRATGAGRY TRTCNCTTGATG
Astl CYC1Ra
GCCC TTKCYCT TGCYCT TTCCCT TG
CYCLOIDEA2
CYC73b
GCNCGNARRT TYT TYGATC TDCAAG
CYCRa
CTTGCTC TTTCYC TYGCYT TYGCCC
CYCLOIDEA3
CYC73b
GCNCGNARRT TYT TYGATC TDCAAG
CYCRa
CTTGCTC TTTCYC TYGCYT TYGCCC
Astl CYC3Fa
GGGAAGAMAGAYMGGCAYAGC
Astl CYC1Ra
GCCC TTKCYCT TGCYCT TTCCCT TG
Campanula persicifolia was wild collected in Fresh
Meadow, New York. Campanula carpatica was bought
from a local nursery garden. Campanula glomerata,
Campanula portenschlagiana, Campanula cochleariifolia, Jasione montana, Platycodon grandiflorus, Phyteuma scheuchzeri, Lobelia anceps, Lobelia bridgesii,
Lobelia cardinalis, Lobelia erinus, Lobelia siphilitica,
Lobelia polyphylla, Lobelia tupa, and Lithotoma axillaris seeds were ordered from online plant nurseries (Botanical Interests ®, Hazzard’s Seeds, and Plant
World Seeds). All DNA was extracted using a DNeasy
Plant Mini Kit (QIAGEN) according to the manufacturer’s instructions and stored in – 20 °C.
Amplification
All PCR reactions were performed using Taq DNA Polymerase (GoTaq® Flexi DNA polymerase, Promega).
All DNAs were amplified in 25 μL PCR reactions
containing: 1 μL DNA, 5 μL 5× buffer, 2.5 μL 25 mM
MgCl2, 0.5 μL 10 mM dNTPs, 1 μL of 10 mM primers,
1 μL Taq polymerase, and distilled water was added to
bring up to total volume. Amplifications utilized the
following cycling program: (1) initial denaturation was
carried out at 94 °C for 2 min; (2) 39 cycles of: 94ºC for
45 s, 51 °C (varied for by different pairs of primers) for
1 min, and 72 °C for 1 min 30 s; (3) a final elongation
step at 72 °C for 20 min. To amplify CYC-like genes in
Campanulaceae, previously designed degenerate primers were used from Howarth and Donoghue [41]. Primers for CamCYC1 were designed based on CYC-like
sequences from other lineages in asterids available from
NCBI. All primer sequences are provided in Table 2.
Cloning was performed using the StrataClone PCR
Cloning Kit (Agilent, Santa Clara, CA), following the
manufacturer’s instructions. We picked four to eight
colonies per plate and amplified them using primer
sites in the construct (M13F and M13R). DNA cleaning utilized the P.E.G. method [72]. Sanger sequencing
Tong et al. EvoDevo
(2022) 13:5
Page 19 of 22
Table 3 The qRT-PCR primers for each species examining CamCYC2A and CamCYC2B gene expression patterns
Efficiency (%)
Lobelia erinus
CamCYC2A
CYC2 37F 5′-GCTAGTAAAACCC TTGATTGGCT-3′
82.7
CYC2A 314R 5′-GCCC TGGACTCTT TTGCAAAGT-3′
CamCYC2B
CYC2 37F 5′-GCTAGTAAAACCC TTGATTGGCT-3′
81.8
CYC2B 291R 5′-GCGATGAGATGCAGGT TTATAACTG-3′
CamActin
Le-act1046F 5′-ATCCACGARACSACCTACAACT-3′
86.0
Le-act1216R 5′- MACCACCT TAATCT TCATGC TGCT-3′
Lobelia siphilitica
CamCYC2A
ls CYC2A-37F 5′-TTCGACAAAGCTAGTAAAACTC TTGATTGG-3′
81.6
Ls CYC2A 264R 5′-TTTC TCT TTGGCTCTCGTTGTAGC-3′
CamCYC2B
ls CYC2B-47F 5′-CTAGTAAAACCCT TGATTGGCT TTTCAC-3′
87.0
Ls CYC2B 298R 5′-CTAGGCGATGAGATGCAGGTTTATAAC-3′
CamActin
Le-act477F 5′-AGAT YTGGCATCAYAC TTTCTACA-3′
89.0
Le-act729R 5′- CCTTCGTARATTGGAACCGTGTG-3′
Lithotoma axillaris
CamCYC2A
Ls CYC2A F41 5′-ACAAAGC TAGTAAAAC TCT TGATTGGCT-3′
89.3
ISCYC2A 260R 5′-TTCTCTT TGGCGC TCGATGTAGCTG-3′
CamCYC2B
ISCYC2B 38F 5′-TTGACAAAGC TAGTAAAACCCT TGATTGG-3′
CamActin
Le-act1046F 5′-ATCCACGARACSACCTACAACT-3′
92.8
ISCYC2B 203R 5′-GCTCCTTCAT TTTGTTCAGCTGC-3′
86.0
Le-act1216R 5′-MACCACCT TAATCT TCATGC TGCT-3′
Lobelia polyphylla
CamCYC2A
LP CYC2AF1a 5′-TCGACAAAGC TAGTAAAAC TCT TGATTGG-3′
89.6
LP CYC2A R4 5′-TTTGCAAGATAAAGTGCAGGTT TATACG-3′
CamCYC2B
Ls CYC2B F43 5′-AAAGCTAGTAAAACCC TTGATTGGC T-3′
85.7
LP CYC2B R1 5′-TTTGTGC TCTCATCGT TTTCGC TTCAC-3′
CamActin
Le-act477F 5′-AGAT YTGGCATCAYAC TTTCTACA-3′
89.0
Le-act729R 5′-CCTTCGTARATTGGAACCGTGTG-3′
The annealing temperature for all primers is 60 ℃
was performed at the Yale University DNA Analysis
Facility, New Haven, CT, using a 3730xl DNA Analyzer
(Applied Biosystems, Thermo Fisher Scientific, Inc.).
All individual colony sequences were edited in Geneious®
Pro v.7.1.2 (http://www.geneious.com), including removing the plasmid and primer sequences. Consensus
sequences were generated from similar clones from the
same DNA sample. To determine orthology, we initially
used BLAST in NCBI. CYC-like genes were determined
by the presence of the TCP and R domains. The specieslevel consensus sequences were aligned in Geneious®
using the MUSCLE Alignment tool (default parameters)
and then manually adjusted according the amino acid
sequences or nucleotide sequences in Mesquite [73]
or Geneious® Pro v.7.1.2. The phylogenetic gene trees
were generated with CIPRES science gateway (https://
www.phylo.org) using Maximum Likelihood by the
Alignment and phylogenetic analyses
RAxML-HPC BlackBox (default parameters, except with
added option to let RA×ML halt bootstrapping automatically and estimate the proportion of invariable sites
(GTRGAMMA + I)). Phylogenetic trees of CYC1 and
CYC3 were midpoint rooted, while in CYC2 the Campanuloideae sequences were used as an outgroup to
Lobelioideae sequences.
Collection and dissection of floral tissues
For expression studies, four Lobelioideae species
were grown in the greenhouse at St. John’s University,
Queens, NY, USA: Lobelia erinus (Fig. 1H), Lo. siphilitica
(Fig. 1G), Lo. polyphylla (Fig. 1I), and Lithotoma axillaris
(Fig. 1F). Living collections are maintained at SJU greenhouse and herbarium specimens are deposited at NYBG.
Flower buds were collected at three different developmental stages: small buds, medium buds, and large buds.
The small buds of Lo. erinus were 2.5–4 mm, medium
buds were 5–6 mm, and large buds were 7–8 mm. For
Tong et al. EvoDevo
(2022) 13:5
Lo. siphilitica, small buds were 5–6 mm, medium buds
were 8–12 mm, and the large buds were 14–18 mm. For
Lo. polyphylla, small buds were 7–10 mm, medium buds
were 15–20 mm, and the large buds were 25–30 mm. For
Li. axillaris, small buds were 10–13 mm, medium buds
were 15–25 mm, and the large buds were 25–35 mm.
Additionally, medium flower buds were dissected, after
resupination, to separate the finally positioned dorsal,
lateral, and ventral corolla lobes. Leaf tissue was separately collected as a control. All tissues were immediately frozen with liquid nitrogen and stored in a – 80 °C
freezer until extraction. Roughly 20–30 mg of tissue was
collected for each RNA extraction. The exception was
tissue from Lo. erinus flower buds, which are extremely
small, with 3–4 mm medium size buds, so therefore, only
roughly 15–20 mg was collected for RNA extraction in
this species. Three biological replicates were collected for
each type of tissue.
Quantitative Real‑Time PCR and statistical analysis
Total RNA was extracted from plant tissues used for qRTPCR using the RNeasy Plant Mini Kit and RNase-free
DNase kit (QIAGEN) according to the manufacturer’s
instructions and then stored at -80 °C. The concentrations and purities of all RNA samples were determined
using a Thermo Scientific NanoDrop 2000 (Thermo
Scientific, Waltham, MA). The qRT-PCR primers were
designed in Geneious® Pro v.7.1.2 based on CamCYC2
gene sequences and ACTIN sequences collected in our
study. Specific primer sets were designed for each species
(Table 3). The qScript™ One-Step SYBR® Green qRTPCR Kit (QuantaBio) was used with manufacturer recommendations to investigate the expression patterns of
CamCYC2A and CamCYC2B gene expression in the collected tissues from Lobelia erinus, Lo. siphilitica, Lithotoma axillaris, and Lo. polyphylla. Each type of tissue
included three biological and two technical replicates.
Samples were run on a Bio-Rad MyIQ Single Color RealTime RCR Detection System (Bio-Rad, Hercules, CA).
The melting curve and threshold cycle (Ct) values were
analyzed by a modified 2−ΔCT method [74]. Because all
of the tissues used were from natural or wild-type plants,
there was no “untreated control” to normalize the second
delta as is standard in these methods. ANOVA and post
hoc Tukey HSD were performed on the web site: https://
astatsa.com/OneWay_Anova_with_TukeyHSD/.
Abbreviations
CYC: CYCLOIDEA; TCP: Teosinte Branched1, CYCLOIDEA, proliferating cell factor; qPCR: Quantitative real-time polymerase chain reaction; RT-PCR: Reverse
transcription polymerase chain reaction; ANOVA: Analysis of variance; HSD:
Honest significant difference; Ct: Threshold cycle; CBS: Group of Lobelioideae
including Centropogon, Burmeistera, and Siphocampylus.
Page 20 of 22
Acknowledgements
The authors thank current and past lab members, especially Brent Berger,
Jiahong Han, Vincent Ricigliano, and Jingbo Zhang for helpful discussion. The
authors additionally thank SJU Departmental of Biological Sciences members,
Ujwala Goasvi Khadtare, Ketan Patil, and Meenhaj Uddin for discussion and
method advice.
Authors’ contributions
JT and DGH designed the research. JT, FM, and ASZ conducted data sequence
generation and analyzes. JT conducted the morphological dissections and
qPCR experiments. JT conducted statistical analyses. JT, EBK, CWM, NC, and
DGH provided interpretations of results. JT and DGH wrote the paper. JT,
EBK, CWM, NC, FM, and ASZ, and DGH read, critiqued, and approved the final
manuscript. All authors read and approved the final manuscript.
Funding
Not applicable.
Availability of data and materials
The datasets supporting the conclusions of this article are available in the
TreeBase repository (https://www.treebase.org/treebase-web/login.jsp) and
GenBank repository (XX-XX); not public until accepted).
Declarations
Ethics approval and consent to participate
Not applicable.
Consent for publication
Not applicable.
Competing interests
The authors declare no competing interests.
Author details
1
Department of Biological Sciences, St. John’s University, Jamaica, NY, USA.
2
Department of Biology, Indiana University, Bloomington, IN, USA. 3 Department of Botany, University of Hawaiʻi at Mānoa, Honolulu, HI, USA. 4 Florida
Museum of Natural History, University of Florida, Gainesville, FL, USA.
Received: 12 August 2021 Accepted: 22 December 2021
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