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1.  Flower Development 
Flowers are the most complex structures of plants. Studies of Arabidopsis thaliana, which has typical eudicot flowers, have been fundamental in advancing the structural and molecular understanding of flower development. The main processes and stages of Arabidopsis flower development are summarized to provide a framework in which to interpret the detailed molecular genetic studies of genes assigned functions during flower development and is extended to recent genomics studies uncovering the key regulatory modules involved. Computational models have been used to study the concerted action and dynamics of the gene regulatory module that underlies patterning of the Arabidopsis inflorescence meristem and specification of the primordial cell types during early stages of flower development. This includes the gene combinations that specify sepal, petal, stamen and carpel identity, and genes that interact with them. As a dynamic gene regulatory network this module has been shown to converge to stable multigenic profiles that depend upon the overall network topology and are thus robust, which can explain the canalization of flower organ determination and the overall conservation of the basic flower plan among eudicots. Comparative and evolutionary approaches derived from Arabidopsis studies pave the way to studying the molecular basis of diverse floral morphologies.
doi:10.1199/tab.0127
PMCID: PMC3244948  PMID: 22303253
2.  A spatial dissection of the Arabidopsis floral transcriptome by MPSS 
BMC Plant Biology  2008;8:43.
Background
We have further characterized floral organ-localized gene expression in the inflorescence of Arabidopsis thaliana by comparison of massively parallel signature sequencing (MPSS) data. Six libraries of RNA sequence tags from immature inflorescence tissues were constructed and matched to their respective loci in the annotated Arabidopsis genome. These signature libraries survey the floral transcriptome of wild-type tissue as well as the floral homeotic mutants, apetala1, apetala3, agamous, a superman/apetala1 double mutant, and differentiated ovules dissected from the gynoecia of wild-type inflorescences. Comparing and contrasting these MPSS floral expression libraries enabled demarcation of transcripts enriched in the petals, stamens, stigma-style, gynoecia, and those with predicted enrichment within the sepal/sepal-petals, petal-stamens, or gynoecia-stamens.
Results
By comparison of expression libraries, a total of 572 genes were found to have organ-enriched expression within the inflorescence. The bulk of characterized organ-enriched transcript diversity was noted in the gynoecia and stamens, whereas fewer genes demonstrated sepal or petal-localized expression. Validation of the computational analyses was performed by comparison with previously published expression data, in situ hybridizations, promoter-reporter fusions, and reverse transcription PCR. A number of well-characterized genes were accurately delineated within our system of transcript filtration. Moreover, empirical validations confirm MPSS predictions for several genes with previously uncharacterized expression patterns.
Conclusion
This extensive MPSS analysis confirms and supplements prior microarray floral expression studies and illustrates the utility of sequence survey-based expression analysis in functional genomics. Spatial floral expression data accrued by MPSS and similar methods will be advantageous in the elucidation of more comprehensive genetic regulatory networks governing floral development.
doi:10.1186/1471-2229-8-43
PMCID: PMC2375892  PMID: 18426585
3.  Within and between Whorls: Comparative Transcriptional Profiling of Aquilegia and Arabidopsis 
PLoS ONE  2010;5(3):e9735.
Background
The genus Aquilegia is an emerging model system in plant evolutionary biology predominantly because of its wide variation in floral traits and associated floral ecology. The anatomy of the Aquilegia flower is also very distinct. There are two whorls of petaloid organs, the outer whorl of sepals and the second whorl of petals that form nectar spurs, as well as a recently evolved fifth whorl of staminodia inserted between stamens and carpels.
Methodology/Principal Findings
We designed an oligonucleotide microarray based on EST sequences from a mixed tissue, normalized cDNA library of an A. formosa x A. pubescens F2 population representing 17,246 unigenes. We then used this array to analyze floral gene expression in late pre-anthesis stage floral organs from a natural A. formosa population. In particular, we tested for gene expression patterns specific to each floral whorl and to combinations of whorls that correspond to traditional and modified ABC model groupings. Similar analyses were performed on gene expression data of Arabidopsis thaliana whorls previously obtained using the Ath1 gene chips (data available through The Arabidopsis Information Resource).
Conclusions/Significance
Our comparative gene expression analyses suggest that 1) petaloid sepals and petals of A. formosa share gene expression patterns more than either have organ-specific patterns, 2) petals of A. formosa and A. thaliana may be independently derived, 3) staminodia express B and C genes similar to stamens but the staminodium genetic program has also converged on aspects of the carpel program and 4) staminodia have unique up-regulation of regulatory genes and genes that have been implicated with defense against microbial infection and herbivory. Our study also highlights the value of comparative gene expression profiling and the Aquilegia microarray in particular for the study of floral evolution and ecology.
doi:10.1371/journal.pone.0009735
PMCID: PMC2843724  PMID: 20352114
4.  Functional recapitulation of transitions in sexual systems by homeosis during the evolution of dioecy in Thalictrum 
Sexual systems are highly variable in flowering plants and an important contributor to floral diversity. The ranunculid genus Thalictrum is especially well-suited to study evolutionary transitions in sexual systems. Homeotic transformation of sexual organs (stamens and carpels) is a plausible mechanism for the transition from hermaphroditic to unisexual flowers in this lineage because flowers of dioecious species develop unisexually from inception. The single-copy gene PISTILLATA (PI) constitutes a likely candidate for rapid switches between stamen and carpel identity. Here, we first characterized the expression pattern of all B class genes in the dioecious species T. dioicum. As expected, all B class orthologs are expressed in stamens from the earliest stages. Certain AP3 lineages were also expressed late in sepal development. We then tested whether orthologs of PI could potentially control sexual system transitions in Thalictrum, by knocking-down their expression in T. dioicum and the hermaphroditic species T. thalictroides. In T. dioicum, we found that ThdPI-1/2 silencing caused stamen primordia to develop into carpels, resulting in male to female flower conversions. In T. thalictroides, we found that ThtPI silencing caused stamen primordia to develop into supernumerary carpels, resulting in hermaphroditic to female flower conversions. These phenotypes illustrate the ability for homeotic mutations to bring about sudden and potentially adaptive changes by altering the function of a single gene. We propose a two-step evolutionary model where transitions from hermaphroditic to unisexual plants in Thalictrum result from two independent mutations at a B class gene locus. Our PI knockdown experiments in T. thalictroides recapitulate the second step in this model: the evolution of female plants as a result of a loss-of-function mutation in a B class gene.
doi:10.3389/fpls.2013.00487
PMCID: PMC3842162  PMID: 24348491
B class genes; PISTILLATA; VIGS; RNAi; ranunculid; ABC model; sex determination; MADS box genes
5.  Comparative Transcriptional Profiling Provides Insights into the Evolution and Development of the Zygomorphic Flower of Vicia sativa (Papilionoideae) 
PLoS ONE  2013;8(2):e57338.
Background
Vicia sativa (the common vetch) possesses a predominant zygomorphic flower and belongs to the subfamily Papilionoideae, which is related to Arabidopsis thaliana in the eurosid II clade of the core eudicots. Each vetch flower consists of 21 concentrically arranged organs: the outermost five sepals, then five petals and ten stamens, and a single carpel in the center.
Methodology/Principal Findings
We explored the floral transcriptome to examine a genome-scale genetic model of the zygomorphic flower of vetch. mRNA was obtained from an equal mixture of six floral organs, leaves and roots. De novo assembly of the vetch transcriptome using Illumina paired-end technology produced 71,553 unigenes with an average length of 511 bp. We then compared the expression changes in the 71,553 unigenes in the eight independent organs through RNA-Seq Quantification analysis. We predominantly analyzed gene expression patterns specific to each floral organ and combinations of floral organs that corresponded to the traditional ABC model domains. Comparative analyses were performed in the floral transcriptomes of vetch and Arabidopsis, and genomes of vetch and Medicago truncatula.
Conclusions/Significance
Our comparative analysis of vetch and Arabidopsis showed that the vetch flowers conform to a strict ABC model. We analyzed the evolution and expression of the TCP gene family in vetch at a whole-genome level, and several unigenes specific to three different vetch petals, which might offer some clues toward elucidating the molecular mechanisms underlying floral zygomorphy. Our results provide the first insights into the genome-scale molecular regulatory network that controls the evolution and development of the zygomorphic flower in Papilionoideae.
doi:10.1371/journal.pone.0057338
PMCID: PMC3578871  PMID: 23437373
6.  An Activated Form of UFO Alters Leaf Development and Produces Ectopic Floral and Inflorescence Meristems 
PLoS ONE  2013;8(12):e83807.
Plants are unique in their ability to continuously produce new meristems and organ primordia. In Arabidopsis, the transcription factor LEAFY (LFY) functions as a master regulator of a gene network that is important for floral meristem and organ specification. UNUSUAL FLORAL ORGANS (UFO) is a co-activator of LEAFY and is required for proper activation of APETALA3 in the floral meristem during the specification of stamens and petals. The ufo mutants display defects in other parts of the flower and the inflorescence, suggestive of additional roles. Here we show that the normal determinacy of the developing Arabidopsis leaves is affected by the expression of a gain-of-function UFO fusion protein with the VP16 transcriptional activator domain. In these lines, the rosette and cauline leaf primordia exhibit reiterated serration, and upon flowering produce ectopic meristems that develop into flowers, bract leaves and inflorescences. These striking phenotypes reveal that developing leaves maintain the competency to initiate flower and inflorescence programs. Furthermore, the gain-of-function phenotypes are dependent on LFY and the SEPALLATA (SEP) MADS-box transcription factors, indicative of their functional interactions with UFO. The findings of this study also suggest that UFO promotes the establishment of the lateral meristems and primordia in the peripheral zone of the apical and floral meristems by enhancing the activity of LFY. These novel phenotypes along with the mutant phenotypes of UFO orthologs in other plant species suggest a broader function for UFO in plants.
doi:10.1371/journal.pone.0083807
PMCID: PMC3871548  PMID: 24376756
7.  Identification and Characterization of RcMADS1, an AGL24 Ortholog from the Holoparasitic Plant Rafflesia cantleyi Solms-Laubach (Rafflesiaceae) 
PLoS ONE  2013;8(6):e67243.
Rafflesia, a holoparasitic genus that produces the largest flower in the world is characterized by the absence of leaves, stem and other macroscopic organs. To better understand the molecular regulation of flower development in this genus we isolated and characterized a floral MADS-box gene, namely, RcMADS1 from Rafflesia cantleyi. Heterologous expression analysis in Arabidopsis was chosen because Rafflesia is not amenable to genetic manipulations. RcMADS1 shares sequence similarity with AGAMOUS-LIKE 24 (AGL24) and SHORT VEGETATIVE PHASE (SVP) of Arabidopsis. Ectopic expression of RcMADS1 in Arabidopsis caused early flowering and conversion of sepals and petals into leaf-like structures, and carpels into inflorescences. In 35S::RcMADS1 plants SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), a downstream target gene of AGL24, was upregulated. 35S::RcMADS1 plants exhibit early flowering and conversion of the floral meristem into inflorescence meristem, as in 35S::AGL24 plants. Similar to AGL24, RcMADS1 could rescue the late flowering phenotypes of agl24-1 and FRIGIDA, but not the early flowering of svp-41. Based on these results, we propose that RcMADS1 is a functional ortholog of Arabidopsis AGL24.
doi:10.1371/journal.pone.0067243
PMCID: PMC3695966  PMID: 23840638
8.  Leaf Development 
The shoot system is the basic unit of development of seed plants and is composed of a leaf, a stem, and a lateral bud that differentiates into a lateral shoot. The most specialized organ in angiosperms, the flower, can be considered to be part of the same shoot system since floral organs, such as the sepal, petal, stamen, and carpel, are all modified leaves. Scales, bracts, and certain kinds of needle are also derived from leaves. Thus, an understanding of leaf development is critical to an understanding of shoot development. Moreover, leaves play important roles in photosynthesis, respiration and photoperception. Thus, a full understanding of leaves is directly related to a full understanding of seed plants.
The details of leaf development remain unclear. The difficulties encountered in studies of leaf development, in particular in dicotyledonous plants such as Arabidopsis thaliana (L.) Henyn., are derived from the complex process of leaf development, during which the division and elongation of cells occur at the same time and in the same region of the leaf primordium (Maksymowych, 1963; Poethig and Sussex, 1985). Thus, we cannot divide the entire process into unit processes in accordance with the tenets of classical anatomy.
Genetic approaches in Arabidopsis, a model plant (Meyerowitz and Pruitt, 1985), have provided a powerful tool for studies of mechanisms of leaf development in dicotyledonous plants, and various aspects of the mechanisms that control leaf development have been revealed in recent developmental and molecular genetic studies of Arabidopsis (for reviews, see Tsukaya, 1995 and 1998; Van Lijsebettens and Clarke, 1998; Sinha, 1999; Van Volkenburgh, 1999; Tsukaya, 2000; Byrne et al., 2001; Dengler and Kang, 2001; Dengler and Tsukaya, 2001; Tsukaya, 2001). In this review, we shall examine the information that is currently available about various mechanisms of leaf development in Arabidopsis. Vascular patterning is also an important factor in the determination of leaf shape, and this topic is reviewed in this resource by Turner (see also Dengler and Kang, 2001). The interested reader is also referred to work on the basic characterization of the vascular patterning in foliage leaves of Arabidopsis has been carried out by Candela et al. (1999) and Semiarti et al. (2001). For terminology, see Fig. 1.
doi:10.1199/tab.0072
PMCID: PMC3243299  PMID: 22303217
9.  Developmental Robustness by Obligate Interaction of Class B Floral Homeotic Genes and Proteins 
PLoS Computational Biology  2009;5(1):e1000264.
DEF-like and GLO-like class B floral homeotic genes encode closely related MADS-domain transcription factors that act as developmental switches involved in specifying the identity of petals and stamens during flower development. Class B gene function requires transcriptional upregulation by an autoregulatory loop that depends on obligate heterodimerization of DEF-like and GLO-like proteins. Because switch-like behavior of gene expression can be displayed by single genes already, the functional relevance of this complex circuitry has remained enigmatic. On the basis of a stochastic in silico model of class B gene and protein interactions, we suggest that obligate heterodimerization of class B floral homeotic proteins is not simply the result of neutral drift but enhanced the robustness of cell-fate organ identity decisions in the presence of stochastic noise. This finding strongly corroborates the view that the appearance of this regulatory mechanism during angiosperm phylogeny led to a canalization of flower development and evolution.
Author Summary
The development of organs, their position, and boundaries in multicellular organisms are defined by genes that can sustain their own activation over long periods of time, termed genetic switches. A good case in point is provided by the genetic machinery controlling the development of flowers in higher plants. In Arabidopsis thaliana and other plants, a particular class of these genes—DEF-like and GLO-like floral homeotic genes—regulates the development of petals and stamens. These genes are self-activating via a heterodimer of their protein products, making the activity of each one of them fully bound to the activity of the other one. The reason for their total functional interdependence has long remained unclear, as the expression of both genes is jointly controlled by shared transcription factors in addition to the heterodimer. In principle, one gene alone could provide their switching functionality. In this study, we use computer modeling to show that the obligate heterodimerization mechanism found in DEF- and GLO-like genes reduces the susceptibility of the genetic switch to failure caused by stochastic noise. This would have provided the system an evolutionary advantage over a single gene with the same functionality.
doi:10.1371/journal.pcbi.1000264
PMCID: PMC2612583  PMID: 19148269
10.  Floral homeotic C function genes repress specific B function genes in the carpel whorl of the basal eudicot California poppy (Eschscholzia californica) 
EvoDevo  2010;1:13.
Background
The floral homeotic C function gene AGAMOUS (AG) confers stamen and carpel identity and is involved in the regulation of floral meristem termination in Arabidopsis. Arabidopsis ag mutants show complete homeotic conversions of stamens into petals and carpels into sepals as well as indeterminacy of the floral meristem. Gene function analysis in model core eudicots and the monocots rice and maize suggest a conserved function for AG homologs in angiosperms. At the same time gene phylogenies reveal a complex history of gene duplications and repeated subfunctionalization of paralogs.
Results
EScaAG1 and EScaAG2, duplicate AG homologs in the basal eudicot Eschscholzia californica show a high degree of similarity in sequence and expression, although EScaAG2 expression is lower than EScaAG1 expression. Functional studies employing virus-induced gene silencing (VIGS) demonstrate that knock down of EScaAG1 and 2 function leads to homeotic conversion of stamens into petaloid structures and defects in floral meristem termination. However, carpels are transformed into petaloid organs rather than sepaloid structures. We also show that a reduction of EScaAG1 and EScaAG2 expression leads to significantly increased expression of a subset of floral homeotic B genes.
Conclusions
This work presents expression and functional analysis of the two basal eudicot AG homologs. The reduction of EScaAG1 and 2 functions results in the change of stamen to petal identity and a transformation of the central whorl organ identity from carpel into petal identity. Petal identity requires the presence of the floral homeotic B function and our results show that the expression of a subset of B function genes extends into the central whorl when the C function is reduced. We propose a model for the evolution of B function regulation by C function suggesting that the mode of B function gene regulation found in Eschscholzia is ancestral and the C-independent regulation as found in Arabidopsis is evolutionarily derived.
doi:10.1186/2041-9139-1-13
PMCID: PMC3012024  PMID: 21122096
11.  Carpeloidy in flower evolution and diversification: a comparative study in Carica papaya and Arabidopsis thaliana 
Annals of Botany  2011;107(9):1453-1463.
Background and Aims
Bisexual flowers of Carica papaya range from highly regular flowers to morphs with various fusions of stamens to the ovary. Arabidopsis thaliana sup1 mutants have carpels replaced by chimeric carpel–stamen structures. Comparative analysis of stamen to carpel conversions in the two different plant systems was used to understand the stage and origin of carpeloidy when derived from stamen tissues, and consequently to understand how carpeloidy contributes to innovations in flower evolution.
Methods
Floral development of bisexual flowers of Carica was studied by scanning electron microscopy and was compared with teratological sup mutants of A. thaliana.
Key Results
In Carica development of bisexual flowers was similar to wild (unisexual) forms up to locule initiation. Feminization ranges from fusion of stamen tissue to the gynoecium to complete carpeloidy of antepetalous stamens. In A. thaliana, partial stamen feminization occurs exclusively at the flower apex, with normal stamens forming at the periphery. Such transformations take place relatively late in development, indicating strong developmental plasticity of most stamen tissues. These results are compared with evo-devo theories on flower bisexuality, as derived from unisexual ancestors. The Arabidopsis data highlight possible early evolutionary events in the acquisition of bisexuality by a patchy transformation of stamen parts into female parts linked to a flower axis-position effect. The Carica results highlight tissue-fusion mechanisms in angiosperms leading to carpeloidy once bisexual flowers have evolved.
Conclusions
We show two different developmental routes leading to stamen to carpel conversions by late re-specification. The process may be a fundamental aspect of flower development that is hidden in most instances by developmental homeostasis.
doi:10.1093/aob/mcr087
PMCID: PMC3108808  PMID: 21504912
Arabidopsis; Carica papaya; bisexual flowers; carpeloidy; ectopic ovules; evo-devo; feminization; floral development; sex conversion; sup1 mutants
12.  Multi-petal cyclamen flowers produced by AGAMOUS chimeric repressor expression 
Scientific Reports  2013;3:2641.
Cyclamen persicum (cyclamen) is a commercially valuable, winter-blooming perennial plant. We cloned two cyclamen orthologues of AGAMOUS (AG), CpAG1 and CpAG2, which are mainly expressed in the stamen and carpel, respectively. Cyclamen flowers have 5 petals, but expression of a chimeric repressor of CpAG1 (CpAG1-SRDX) caused stamens to convert into petals, resulting in a flower with 10 petals. By contrast, CpAG2-SRDX only caused incomplete formation of stamens and carpels. Expression in Arabidopsis thaliana showed similar effects on flower organ specification. Simultaneous expression of CpAG1-SRDX and CpAG2-SRDX in cyclamen induced rose-like, multi-petal flowers, a potentially valuable trait in commercial ornamental varieties. Expression of CpAG2-SRDX in a cyclamen mutant lacking expression of CpAG1 more effectively produced multi-petal flowers. Here, we controlled the number of petals in cyclamen by simple genetic engineering with a chimeric repressor. This strategy may be applicable useful for other ornamental plants with two distinct AG orthologues.
doi:10.1038/srep02641
PMCID: PMC3770964  PMID: 24026510
13.  Quantitative Developmental Analysis of Homeotic Changes in the Inflorescence of Philodendron (Araceae) 
Annals of Botany  2008;101(7):1027-1034.
Background and Aims
The inflorescence of Philodendron constitutes an interesting morphological model to analyse the phenomenon of homeosis quantitatively at the floral level. The specific goals of this study were (1) to characterize and quantify the range of homeotic transformation in Philodendron billietiae, and (2) to test the hypothesis that the nature of flowers surrounding atypical bisexual flowers (ABFs) channel the morphological potentialities of atypical bisexual flowers.
Methods
Inflorescences of P. billietiae at different stages of development were observed using SEM. The number of appendices in male, female and sterile flowers were counted on 11 young inflorescences (5–6 flowers per inflorescence). The number of staminodes and carpels on ABFs were counted on 19 inflorescences (n = 143). These data were used for regression and ANOVA analyses.
Results
There was an average of 4·1 stamens per male flower, 9·8 carpels per female flower and 6·8 staminodes per sterile male flower. There was an average of 7·3 floral appendices per atypical flower. Staminodes and carpels are inserted on the same whorl in ABFs. A negative exponential relationship was found between the average number of staminodes and the number of carpels in ABFs. If only the ABFs consisting of less than six carpels are considered, there is a linear relationship between the number of carpels and the average number of staminodes. The value of the slope of the regression equation indicates that on average, in P. billietiae, 1·36 carpels are replaced by one staminode.
Conclusions
In P. billietiae, the number of appendages in female flowers imposes a constraint on the maximum total number of appendages (carpels and staminodes) that can develop on ABFs. The quantitative analyses indicate that the average number of different types of floral appendages on an ABF and the number of organs involved in a homeotic transformation are two independent phenomena.
doi:10.1093/aob/mcn031
PMCID: PMC2710224  PMID: 18356291
Philodendron; positional information; gradient; flower; homeosis; developmental constraint
14.  Developmental Genetics of the Perianthless Flowers and Bracts of a Paleoherb Species, Saururus chinensis 
PLoS ONE  2013;8(1):e53019.
Saururus chinensis is a core member of Saururaceae, a perianthless (lacking petals or sepals) family. Due to its basal phylogenetic position and unusual floral composition, study of this plant family is important for understanding the origin and evolution of perianthless flowers and petaloid bracts among angiosperm species. To isolate genes involved in S. chinensis flower development, subtracted floral cDNA libraries were constructed by using suppression subtractive hybridization (SSH) on transcripts isolated from developing inflorescences and seedling leaves. The subtracted cDNA libraries contained a total of 1,141 ESTs and were used to create cDNA microarrays to analyze transcript profiles of developing inflorescence tissues. Subsequently, qRT-PCR analyses of eight MADS-box transcription factors and in situ hybridizations of two B-class MADS-box transcription factors were performed to verify and extend the cDNA microarray results. Finally, putative phylogenetic relationships within the B-class MADS-box gene family were determined using the discovered S. chinensis B-class genes to compare K-domain sequences with B genes from other basal angiosperms. Two hundred seventy-seven of the 1,141 genes were found to be expressed differentially between S. chinensis inflorescence tissues and seedling leaves, 176 of which were grouped into at least one functional category, including transcription (14.75%), energy (12.59%), metabolism (9.12%), protein-related function (8.99%), and cellular transport (5.76%). qRT-PCR and in situ hybridization of selected MADS-box genes supported our microarray data. Phylogenetic analysis indicated that a total of six B-class MADS-box genes were isolated from S. chinensis. The differential regulation of S. chinensis B-class MADS-box transcription factors likely plays a role during the development of subtending bracts and perianthless flowers. This study contributes to our understanding of inflorescence development in Saururus, and represents an initial step toward understanding the formation of petaloid bracts in this species.
doi:10.1371/journal.pone.0053019
PMCID: PMC3559744  PMID: 23382831
15.  Cucumber SUPERMAN Has Conserved Function in Stamen and Fruit Development and a Distinct Role in Floral Patterning 
PLoS ONE  2014;9(1):e86192.
The Arabidopsis SUPERMAN (SUP) gene encodes a C2H2 type zinc finger protein that is required for maintaining the boundaries between stamens and carpels, and for regulating development of ovule outer integument. Orthologs of SUP have been characterized in bisexual flowers as well as dioecious species, but it remains elusive in monoecious plants with unisexual flowers on the same individual. Here we isolate the SUP ortholog in Cucumis sativus L (CsSUP), a monoecious vegetable. CsSUP is predominantly expressed in female specific organs: the female flower buds and ovules. Ectopic expression of CsSUP in Arabidopsis can partially complement the fruit development in sup-5 mutant, and its over-expression in wide-type leads to reduced silique length, suppressed stamen development and distorted petal patterning. Our data suggest that CsSUP plays conserved as well as distinct roles during flower and fruit development, and it may function in the boundaries and ovules to balance petal patterning, stamen and ovule development in Arabidopsis.
doi:10.1371/journal.pone.0086192
PMCID: PMC3900519  PMID: 24465952
16.  Are Petals Sterile Stamens or Bracts? The Origin and Evolution of Petals in the Core Eudicots 
Annals of Botany  2007;100(3):621-630.
Background
The aim of this paper is to discuss the controversial origins of petals from tepals or stamens and the links between the morphological expression of petals and floral organ identity genes in the core eudicots.
Scope
I challenge the widely held classical view that petals are morphologically derived from stamens in the core eudicots, and sepals from tepals or bracts. Morphological data suggest that tepal-derived petals have evolved independently in the major lineages of the core eudicots (i.e. asterids, Santalales and rosids) from Berberidopsis-like prototypes, and that staminodial petals have arisen only in few isolated cases where petals had been previously lost (Caryophyllales, Rosales). The clear correlation between continuous changes in petal morphology, and a scenario that indicates numerous duplications to have taken place in genes controlling floral organ development, can only be fully understood within a phylogenetic context. B-gene expression plays a fundamental role in the evolution of the petals by controlling petaloidy, but it does not clarify petal homology.
Conclusions
An increased synorganization of the flower in the core eudicots linked with the establishment of floral whorls restricts the petaloid gene expression to the second whorl, reducing the similarities of petals with tepals from which they were originally derived. An increased flower size linked with secondary polyandry or polycarpelly may lead to a breakdown of the restricted gene expression and a reversal to ancestral characteristics of perianth development. An altered ‘sliding boundary’ hypothesis is proposed for the core eudicots to explain shifts in petaloidy of the perianth and the event of staminodial petals. The repetitive changes of function in the perianth of the core eudicots are linked with shifts in petaloidy to the outer perianth whorl, or losses of petal or sepal whorls that can be secondarily compensated for by the inclusion of bracts in the flower. The origin and evolution of petals appears to be as complex on a molecular basis as it is from a morphological point of view.
doi:10.1093/aob/mcm076
PMCID: PMC2533615  PMID: 17513305
Apetala 3; Berberidopsis; bract-derived petals; core eudicots; gene expression; perianth evolution; petaloidy; phylogeny; staminodial petals
17.  Functional divergence within class B MADS-box genes TfGLO and TfDEF in Torenia fournieri Lind 
Molecular Genetics and Genomics  2010;284(5):399-414.
Homeotic class B genes GLOBOSA (GLO)/PISTILLATA (PI) and DEFICIENS (DEF)/APETALA3 (AP3) are involved in the development of petals and stamens in Arabidopsis. However, functions of these genes in the development of floral organs in torenia are less well known. Here, we demonstrate the unique floral phenotypes of transgenic torenia formed due to the modification of class B genes, TfGLO and TfDEF. TfGLO-overexpressing plants showed purple-stained sepals that accumulated anthocyanins in a manner similar to that of petals. TfGLO-suppressed plants showed serrated petals and TfDEF-suppressed plants showed partially decolorized petals. In TfGLO-overexpressing plants, cell shapes on the surfaces of sepals were altered to petal-like cell shapes. Furthermore, TfGLO- and TfDEF-suppressed plants partially had sepal-like cells on the surfaces of their petals. We isolated putative class B gene-regulated genes and examined their expression in transgenic plants. Three xyloglucan endo-1,4-beta-d-glucanase genes were up-regulated in TfGLO- and TfDEF-overexpressing plants and down-regulated in TfGLO- and TfDEF-suppressed plants. In addition, 10 anthocyanin biosynthesis-related genes, including anthocyanin synthase and chalcone isomerase, were up-regulated in TfGLO-overexpressing plants and down-regulated in TfGLO-suppressed plants. The expression patterns of these 10 genes in TfDEF transgenic plants were diverse and classified into several groups. HPLC analysis indicated that sepals of TfGLO-overexpressing plants accumulate the same type of anthocyanins and flavones as wild-type plants. The difference in phenotypes and expression patterns of the 10 anthocyanin biosynthesis-related genes between TfGLO and TfDEF transgenic plants indicated that TfGLO and TfDEF have partial functional divergence, while they basically work synergistically in torenia.
Electronic supplementary material
The online version of this article (doi:10.1007/s00438-010-0574-z) contains supplementary material, which is available to authorized users.
doi:10.1007/s00438-010-0574-z
PMCID: PMC2955243  PMID: 20872230
Torenia; TfGLO; TfDEF; Class B gene; Anthocyanin
18.  Flower-specific KNOX phenotype in the orchid Dactylorhiza fuchsii  
Journal of Experimental Botany  2012;63(13):4811-4819.
The KNOTTED1-like homeobox (KNOX) genes are best known for maintaining a pluripotent stem-cell population in the shoot apical meristem that underlies indeterminate vegetative growth, allowing plants to adapt their development to suit the prevailing environmental conditions. More recently, the function of the KNOX gene family has been expanded to include additional roles in lateral organ development such as complex leaf morphogenesis, which has come to dominate the KNOX literature. Despite several reports implicating KNOX genes in the development of carpels and floral elaborations such as petal spurs, few authors have investigated the role of KNOX genes in flower development. Evidence is presented here of a flower-specific KNOX function in the development of the elaborate flowers of the orchid Dactylorhiza fuchsii, which have a three-lobed labellum petal with a prominent spur. Using degenerate PCR, four Class I KNOX genes (DfKN1–4) have been isolated, one from each of the four major Class I KNOX subclades and by reverse transcription PCR (RT-PCR), it is demonstrated that DfKNOX transcripts are detectable in developing floral organs such as the spur-bearing labellum and inferior ovary. Although constitutive expression of the DfKN2 transcript in tobacco produces a wide range of floral abnormalities, including serrated petal margins, extra petal tissue, and fused organs, none of the vegetative phenotypes typical of constitutive KNOX expression were produced. These data are highly suggestive of a role for KNOX expression in floral development that may be especially important in taxa with elaborate flowers.
doi:10.1093/jxb/ers152
PMCID: PMC3428008  PMID: 22771852
Dactylorhiza fuchsii, evolution, flower development, KNOX genes, labellum, orchids, petal shape, petal spur.
19.  Floral Anatomy of Paepalanthoideae (Eriocaulaceae, Poales) and their Nectariferous Structures 
Annals of Botany  2006;99(1):131-139.
Background and Aims
Eriocaulaceae (Poales) is currently divided in two subfamilies: Eriocauloideae, which comprises two genera and Paepalanthoideae, with nine genera. The floral anatomy of Actinocephalus polyanthus, Leiothrix fluitans, Paepalanthus chlorocephalus, P. flaccidus and Rondonanthus roraimae was studied here. The flowers of these species of Paepalanthoideae are unisexual, and form capitulum-type inflorescences. Staminate and pistillate flowers are randomly distributed in the capitulum and develop centripetally. This work aims to establish a floral nomenclature for the Eriocaulaceae to provide more information about the taxonomy and phylogeny of the family.
Methods
Light microscopy, scanning electron microscopy and chemical tests were used to investigate the floral structures.
Key Results
Staminate and pistillate flowers are trimerous (except in P. flaccidus, which presents dimerous flowers), and the perianth of all species is differentiated into sepals and petals. Staminate flowers present an androecium with scale-like staminodes (not in R. roraimae) and fertile stamens, and nectariferous pistillodes. Pistillate flowers present scale-like staminodes (except for R. roraimae, which presents elongated and vascularized staminodes), and a gynoecium with a hollow style, ramified in stigmatic and nectariferous portions.
Conclusions
The scale-like staminodes present in the species of Paepalanthoideae indicate a probable reduction of the outer whorl of stamens present in species of Eriocauloideae. Among the Paepalanthoideae genera, Rondonanthus, which is probably basal, shows vascularized staminodes in their pistillate flowers. The occurrence of nectariferous pistillodes in staminate flowers and that of nectariferous portions of the style in pistillate flowers of Paepalanthoideae are emphasized as nectariferous structures in Eriocaulaceae.
doi:10.1093/aob/mcl231
PMCID: PMC2802974  PMID: 17085472
Eriocaulaceae; Paepalanthoideae; nectariferous structures; staminodes; staminate flowers; pistillate flowers; floral anatomy; monocotyledons; Poales
20.  Correlation between number and position of floral organs in Arabidopsis 
Annals of Botany  2011;108(1):123-131.
Background and Aims
The study of variation in number, position and type of floral organs may serve as a key to understanding the mechanisms underlying their variation, and will make it possible to improve the analysis of gene function in model plant species by means of a more accurate characterization of mutant phenotypes. The present analysis was carried out in order to understand the correlation between number and position of floral organs in Arabidopsis thaliana.
Methods
An analysis of number and position of organs in flowers of wild type as well as in a series of mutations with floral organ position alterations was carried out, using light and electron microscopy. Variation common to different genotypes was analysed by means of individual diagrams, upon which generalized diagrams depicting variation in number and position of organs, were built by superimposition.
Key Results and Conclusions
It is shown that in the Arabidopsis flower a correlation exists between positions of petals and sepals, as well as between positions of stamens and carpels, whereas the position of carpels does not seem to depend on number and position of petals and stamens. This suggests that the position of organs in the basal (sepals) and apical (carpels) parts of the flower are determined before that in the intermediate zone. This assumption is consistent with the results of mathematical modelling and is supposed to be the consequence of stem-cell activity in the flower.
doi:10.1093/aob/mcr115
PMCID: PMC3119622  PMID: 21693667
Flower organ position; Arabidopsis thaliana; flower development; floral patterning
21.  Expression of ethylene biosynthetic and receptor genes in rose floral tissues during ethylene-enhanced flower opening 
Journal of Experimental Botany  2008;59(8):2161-2169.
Ethylene production, as well as the expression of ethylene biosynthetic (Rh-ACS1–4 and Rh-ACO1) and receptor (Rh-ETR1–5) genes, was determined in five different floral tissues (sepals, petals, stamens, gynoecia, and receptacles) of cut rose (Rosa hybrida cv. Samantha upon treatment with ethylene or the ethylene inhibitor 1-methylcyclopropene (1-MCP). Ethylene-enhanced ethylene production occurred only in gynoecia, petals, and receptacles, with gynoecia showing the greatest enhancement in the early stage of ethylene treatment. However, 1-MCP did not suppress ethylene production in these three tissues. In sepals, ethylene production was highly decreased by ethylene treatment, and increased dramatically by 1-MCP. Ethylene production in stamens remained unchanged after ethylene or 1-MCP treatment. Induction of certain ethylene biosynthetic genes by ethylene in different floral tissues was positively correlated with the ethylene production, and this induction was also not suppressed by 1-MCP. The expression of Rh-ACS2 and Rh-ACS3 was quickly induced by ethylene in gynoecia, but neither Rh-ACS1 nor Rh-ACS4 was induced by ethylene in any of the five tissues. In addition, Rh-ACO1 was induced by ethylene in all floral tissues except sepals. The induced expression of ethylene receptor genes by ethylene was much faster in gynoecia than in petals, and the expression of Rh-ETR3 was strongly suppressed by 1-MCP in all floral tissues. These results indicate that ethylene biosynthesis in gynoecia is regulated developmentally, rather than autocatalytically. The response of rose flowers to ethylene occurs initially in gynoecia, and ethylene may regulate flower opening mainly through the Rh-ETR3 gene in gynoecia.
doi:10.1093/jxb/ern078
PMCID: PMC2413286  PMID: 18535299
Cut roses; ethylene biosynthesis; ethylene receptor; floral tissues; flower opening; gene expression; Rosa hybrida
22.  Stochastic properties of the plant circadian clock 
Circadian clocks are gene regulatory networks whose role is to help the organisms to cope with variations in environmental conditions such as the day/night cycle. In this work, we explored the effects of molecular noise in single cells on the behaviour of the circadian clock in the plant model species Arabidopsis thaliana. The computational modelling language Bio-PEPA enabled us to give a stochastic interpretation of an existing deterministic model of the clock, and to easily compare the results obtained via stochastic simulation and via numerical solution of the deterministic model. First, the introduction of stochasticity in the model allowed us to estimate the unknown size of the system. Moreover, stochasticity improved the description of the available experimental data in several light conditions: noise-induced fluctuations yield a faster entrainment of the plant clock under certain photoperiods and are able to explain the experimentally observed dampening of the oscillations in plants under constant light conditions. The model predicts that the desynchronization between noisy oscillations in single cells contributes to the observed damped oscillations at the level of the cell population. Analysis of the phase, period and amplitude distributions under various light conditions demonstrated robust entrainment of the plant clock to light/dark cycles which closely matched the available experimental data.
doi:10.1098/rsif.2011.0378
PMCID: PMC3284129  PMID: 21880617
circadian clock; Arabidopsis thaliana; discrete stochastic model; Bio-PEPA process algebra; oscillatory systems
23.  Developmental Changes in the Metabolic Network of Snapdragon Flowers 
PLoS ONE  2012;7(7):e40381.
Evolutionary and reproductive success of angiosperms, the most diverse group of land plants, relies on visual and olfactory cues for pollinator attraction. Previous work has focused on elucidating the developmental regulation of pathways leading to the formation of pollinator-attracting secondary metabolites such as scent compounds and flower pigments. However, to date little is known about how flowers control their entire metabolic network to achieve the highly regulated production of metabolites attracting pollinators. Integrative analysis of transcripts and metabolites in snapdragon sepals and petals over flower development performed in this study revealed a profound developmental remodeling of gene expression and metabolite profiles in petals, but not in sepals. Genes up-regulated during petal development were enriched in functions related to secondary metabolism, fatty acid catabolism, and amino acid transport, whereas down-regulated genes were enriched in processes involved in cell growth, cell wall formation, and fatty acid biosynthesis. The levels of transcripts and metabolites in pathways leading to scent formation were coordinately up-regulated during petal development, implying transcriptional induction of metabolic pathways preceding scent formation. Developmental gene expression patterns in the pathways involved in scent production were different from those of glycolysis and the pentose phosphate pathway, highlighting distinct developmental regulation of secondary metabolism and primary metabolic pathways feeding into it.
doi:10.1371/journal.pone.0040381
PMCID: PMC3394800  PMID: 22808147
24.  Are binary synapses superior to graded weight representations in stochastic attractor networks? 
Cognitive Neurodynamics  2009;3(3):243-250.
Synaptic plasticity is an underlying mechanism of learning and memory in neural systems, but it is controversial whether synaptic efficacy is modulated in a graded or binary manner. It has been argued that binary synaptic weights would be less susceptible to noise than graded weights, which has impelled some theoretical neuroscientists to shift from the use of graded to binary weights in their models. We compare retrieval performance of models using both binary and graded weight representations through numerical simulations of stochastic attractor networks. We also investigate stochastic attractor models using multiple discrete levels of weight states, and then investigate the optimal threshold for dilution of binary weight representations. Our results show that a binary weight representation is not less susceptible to noise than a graded weight representation in stochastic attractor models, and we find that the load capacities with an increasing number of weight states rapidly reach the load capacity with graded weights. The optimal threshold for dilution of binary weight representations under stochastic conditions occurs when approximately 50% of the smallest weights are set to zero.
doi:10.1007/s11571-009-9083-3
PMCID: PMC2727164  PMID: 19424822
Synaptic plasticity; Binary versus graded; Associative memory; Point attractor networks
25.  Determination of Flower Structure in Elaeis guineensis: Do Palms use the Same Homeotic Genes as Other Species? 
Annals of Botany  2007;100(1):1-12.
Aims
In this article a review is made of data recently obtained on the structural diversity and possible functions of MADS box genes in the determination of flower structure in the African oil palm (Elaeis guineensis). MADS box genes play a dominant role in the ABC model established to explain how floral organ identity is determined in model dicotyledon species such as Arabidopsis thaliana and Antirrhinum majus. In the monocotyledons, although there appears to be a broad general conservation of ABC gene functions, the model itself needs to be adapted in some cases, notably for certain species which produce flowers with sepals and petals of similar appearance. For the moment, ABC genes remain unstudied in a number of key monocot clades, so only a partial picture is available for the Liliopsida as a whole. The aim of this article is to summarize data recently obtained for the African oil palm Elaeis guineensis, a member of the family Arecaceae (Arecales), and to discuss their significance with respect to knowledge gained from other Angiosperm groups, particularly within the monocotyledons.
Scope
The essential details of reproductive development in oil palm are discussed and an overview is provided of the structural and functional characterization of MADS box genes likely to play a homeotic role in flower development in this species.
Conclusions
The structural and functional data provide evidence for a general conservation of the generic ‘ABC’ model in oil palm, rather than the ‘modified ABC model’ proposed for some other monocot species which produce homochlamydeous flowers (i.e. with morphologically similar organs in both perianth whorls), such as members of the Liliales. Our oil palm data therefore follow a similar pattern to those obtained for other Commelinid species in the orders Commelinales and Poales. The significance of these findings is discussed.
doi:10.1093/aob/mcm027
PMCID: PMC2735288  PMID: 17355996
Palm; MADS box; flower; Elaeis; monoecious; homeotic

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