Roles of synorganisation, zygomorphy and heterotopy in floral evolution: the gynostemium and labellum of orchids and other lilioid monocots

A de novo floral transcriptome reveals clues into Phalaenopsis orchid flower development

Phalaenopsis has a zygomorphic floral structure, including three outer tepals, two lateral inner tepals and a highly modified inner median tepal called labellum or lip; however, the regulation of its organ development remains unelucidated. We generated RNA-seq reads with the Illumina platform for floral organs of the Phalaenopsis wild-type and peloric mutant with a lip-like petal. A total of 43,552 contigs were obtained after de novo assembly. We used differentially expressed gene profiling to compare the transcriptional changes in floral organs for both the wild-type and peloric mutant. Pair-wise comparison of sepals, petals and labellum between peloric mutant and its wild-type revealed 1,838, 758 and 1,147 contigs, respectively, with significant differential expression. PhAGL6a (CUFF.17763), PhAGL6b (CUFF.17763.1), PhMADS1 (CUFF.36625.1), PhMADS4 (CUFF.25909) and PhMADS5 (CUFF.39479.1) were significantly upregulated in the lip-like petal of the peloric mutant. We used real-time PCR analysis of lip-like petals, lip-like sepals and the big lip of peloric mutants to confirm the five genes' expression patterns. PhAGL6a, PhAGL6b and PhMADS4 were strongly expressed in the labellum and significantly upregulated in lip-like petals and lip-like sepals of peloric-mutant flowers. In addition, PhAGL6b was significantly downregulated in the labellum of the big lip mutant, with no change in expression of PhAGL6a. We provide a comprehensive transcript profile and functional analysis of Phalaenopsis floral organs. PhAGL6a PhAGL6b, and PhMADS4 might play crucial roles in the development of the labellum in Phalaenopsis. Our study provides new insights into how the orchid labellum differs and why the petal or sepal converts to a labellum in Phalaenopsis floral mutants.

Histone acetylation accompanied with promoter sequences displaying differential expression profiles of B-class MADS-box genes for phalaenopsis floral morphogenesis

Five B-class MADS-box genes, including four APETALA3 (AP3)-like PeMADS2∼5 and one PISTILLATA (PI)-like PeMADS6, specify the spectacular flower morphology in orchids. The PI-like PeMADS6 ubiquitously expresses in all floral organs. The four AP3-like genes, resulted from two duplication events, express ubiquitously at floral primordia and early floral organ stages, but show distinct expression profiles at late floral organ primordia and floral bud stages. Here, we isolated the upstream sequences of PeMADS2∼6 and studied the regulatory mechanism for their distinct gene expression. Phylogenetic footprinting analysis of the 1.3-kb upstream sequences of AP3-like PeMADS2∼5 showed that their promoter regions have sufficiently diverged and contributed to their subfunctionalization. The amplified promoter sequences of PeMADS2∼6 could drive beta-glucuronidase (GUS) gene expression in all floral organs, similar to their expression at the floral primordia stage. The promoter sequence of PeMADS4, exclusively expressed in lip and column, showed a 1.6∼3-fold higher expression in lip/column than in sepal/petal. Furthermore, we noted a 4.9-fold increase in histone acetylation (H3K9K14ac) in the translation start region of PeMADS4 in lip as compared in petal. All these results suggest that the regulation via the upstream sequences and increased H3K9K14ac level may act synergistically to display distinct expression profiles of the AP3-like genes at late floral organ primordia stage for Phalaenopsis floral morphogenesis.

Comparative proteomic analysis of labellum and inner lateral petals in Cymbidium ensifolium flowers

The labellum in orchids shares homology with the inner lateral petals of the flower. The labellum is a modified petal and often distinguished from other petals and sepals due to its large size and irregular shape. Herein, we combined two-dimensional gel electrophoresis (2-DE) and matrix assisted laser desorption/ionization time of flight/time of flight (MALDI-TOF/TOF) approaches to identify the differentially expressed proteome between labellum and inner lateral petal in one of Orchid species (C. ensifolium). A total of 30 protein spots were identified, which showed more than a two-fold significant difference (p < 0.05) in their expression. Compared with C. ensifolium transcriptome (sequenced in house), 21 proteins matched the translated nucleotide. The proteins identified were classified into 48 categories according to gene ontology (GO). Additionally, these proteins were involved in 18 pathways and 9 possible protein-protein interactions. Serine carboxypeptidase and beta-glucosidase were involved in the phenylpropanoid pathway, which could regulate biosynthesis of floral scent components. Malate dehydrogenase (maeB) and triosephosphate isomerase (TPI) in carbon fixation pathway could regulate the energy metabolism. Xyloglucan endotransglucosylase/hydrolase (XET/XTH) could promote cell wall formation and aid the petal’s morphogenesis. The identification of such differentially expressed proteins provides new targets for future studies; these will assess the proteins’ physiological roles and significance in labellum and inner lateral petals.

De novo transcriptome assembly from inflorescence of Orchis italica: analysis of coding and non-coding transcripts

The floral transcriptome of Orchis italica, a wild orchid species, was obtained using Illumina RNA-seq technology and specific de novo assembly and analysis tools. More than 100 million raw reads were processed resulting in 132,565 assembled transcripts and 86,079 unigenes with an average length of 606 bp and N50 of 956 bp. Functional annotation assigned 38,984 of the unigenes to records present in the NCBI non-redundant protein database, 32,161 of them to Gene Ontology terms, 15,775 of them to Eukaryotic Orthologous Groups (KOG) and 7,143 of them to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The in silico expression analysis based on the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) was confirmed by real-time RT-PCR experiments on 10 selected unigenes, which showed high and statistically significant positive correlation with the RNA-seq based expression data. The prediction of putative long non-coding RNAs was assessed using two different software packages, CPC and Portrait, resulting in 7,779 unannotated unigenes that matched the threshold values for both of the analyses. Among the predicted long non-coding RNAs, one is the homologue of TAS3, a long non-coding RNA precursor of trans-acting small interfering RNAs (ta-siRNAs). The differential expression pattern observed for the selected putative long non-coding RNAs suggests their possible functional role in different floral tissues.

Flower development of Phalaenopsis orchid involves functionally divergent SEPALLATA-like genes

The Phalaenopsis orchid produces complex flowers that are commercially valuable, which has promoted the study of its flower development. E-class MADS-box genes, SEPALLATA (SEP), combined with B-, C- and D-class MADS-box genes, are involved in various aspects of plant development, such as floral meristem determination, organ identity, fruit maturation, seed formation and plant architecture. Four SEP-like genes were cloned from Phalaenopsis orchid, and the duplicated PeSEPs were grouped into PeSEP1/3 and PeSEP2/4. All PeSEPs were expressed in all floral organs. PeSEP2 expression was detectable in vegetative tissues. The study of protein-protein interactions suggested that PeSEPs may form higher order complexes with the B-, C-, D-class and AGAMOUS LIKE6-related MADS-box proteins to determine floral organ identity. The tepal became a leaf-like organ when PeSEP3 was silenced by virus-induced silencing, with alterations in epidermis identity and contents of anthocyanin and chlorophyll. Silencing of PeSEP2 had minor effects on the floral phenotype. Silencing of the E-class genes PeSEP2 and PeSEP3 resulted in the downregulation of B-class PeMADS2-6 genes, which indicates an association of PeSEP functions and B-class gene expression. These findings reveal the important roles of PeSEP in Phalaenopsis floral organ formation throughout the developmental process by the formation of various multiple protein complexes.

Identification and characterization of the microRNA transcriptome of a moth orchid Phalaenopsis aphrodite

Orchids display unique phenotypes, functional characteristics and ecological adaptations that are not found in model plants. In this study, we aimed to characterize the microRNA (miRNA) transcriptome and identify species- and tissue-specific miRNAs in Phalaenopsis aphrodite. After data filtering and cleanup, a total of 59,387,374 reads, representing 1,649,996 unique reads, were obtained from four P. aphrodite small RNA libraries. A systematic bioinformatics analysis pipeline was developed that can be used for miRNA and precursor mining, and target gene prediction in non-model plants. A total of 3,251 unique reads for 181 known plant miRNAs (belonging to 88 miRNA families), 23 new miRNAs and 91 precursors were identified. All the miRNA star sequences (miRNA*), the complementary strands of miRNA that from miRNA/miRNA* duplexes, of the predicted new miRNAs were detected in our small RNA libraries, providing additional evidence for their existence as new miRNAs in P. aphrodite. Furthermore, 240 potential miRNA-targets that appear to be involved in many different biological activities and molecular functions, especially transcription factors, were identified, suggesting that miRNAs can impact multiple processes in P. aphrodite. We also verified the cleavage sites for six targets using RNA ligase-mediated rapid amplification of 5' ends assay. The results provide valuable information about the composition, expression and function of miRNA in P. aphrodite, and will aid functional genomics studies of orchids.

New insight into the regulation of floral morphogenesis

The beauty and complexity of flowers have held the fascination of scientists for centuries, from Linnaeus, to Goethe, to Darwin, through to the present. During the past decade, enormous progress has been made in understanding the molecular regulation of flower morphogenesis. It seems likely that there are both highly conserved aspects to flower development in addition to significant differences in developmental patterning that can contribute to the unique morphologies of different species. Furthermore, floral development is attractive in that several key genes regulating fundamental processes have been identified. Crucial functional studies of floral organ identity genes in diverse taxa are allowing the real insight into the conservation of gene function, while findings on the genetic control of organ elaboration open up new avenues for investigation. These fundamentals of floral organ differentiation and growth are therefore an ideal subject for comparative analyses of flower development, which will lead to a better understanding of molecular mechanisms that control flower morphogenesis.

Expression of paralogous SEP-, FUL-, AG- and STK-like MADS-box genes in wild-type and peloric Phalaenopsis flowers

The diverse flowers of Orchidaceae are the result of several major morphological transitions, among them the most studied is the differentiation of the inner median tepal into the labellum, a perianth organ key in pollinator attraction. Type A peloria lacking stamens and with ectopic labella in place of inner lateral tepals are useful for testing models on the genes specifying these organs by comparing their patterns of expression between wild-type and peloric flowers. Previous studies focused on DEFICIENS- and GLOBOSA-like MADS-box genes because of their conserved role in perianth and stamen development. The "orchid code" model summarizes this work and shows in Orchidaceae there are four paralogous lineages of DEFICIENS/AP3-like genes differentially expressed in each floral whorl. Experimental tests of this model showed the conserved, higher expression of genes from two specific DEF-like gene lineages is associated with labellum development. The present study tests whether eight MADS-box candidate SEP-, FUL-, AG-, and STK-like genes have been specifically duplicated in the Orchidaceae and are also differentially expressed in association with the distinct flower organs of Phalaenopsis hyb. "Athens." The gene trees indicate orchid-specific duplications. In a way analogous to what is observed in labellum-specific DEF-like genes, a two-fold increase in the expression of SEP3-like gene PhaMADS7 was measured in the labellum-like inner lateral tepals of peloric flowers. The overlap between SEP3-like and DEF-like genes suggests both are associated with labellum specification and similar positional cues determine their domains of expression. In contrast, the uniform messenger levels of FUL-like genes suggest they are involved in the development of all organs and their expression in the ovary suggests cell differentiation starts before pollination. As previously reported AG-like and STK-like genes are exclusively expressed in gynostemium and ovary, however no evidence for transcriptional divergence was found in the stage investigated. Gene expression suggests a developmental regulatory system based on the combined activity of duplicate MADS-box genes. We discuss its feasibility based on documented protein interactions and patterns of expression.

A modified ABCDE model of flowering in orchids based on gene expression profiling studies of the moth orchid Phalaenopsis aphrodite

Previously we developed genomic resources for orchids, including transcriptomic analyses using next-generation sequencing techniques and construction of a web-based orchid genomic database. Here, we report a modified molecular model of flower development in the Orchidaceae based on functional analysis of gene expression profiles in Phalaenopsis aphrodite (a moth orchid) that revealed novel roles for the transcription factors involved in floral organ pattern formation. Phalaenopsis orchid floral organ-specific genes were identified by microarray analysis. Several critical transcription factors including AP3, PI, AP1 and AGL6, displayed distinct spatial distribution patterns. Phylogenetic analysis of orchid MADS box genes was conducted to infer the evolutionary relationship among floral organ-specific genes. The results suggest that gene duplication MADS box genes in orchid may have resulted in their gaining novel functions during evolution. Based on these analyses, a modified model of orchid flowering was proposed. Comparison of the expression profiles of flowers of a peloric mutant and wild-type Phalaenopsis orchid further identified genes associated with lip morphology and peloric effects. Large scale investigation of gene expression profiles revealed that homeotic genes from the ABCDE model of flower development classes A and B in the Phalaenopsis orchid have novel functions due to evolutionary diversification, and display differential expression patterns.

Perspectives on MADS-box expression during orchid flower evolution and development

The diverse morphology of orchid flowers and their complex, often deceptive strategies to become pollinated have fascinated researchers for a long time. However, it was not until the 20th century that the ontogeny of orchid flowers, the genetic basis of their morphology and the complex phylogeny of Orchidaceae were investigated. In parallel, the improvement of techniques for in vitro seed germination and tissue culture, together with studies on biochemistry, physiology, and cytology supported the progress of what is now a highly productive industry of orchid breeding and propagation. In the present century both basic research in orchid flower evo-devo and the interest for generating novel horticultural varieties have driven the characterization of many members of the MADS-box family encoding key regulators of flower development. This perspective summarizes the picture emerging from these studies and discusses the advantages and limitations of the comparative strategy employed so far. I address the growing role of natural and horticultural mutants in these studies and the emergence of several model species in orchid evo-devo and genomics. In this context, I make a plea for an increasingly integrative approach.

Organ homologies in orchid flowers re-interpreted using the Musk Orchid as a model

Background and Aims. The presence of novel structures in orchid flowers, including auricles, rostellum and bursicles on the gynostemium and a lobed labellum, has prompted long-standing homology disputes, fuelled by conflicting evidence from a wide range of sources. Re-assessment of this debate using an improved model is timely, following recent phylogenetic insights and on the cusp of a revolution in developmental genetics.

Methods. We use new data from floral development and anatomy in the small-flowered terrestrial orchid Herminium monorchis as a model to explore organ homologies in orchid flowers within the context of a review of recent literature on developmental genetics.

Key Results. The apex of the median carpel of Herminium is trilobed, and the bursicles develop from its lateral lobes, relatively late in flower ontogeny. The bursicles enclose the viscidia, which adhere to the tapetal remnants to form a caudicle linking the viscidium with the pollinium. The auricles are initiated earlier than the bursicles, but they also remain unvascularized. The deeply trilobed labellum possesses three vascular traces, in contrast with the lateral petals, each of which contains a single vascular trace. The two lateral labellum traces diverge from the traces supplying the two adjacent lateral sepals. Data from flower ontogeny and anatomy conflict with respect to organ homologies.

Conclusions. Much progress has recently been made in understanding the exceptional differentiation shown by orchids among perianth segments, focusing on multiple copies of the DEF/AP3 subclass of B-class MADS-box genes. In contrast, untangling homologies of profound congenital union of multiple floral organs forming the orchid gynostemium is hampered by their profound congenital union, which we ascribe to overlap in gene expression between organs. Thus, the functional morphology of the orchid flower could ultimately reflect extreme synorganization and associated genetic integration. Analogizing the deeply lobed orchid labellum with a compound leaf, we speculate that KNOX genes could be implicated not only in their demonstrated role in spur development but also in the development of both the characteristic lobed morphology of the orchid labellum and the lobing of the median carpel that differentiates the bursicles and rostellum.

The OitaAG and OitaSTK genes of the orchid Orchis italica: a comparative analysis with other C- and D-class MADS-box genes

According to the ABCDE model of flower development, the C- and D- class MADS box genes are involved in the formation of male and female reproductive organs (fused to form the column in orchids) and in ovule maturation (triggered by fertilization in orchids). In the present study, we report the isolation of the Orchis italica genes OitaAG and OitaSTK, homologs of the C-class AGAMOUS and the D-class SEEDSTICK genes of Arabidopsis, respectively. Analysis of their expression profiles reveals high levels of mRNA in columns and ovaries, particularly after pollination. However, weak expression is also detectable in the inner tepals (OitaAG) and the lip and root (OitaSTK). This expression profile is only partially overlapping with those reported in other orchid species and may be the consequence of a different evolutionary history of these functional gene classes in orchids. The genomic characterization of the OitaAG and OitaSTK genes shows that a high number of traces of mobile elements are present in introns and could have contributed to the size expansion of some of them (e.g., intron 2 and 3 of OitaAG and intron 3, 4 and 5 of OitaSTK). Nucleotide sequences of intron 1 of the OitaSTK gene and other STK-like genes do not share regulatory motifs, whereas sequence comparison of intron 2 of the OitaAG gene with that of intron 2 of other AG-like genes reveals, for the first time in an orchid species, the presence of conserved cis-regulatory boxes and binding sites for transcription factors that positively (e.g., LEAFY and WUSCHEL) or negatively (e.g., BELLRINGER) regulate the expression of the AG homologs in dicots and monocots.

The mirror crack'd: both pigment and structure contribute to the glossy blue appearance of the mirror orchid, Ophrys speculum

The Mediterranean orchid genus Ophrys is remarkable for its pseudocopulatory pollination mechanism; naïve male pollinators are attracted to the flowers by olfactory, visual and tactile cues. The most striking visual cue is a highly reflective, blue speculum region at the centre of the labellum, which mimics the corresponding female insect and reaches its strongest development in the mirror orchid, O. speculum. We explored the structure and properties of the much-discussed speculum by scanning and transmission electron microscopic examination of its ultrastructure, visible and ultraviolet (UV) angle-resolved spectrophotometry of the intact tissue, and mass spectrometry of extracted pigments. The speculum contrasts with the surrounding labellar epidermis in being flat-celled with a thick, smooth cuticle. The speculum is extremely glossy, reflecting intense white light in a specular direction, but at more oblique angles it predominantly reflects blue and UV light. Pigments in the speculum, dominantly the cyanidin 3-(3''-malonylglucoside), are less diverse than in the surrounding regions of the labellar epidermis and lack quercetin copigments. Several physical and biochemical processes interact to produce the striking and much-discussed optical effects in these flowers, but the blue colour is not produced by structural means and is not iridescent.

Reconstructing the origin and elaboration of insect-trapping inflorescences in the Araceae

PREMISE OF THE STUDY

Floral traps are among the most sophisticated devices that have evolved in angiosperms in the context of pollination, but the evolution of trap pollination has not yet been studied in a phylogenetic context. We aim to determine the evolutionary history of morphological traits that facilitate trap pollination and to elucidate the impact of pollinators on the evolution of inflorescence traps in the family Araceae. •

METHODS

Inflorescence morphology was investigated to determine the presence of trapping devices and to classify functional types of traps. We inferred phylogenetic relationships in the family using maximum likelihood and Bayesian methods. Character evolution of trapping devices, trap types, and pollinator types was then assessed with maximum parsimony and Bayesian methods. We also tested for an association of trap pollination with specific pollinator types. •

KEY RESULTS

Inflorescence traps have evolved independently at least 10 times within the Araceae. Trapping devices were found in 27 genera. On the basis of different combinations of trapping devices, six functional types of traps were identified. Trap pollination in Araceae is correlated with pollination by flies. •

CONCLUSIONS

Trap pollination in the Araceae is more common than was previously thought. Preadaptations such as papillate cells or elongated sterile flowers facilitated the evolution of inflorescence traps. In some clades, imperfect traps served as a precursor for the evolution of more elaborate traps. Traps that evolved in association with fly pollination were most probably derived from mutualistic ancestors, offering a brood-site to their pollinators.

The MADS and the Beauty: Genes Involved in the Development of Orchid Flowers

Since the time of Darwin, biologists have studied the origin and evolution of the Orchidaceae, one of the largest families of flowering plants. In the last two decades, the extreme diversity and specialization of floral morphology and the uncoupled rate of morphological and molecular evolution that have been observed in some orchid species have spurred interest in the study of the genes involved in flower development in this plant family. As part of the complex network of regulatory genes driving the formation of flower organs, the MADS-box represents the most studied gene family, both from functional and evolutionary perspectives. Despite the absence of a published genome for orchids, comparative genetic analyses are clarifying the functional role and the evolutionary pattern of the MADS-box genes in orchids. Various evolutionary forces act on the MADS-box genes in orchids, such as diffuse purifying selection and the relaxation of selective constraints, which sometimes reveals a heterogeneous selective pattern of the coding and non-coding regions. The emerging theory regarding the evolution of floral diversity in orchids proposes that the diversification of the orchid perianth was a consequence of duplication events and changes in the regulatory regions of the MADS-box genes, followed by sub- and neo-functionalization. This specific developmental-genetic code is termed the "orchid code."

Flower-specific KNOX phenotype in the orchid Dactylorhiza fuchsii

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.

Characterization of Linaria KNOX genes suggests a role in petal-spur development

Spurs are tubular outgrowths of perianth organs that have evolved iteratively among angiosperms. They typically contain nectar and often strongly influence pollinator specificity, potentially mediating reproductive isolation. The identification of Antirrhinum majus mutants with ectopic petal spurs suggested that petal-spur development is dependent on the expression of KNOTTED 1-like homeobox (KNOX) genes, which are better known for their role in maintaining the shoot apical meristem. Here, we tested the role of KNOX genes in petal-spur development by isolating orthologs of the A. majus KNOX genes Hirzina (AmHirz) and Invaginata (AmIna) from Linaria vulgaris, a related species that differs from A. majus in possessing long, narrow petal spurs. We name these genes LvHirz and LvIna, respectively. Using quantitative reverse-transcription PCR, we show that LvHirz is expressed at high levels in the developing petals and demonstrate that the expression of petal-associated KNOX genes is sufficient to induce sac-like outgrowths on petals in a heterologous host. We propose a model in which KNOX gene expression during early petal-spur development promotes and maintains further morphogenetic potential of the petal, as previously described for KNOX gene function in compound leaf development. These data indicate that petal spurs could have evolved by changes in regulatory gene expression that cause rapid and potentially saltational phenotypic modifications. Given the morphological similarity of spur ontogeny in distantly related taxa, changes in KNOX gene expression patterns could be a shared feature of spur development in angiosperms.

The duplicated B-class MADS-box genes display dualistic characters in orchid floral organ identity and growth

Orchidaceae are an excellent model to examine perianth development because of their sophisticated floral architecture. In this study, we identified 24 APETALA3 (AP3)-like and 13 PISTILLA (PI)-like genes from 11 species of orchids and characterized them into four AP3- and two PI-duplicated homologs. The first duplication event in AP3 homologs occurring in the early evolutionary history of the Orchidaceae gave rise to AP3A and AP3B clades. Further duplication events resulted in four subclades, namely AP3A1, AP3A2, AP3B1 and AP3B2, during the evolution of Orchidaceae. The AP3 paralogous genes were expressed throughout inflorescence and floral bud development. From the in situ hybridization results, we noticed that the transition timings from ubiquitous to constrained expression in floral organs for both clades are different. The transition point of expression of the AP3A clade (clades 3 and 4) was at the late floral organ primordia stage. In contrast, that for the AP3B clade (clades 1 and 2) was not observed until the late inflorescence and floral bud stages. In addition, the AP3 orthologous genes revealed diverse expression patterns in various species of orchids, whereas the PI homologs were uniformly expressed in all floral whorls. AP3A2 orthologs play a noticeable role in lip formation because of their exclusive expression in the lip. Further evidence comes from the ectopic expression of AP3A2 detected in the lip-like petals extending from the lip in four sets of peloric mutants. Finally, a Homeotic Orchid Tepal (HOT) model is proposed, in which dualistic characters of duplicated B-class MADS-box genes are involved in orchid perianth development and growth.

De novo assembly of expressed transcripts and global analysis of the Phalaenopsis aphrodite transcriptome

Being one of the largest families in the angiosperms, Orchidaceae display a great biodiversity resulting from adaptation to diverse habitats. Genomic information on orchids is rather limited, despite their unique and interesting biological features, thus impeding advanced molecular research. Here we report a strategy to integrate sequence outputs of the moth orchid, Phalaenopsis aphrodite, from two high-throughput sequencing platform technologies, Roche 454 and Illumina/Solexa, in order to maximize assembly efficiency. Tissues collected for cDNA library preparation included a wide range of vegetative and reproductive tissues. We also designed an effective workflow for annotation and functional analysis. After assembly and trimming processes, 233,823 unique sequences were obtained. Among them, 42,590 contigs averaging 875 bp in length were annotated to protein-coding genes, of which 7,263 coding genes were found to be nearly full length. The sequence accuracy of the assembled contigs was validated to be as high as 99.9%. Genes with tissue-specific expression were also categorized by profiling analysis with RNA-Seq. Gene products targeted to specific subcellular localizations were identified by their annotations. We concluded that, with proper assembly to combine outputs of next-generation sequencing platforms, transcriptome information can be enriched in gene discovery, functional annotation and expression profiling of a non-model organism.

Gene discovery using next-generation pyrosequencing to develop ESTs for Phalaenopsis orchids

BACKGROUND

Orchids are one of the most diversified angiosperms, but few genomic resources are available for these non-model plants. In addition to the ecological significance, Phalaenopsis has been considered as an economically important floriculture industry worldwide. We aimed to use massively parallel 454 pyrosequencing for a global characterization of the Phalaenopsis transcriptome.

RESULTS

To maximize sequence diversity, we pooled RNA from 10 samples of different tissues, various developmental stages, and biotic- or abiotic-stressed plants. We obtained 206,960 expressed sequence tags (ESTs) with an average read length of 228 bp. These reads were assembled into 8,233 contigs and 34,630 singletons. The unigenes were searched against the NCBI non-redundant (NR) protein database. Based on sequence similarity with known proteins, these analyses identified 22,234 different genes (E-value cutoff, e-7). Assembled sequences were annotated with Gene Ontology, Gene Family and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Among these annotations, over 780 unigenes encoding putative transcription factors were identified.

CONCLUSION

Pyrosequencing was effective in identifying a large set of unigenes from Phalaenopsis. The informative EST dataset we developed constitutes a much-needed resource for discovery of genes involved in various biological processes in Phalaenopsis and other orchid species. These transcribed sequences will narrow the gap between study of model organisms with many genomic resources and species that are important for ecological and evolutionary studies.

Conserved differential expression of paralogous DEFICIENS- and GLOBOSA-like MADS-box genes in the flowers of Orchidaceae: refining the 'orchid code'

In flowering plants, class-B floral homeotic genes encode MADS-domain transcription factors, which are key in the specification of petal and stamen identity, and have two ancient clades: DEF-like and GLO-like genes. Many species have one gene of each clade, but orchids have typically four DEF-like genes, representing ancient gene clades 1, 2, 3 and 4. We tested the 'orchid code', a combinatorial genetic model suggesting that differences between the organs of the orchid perianth (outer tepals, inner lateral tepals and labellum) are generated by the combinatorial differential expression of four DEF-like genes. Our experimental test involves highly sensitive and specific measurements, with qRT-PCR of the expression of DEF- and GLO-like genes from the distantly related Vanilla planifolia and Phragmipedium longifolium, as well as from wild-type and peloric Phalaenopsis hybrid flowers. Our findings support the first 'orchid code' hypothesis, in that absence of clade-3 and -4 gene expression distinguishes the outer tepals from the inner tepals. In contrast to the original hypothesis, however, mRNA of both clade-3 and -4 genes accumulates in wild-type inner lateral tepals and the labellum, and in labellum-like inner lateral tepals of peloric flowers, albeit in different quantities. Our data suggest a revised hypothesis where high levels of clade-1 and -2, and low levels of clade-3 and -4, gene expression specify inner lateral tepals, whereas labellum development requires low levels of clade-1 and -2 expression and high levels of clade-3 and -4 expression.

The PI/GLO-like locus in orchids: duplication and purifying selection at synonymous sites within Orchidinae (Orchidaceae)

Positive selection and relaxation of purifying constraints after duplication events have driven the functional diversification of gene families involved in development. One example of this occurred within the plant MADS-box genes. The evolution of the orchid flower was driven by duplication events followed by sub- and neo-functionalization of class B DEF-like MADS-box genes, which are present at three to four copies in the orchid genome. In contrast, the orchid PI/GLO-like class B MADS-box genes have been reported thus far as single-copy loci, with the only exception of Habenaria radiata. We isolated a novel PI/GLO-like gene (OrcPI2) in Orchis italica, which is different than the previously characterized OrcPI locus. The presence of two functional paralogs of PI/GLO-like genes in orchids is detectable only within the tribe Orchidinae. Evolutionary analyses revealed an apparent relaxation of purifying selection acting on the two PI/GLO-like paralogs of the Orchidinae when compared to the single-copy PI/GLO-like genes found in other orchid species. Furthermore, by measuring dN/dS (ω) ratios, we show that a high percentage of sites between the two PI/GLO-like paralogs have different evolutionary pressures. Interestingly, the apparent relaxation of selective constraints on the two PI/GLO-like paralogs is due to strong purifying selection at synonymous sites rather than to a high value of nonsynonymous substitution rate. This peculiar evolutionary pattern might be related to molecular processes such as mRNA folding and/or translational efficiency control. These processes could potentially be involved in or predate the functional diversification of the two PI/GLO-like paralogs within Orchidinae.

Duplicated C-class MADS-box genes reveal distinct roles in gynostemium development in Cymbidium ensifolium (Orchidaceae)

The orchid floral organs represent novel and effective structures for attracting pollination vectors. In addition, to avoid inbreeding, the androecium and gynoecium are united in a single structure termed the gynostemium. Identification of C-class MADS-box genes regulating reproductive organ development could help determine the level of homology with the current ABC model of floral organ identity in orchids. In this study, we isolated and characterized two C-class AGAMOUS-like genes, denoted CeMADS1 and CeMADS2, from Cymbidium ensifolium. These two genes showed distinct spatial and temporal expression profiles, which suggests their functional diversification during gynostemium development. Furthermore, the expression of CeMADS1 but not CeMADS2 was eliminated in the multitepal mutant whose gynostemium is replaced by a newly emerged flower, and this ecotopic flower continues to produce sepals and petals centripetally. Protein interaction relationships among CeMADS1, CeMADS2 and E-class PeMADS8 proteins were assessed by yeast two-hybrid analysis. Both CeMADS1 and CeMADS2 formed homodimers and heterodimers with each other and the E-class PeMADS protein. Furthermore, transgenic Arabidopsis plants overexpressing CeMADS1 or CeMADS2 showed limited growth of primary inflorescence. Thus, CeMADS1 may have a pivotal C function in reproductive organ development in C. ensifolium.

Synorganisation without organ fusion in the flowers of Geranium robertianum (Geraniaceae) and its not so trivial obdiplostemony

BACKGROUND AND AIMS

Synorganisation of floral organs, an important means in angiosperm flower evolution, is mostly realized by congenital or post-genital organ fusion. Intimate synorganisation of many floral organs without fusion, as present in Geranium robertianum, is poorly known and needs to be studied. Obdiplostemony, the seemingly reversed position of two stamen whorls, widely distributed in core eudicots, has been the subject of much attention, but there is confusion in the literature. Obdiplostemony occurs in Geranium and whether and how it is involved in this synorganisation is explored here.

METHODS

Floral development and architecture were studied with light microscopy based on microtome section series and with scanning electron microscopy.

KEY RESULTS

Intimate synorganisation of floral organs is effected by the formation of five separate nectar canals for the proboscis of pollinators. Each nectar canal is formed by six adjacent organs from four organ whorls. In addition, the sepals are hooked together by the formation of longitudinal ribs and grooves, and provide a firm scaffold for the canals. Obdiplostemony provides a guide rail within each canal formed by the flanks of the antepetalous stamen filaments.

CONCLUSIONS

Intimate synorganisation in flowers can be realized without any fusion, and obdiplostemony may play a role in this synorganisation.

Evidence for the involvement of Globosa-like gene duplications and expression divergence in the evolution of floral morphology in the Zingiberales

*The MADS box transcription factor family has long been identified as an important contributor to the control of floral development. It is often hypothesized that the evolution of floral development across angiosperms and within specific lineages may occur as a result of duplication, functional diversification, and changes in regulation of MADS box genes. Here we examine the role of Globosa (GLO)-like genes, members of the B-class MADS box gene lineage, in the evolution of floral development within the monocot order Zingiberales. *We assessed changes in perianth and stamen whorl morphology in a phylogenetic framework. We identified GLO homologs (ZinGLO1-4) from 50 Zingiberales species and investigated the evolution of this gene lineage. Expression of two GLO homologs was assessed in Costus spicatus and Musa basjoo. *Based on the phylogenetic data and expression results, we propose several family-specific losses and gains of GLO homologs that appear to be associated with key morphological changes. The GLO-like gene lineage has diversified concomitant with the evolution of the dimorphic perianth and the staminodial labellum. *Duplications and expression divergence within the GLO-like gene lineage may have played a role in floral diversification in the Zingiberales.

Isolation and phylogenetic footprinting analysis of the 5'-regulatory region of the floral homeotic gene OrcPI from Orchis italica (Orchidaceae)

The nucleotide sequences of regulatory elements from homologous genes can be strongly divergent. Phylogenetic footprinting, a comparative analysis of noncoding regions, can detect putative transcription factor binding sites (TFBSs) shared among the regulatory regions of 2 or more homologous genes. These conserved motifs have the potential to serve the same regulatory function in distantly related taxa. We isolated the 5'-noncoding region of the OrcPI gene, a MADS-box transcription factor involved in flower development in Orchis italica, using the thermal asymmetric interlaced polymerase chain reaction technique. This region (comprising 1352 bp) induced transient beta-glucuronidase expression in the petal tissue of white Rosa hybrida flowers and represents the 5'-regulatory sequence of the OrcPI gene. Phylogenetic footprinting analysis detected conserved regions within the 5'-regulatory sequence of OrcPI and the homologous regions of Oryza sativa, Lilium regale, and Arabidopsis thaliana. Some of these sequences are known TFBSs described in databases of plant regulatory elements. Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the following accession numbers: AF198055 promoter region of the PISTILLATA (PI) gene of A. thaliana; AB094985 cDNA of OrcPI (PI/GLOBOSA [PI/GLO] homologue) of O. italica; AB378089 5'-regulatory region of the OrcPI gene of O. italica; AP008211 putative promoter region of OSMADS2 (PI/GLO homologue) of O. sativa; AP008207 putative promoter region of OSMADS4 (PI/GLO homologue) of O. sativa; and AB158292 putative promoter region of the PI/GLO homologue of L. regale.

Molecular phylogenetics and morphological reappraisal of the Platanthera clade (Orchidaceae: Orchidinae) prompts expansion of the generic limits of Galearis and Platanthera

BACKGROUND AND AIMS

The Platanthera clade dominates the North American orchid flora and is well represented in eastern Asia. It has also generated some classic studies of speciation in Platanthera sections Platanthera and Limnorchis. However, it has proved rich in taxonomic controversy and near-monotypic genera. The clade is reviewed via a new molecular phylogenetic analysis and those results are combined with brief reconsideration of morphology in the group, aiming to rationalize the species into a smaller number of larger monophyletic genera and sections.

METHODS

Nuclear ribosomal internal transcribed spacer (ITS) sequences were obtained from 86 accessions of 35 named taxa, supplemented from GenBank with five accessions encompassing a further two named taxa.

KEY RESULTS

Using Pseudorchis as outgroup, and scoring indels, the data matrix generated 30 most-parsimonious trees that differed in the placement of two major groups plus two closely related species. Several other internal nodes also attracted only indifferent statistical support. Nonetheless, by combining implicit assessment of morphological divergence with explicit assessment of molecular divergence (when available), nine former genera can be rationalized into four revised genera by sinking the monotypic Amerorchis, together with Aceratorchis and Chondradenia (neither yet sequenced), into Galearis, and by amalgamating Piperia, Diphylax and the monotypic Tsaiorchis into the former Platanthera section Platanthera. After further species sampling, this section will require sub-division into at least three sections. The present nomenclatural adjustments prompt five new combinations.

CONCLUSIONS

Resolution of major groups should facilitate future species-level research on the Platanthera clade. Recent evidence suggests that ITS sequence divergence characterizes most species other than the P. bifolia group. The floral differences that distinguished Piperia, Diphylax and Tsaiorchis from Platanthera, and Aceratorchis and Chondradenia from Galearis, reflect various forms of heterochrony (notably paedomorphosis); this affected both the perianth and the gynostemium, and may have proved adaptive in montane habitats. Floral reduction was combined with lateral expansion of the root tubers in Piperia and Diphylax (including Tsaiorchis), whereas root tubers were minimized in the putative (but currently poorly supported) Neolindleya-Galearis clade. Allopolyploidy and/or autogamy strongly influenced speciation in Platanthera section Limnorchis and perhaps also Neolindleya. Reproductive biology remains an important driver of evolution in the clade, though plant-pollinator specificity and distinctness of the species boundaries have often been exaggerated.

Why are orchid flowers so diverse? Reduction of evolutionary constraints by paralogues of class B floral homeotic genes

BACKGROUND

The nearly 30 000 species of orchids produce flowers of unprecedented diversity. However, whether specific genetic mechanisms contributed to this diversity is a neglected topic and remains speculative. We recently published a theory, the 'orchid code', maintaining that the identity of the different perianth organs is specified by the combinatorial interaction of four DEF-like MADS-box genes with other floral homeotic genes.

SCOPE

Here the developmental and evolutionary implications of our theory are explored. Specifically, it is shown that all frequent floral terata, including all peloric types, can be explained by monogenic gain- or-loss-of-function mutants, changing either expression of a DEF-like or CYC-like gene. Supposed dominance or recessiveness of mutant alleles is correlated with the frequency of terata in both cultivation and nature. Our findings suggest that changes in DEF- and CYC-like genes not only underlie terata but also the natural diversity of orchid species. We argue, however, that true changes in organ identity are rare events in the evolution of orchid flowers, even though we review some likely cases.

CONCLUSIONS

The four DEF paralogues shaped floral diversity in orchids in a dramatic way by modularizing the floral perianth based on a complex series of sub- and neo-functionalization events. These genes may have eliminated constraints, so that different kinds of perianth organs could then evolve individually and thus often in dramatically different ways in response to selection by pollinators or by genetic drift. We therefore argue that floral diversity in orchids may be the result of an unprecedented developmental genetic predisposition that originated early in orchid evolution.

Positive selection and ancient duplications in the evolution of class B floral homeotic genes of orchids and grasses

BACKGROUND

Positive selection is recognized as the prevalence of nonsynonymous over synonymous substitutions in a gene. Models of the functional evolution of duplicated genes consider neofunctionalization as key to the retention of paralogues. For instance, duplicate transcription factors are specifically retained in plant and animal genomes and both positive selection and transcriptional divergence appear to have played a role in their diversification. However, the relative impact of these two factors has not been systematically evaluated. Class B MADS-box genes, comprising DEF-like and GLO-like genes, encode developmental transcription factors essential for establishment of perianth and male organ identity in the flowers of angiosperms. Here, we contrast the role of positive selection and the known divergence in expression patterns of genes encoding class B-like MADS-box transcription factors from monocots, with emphasis on the family Orchidaceae and the order Poales. Although in the monocots these two groups are highly diverse and have a strongly canalized floral morphology, there is no information on the role of positive selection in the evolution of their distinctive flower morphologies. Published research shows that in Poales, class B-like genes are expressed in stamens and in lodicules, the perianth organs whose identity might also be specified by class B-like genes, like the identity of the inner tepals of their lily-like relatives. In orchids, however, the number and pattern of expression of class B-like genes have greatly diverged.

RESULTS

The DEF-like genes from Orchidaceae form four well-supported, ancient clades of orthologues. In contrast, orchid GLO-like genes form a single clade of ancient orthologues and recent paralogues. DEF-like genes from orchid clade 2 (OMADS3-like genes) are under less stringent purifying selection than the other orchid DEF-like and GLO-like genes. In comparison with orchids, purifying selection was less stringent in DEF-like and GLO-like genes from Poales. Most importantly, positive selection took place before the major organ reduction and losses in the floral axis that eventually yielded the zygomorphic grass floret.

CONCLUSION

In DEF-like genes of Poales, positive selection on the region mediating interactions with other proteins or DNA could have triggered the evolution of the regulatory mechanisms behind the development of grass-specific reproductive structures. Orchidaceae show a different trend, where gene duplication and transcriptional divergence appear to have played a major role in the canalization and modularization of perianth development.

Saltational evolution: hopeful monsters are here to stay

Since 150 years it is hypothesized now that evolution always proceeds in a countless number of very small steps (Darwin in On the origin of species by means of natural selection or the preservation of favoured races in the struggle of life, Murray, London, 1859), a view termed "gradualism". Few contemporary biologists will doubt that gradualism reflects the most frequent mode of evolution, but whether it is the only one remains controversial. It has been suggested that in some cases profound ("saltational") changes may have occurred within one or a few generations of organisms. Organisms with a profound mutant phenotype that have the potential to establish a new evolutionary lineage have been termed "hopeful monsters". Recently I have reviewed the concept of hopeful monsters in this journal mainly from a historical perspective, and provided some evidence for their past and present existence. Here I provide a brief update on data and discussions supporting the view that hopeful monsters and saltational evolution are valuable biological concepts. I suggest that far from being mutually exclusive scenarios, both gradual and saltational evolution are required to explain the complexity and diversity of life on earth. In my view, gradual changes represent the usual mode of evolution, but are unlikely to be able to explain all key innovations and changes in body plans. Saltational changes involving hopeful monsters are probably very exceptional events, but since they have the potential to establish profound novelties sometimes facilitating adaptive radiations, they are of quite some importance, even if they would occur in any evolutionary lineage less than once in a million years. From that point of view saltational changes are not more bizarre scenarios of evolutionary change than whole genome duplications, endosymbiosis or impacts of meteorites. In conclusion I argue that the complete dismissal of saltational evolution is a major historical error of evolutionary biology tracing back to Darwin that needs to be rectified.

The OrcPI locus: genomic organization, expression pattern, and noncoding regions variability in Orchis italica (Orchidaceae) and related species

OrcPI is a class B MADS-box gene of Orchis italica (Orchidaceae), homologous of the PISTILLATA/GLOBOSA gene isolated in Arabidopsis and Antirrhinum. Its role in determining petals and stamens is conserved in orchids, where it seems to be involved also in other functions, such as flower longevity and ovary development. The present study reports the genomic characterization of the OrcPI locus in O. italica including coding and noncoding regions (introns, 5'- and 3' untranslated regions, and putative promoter). Nucleotide polymorphism distribution confirmed that this gene is subjected to different evolutionary forces, phylogenetic and distance analyses demonstrated that OrcPI is a useful nuclear marker at low taxonomic level in orchids. The expression pattern analysis showed that OrcPI transcripts are present in all the floral structures, undetected in the vegetative tissues, and decreased in the natural senescent flower. Finally, micro-RNAs putative target sites were identified within the OrcPI gene, conserved among orchids.

Molecular mechanisms of floral mimicry in orchids

Deceptive plants do not produce floral rewards, but attract pollinators by mimicking signals of other organisms, such as food plants or female insects. Such floral mimicry is particularly common in orchids, in which flower morphology, coloration and odour play key roles in deceiving pollinators. A better understanding of the molecular bases for these traits should provide new insights into the occurrence, mechanisms and evolutionary consequences of floral mimicry. It should also reveal the molecular bases of pollinator-attracting signals, in addition to providing strategies for manipulating insect behaviour in general. Here, we review data on the molecular bases for traits involved in floral mimicry, and we describe methodological advances helpful for the functional evaluation of key genes.

MADS about the evolution of orchid flowers

Orchids have unique flowers involving three types of perianth organs: outer tepals, lateral inner tepals, and a lip. Expression studies indicate that the identity of these organs is specified by the combinatorial interaction of four different DEFICIENS-like MADS-box genes. We suggest that clarifying the evolution of these genes provides a rational framework for reconstructing the enigmatic origin and unique diversification of the orchid flower. For example, two rounds of gene duplications during early orchid evolution might have generated the genes that were probably recruited to distinguish the different types of perianth organs. This hypothesis suggests intriguing, experimentally testable mechanisms by which gene duplications followed by sub- and neo-functionalization events might have contributed to the evolutionary origin of morphological novelties in orchids - and well beyond.

The discovery of polyandry in Curculigo (Hypoxidaceae): implications for androecium evolution of asparagoid monocotyledons

BACKGROUND AND AIMS

Individual flowers of the monocot Curculigo racemosa (Hypoxidaceae, Asparagales) are regularly polyandrous. To evaluate the significance of this almost unique character among Asparagales for flower evolution of asparagoid monocots, flowers of C. racemosa were studied comparatively.

METHODS

Anthetic flowers as well as early floral developmental stages were studied by light and scanning electron microscopy.

KEY RESULTS

Despite the polyandry, floral development is similar to that of other Asparagales with a developmental gradient from adaxial to abaxial. Stamens initiate simultaneously and the diameter of staminal primordia is about half of that in species with six anthers. The number of stamens is not fixed (12-26) and varies within the same inflorescence. Surprisingly, the gynoecium can be four- or six-locular, besides the normal trimerous state.

CONCLUSIONS

The discovery of a polyandrous Curculigo reveals plasticity of stamen number at the base of Asparagales. Orchidaceae - sister to all other Asparagales - has a reduced stamen number (three, two or one), whereas in Hypoxidaceae - part of the next diverging clade - either the normal monocot stamen number (six), polyandry (this study) or the loss of three anthers (Pauridia) occurs. However, at present it is impossible to decide whether the flexibility in stamen number is autapomorphic for each group or whether it is a synapomorphy. The small size of stamen primordia of Curculigo is conspicuous. It allows more space for additional androecial primordia. Stamens are initiated as independent organs, and filaments are not in bundles, hence C. racemosa is not secondarily polyandrous as may be the case in the distantly related Gethyllis of asparagoid Amaryllidaceae. The increase in carpel number is a rare phenomenon in angiosperms. A possible explanation for the polyandry of C. racemosa is that it is a natural SUPERMAN-deficient mutant, which shows an increase of stamens, or ULTRAPETALA or CARPEL FACTORY mutants, which are polyandrous and changed in carpel number.

Bilabiate flowers: the ultimate response to bees?

BACKGROUND AND AIMS

Bilabiate flowers have evolved in many lineages of the angiosperms, thus representing a convincing example of parallel evolution. Similar to keel blossoms, they have obviously evolved in order to protect pollen against pollen-collecting bees. Although many examples are known, a comprehensive survey on floral diversity and functional constraints of bilabiate flowers is lacking. Here, the concept is widened and described as a general pattern.

METHODS

The present paper is a conceptional review including personal observations of the authors. To form a survey on the diversity of bilabiate blossoms, a search was made for examples across the angiosperms and these were combined with personal observations collected during the last 25 years, coupled with knowledge from the literature. New functional terms are introduced that are independent of morphological and taxonomic associations.

KEY RESULTS

Bilabiate constructions occur in at least 38 angiosperm families. They are characterized by dorsiventral organization and dorsal pollen transfer. They are most often realised on the level of a single flower, but may also be present in an inflorescence or as part of a so-called 'walk-around flower'. Interestingly, in functional terms all nototribic blossoms represent bilabiate constructions. The great majority of specialized bee-flowers can thus be included under bilabiate and keel blossoms. The syndrome introduced here, however, also paves the way for the inclusion of larger animals such as birds and bats. The most important evolutionary trends appear to be in the saving of pollen and the precision of its transfer. With special reference to the Lamiales, selected examples of bilabiate flowers are presented and their functional significance is discussed.

CONCLUSIONS

Bilabiate blossoms protect their pollen against pollen-collecting bees and at the same time render their pollination more precisely. The huge diversity of realised forms indicate the high selection pressure towards the bilabiate syndrome. As bees are very inventive, however, bilabiate constructions will not represent the ultimate response to bees.

Floral organ identity genes in the orchid Dendrobium crumenatum

Orchids are members of Orchidaceae, one of the largest families in the flowering plants. Among the angiosperms, orchids are unique in their floral patterning, particularly in floral structures and organ identity. The ABCDE model was proposed as a general model to explain flower development in diverse plant groups, however the extent to which this model is applicable to orchids is still unknown. To investigate the regulatory mechanisms underlying orchid flower development, we isolated candidates for A, B, C, D and E function genes from Dendrobium crumenatum. These include AP2-, PI/GLO-, AP3/DEF-, AG- and SEP-like genes. The expression profiles of these genes exhibited different patterns from their Arabidopsis orthologs in floral patterning. Functional studies showed that DcOPI and DcOAG1 could replace the functions of PI and AG in Arabidopsis, respectively. By using chimeric repressor silencing technology, DcOAP3A was found to be another putative B function gene. Yeast two-hybrid analysis demonstrated that DcOAP3A/B and DcOPI could form heterodimers. These heterodimers could further interact with DcOSEP to form higher protein complexes, similar to their orthologs in eudicots. Our findings suggested that there is partial conservation in the B and C function genes between Arabidopsis and orchid. However, gene duplication might have led to the divergence in gene expression and regulation, possibly followed by functional divergence, resulting in the unique floral ontogeny in orchids.

The proper place of hopeful monsters in evolutionary biology

Hopeful monsters are organisms with a profound mutant phenotype that have the potential to establish a new evolutionary lineage. The Synthetic Theory of evolutionary biology has rejected the evolutionary relevance of hopeful monsters, but could not fully explain the mechanism and mode of macroevolution. On the other hand, several lines of evidence suggest that hopeful monsters played an important role during the origin of key innovations and novel body plans by saltational rather than gradual evolution. Homeotic mutants are identified as an especially promising class of hopeful monsters. Examples for animal and plant lineages that may have originated as hopeful monsters are given. Nevertheless, a brief review of the history of the concept of hopeful monsters reveals that it needs refinements and empirical tests if it is to be a useful addition to evolutionary biology. While evolutionary biology is traditionally zoocentric, hopeful monsters might be more relevant for plant than for animal evolution. Even though during recent years developmental genetics has provided detailed knowledge about how hopeful monsters can originate in the first place, we know almost nothing about their performance in natural populations and thus the ultimate difference between hopeful and hopeless. Studying the fitness of candidate hopeful monsters (suitable mutants with profound phenotype) in natural habitats thus remains a considerable challenge for the future.

Orchid diversity: an evolutionary consequence of deception?

The Orchidaceae are one of the most species-rich plant families and their floral diversity and pollination biology have long intrigued evolutionary biologists. About one-third of the estimated 18,500 species are thought to be pollinated by deceit. To date, the focus has been on how such pollination evolved, how the different types of deception work, and how it is maintained, but little progress has been made in understanding its evolutionary consequences. To address this issue, we discuss here how deception affects orchid mating systems, the evolution of reproductive isolation, speciation processes and neutral genetic divergence among species. We argue that pollination by deceit is one of the keys to orchid floral and species diversity. A better understanding of its evolutionary consequences could help evolutionary biologists to unravel the reasons for the evolutionary success of orchids.

Floral zygomorphy, the recurring evolution of a successful trait

The flowers of the primitive angiosperm plants were radially symmetrical (actinomorphic). Flowers with bilateral symmetry (zygomorphic) evolved in several clades independently as an adaptation to specialized methods of pollination and played an important role in the diversification of flowering plants. In the model species Antirrhinum majus (snapdragon), the related genes CYCLOIDEA (CYC) and DICHOTOMA (DICH) are key in the development of this trait. This raises the question of whether they played a role in the evolution of floral bilateral symmetry. To address this, the evolution of CYC in relation to the evolution of zygomorphy is being investigated. Phylogenetic and functional analyses of CYC-like genes are being carried out in groups either closely related to Antirhinum or in families where zygomorphy evolved as an independent event. In addition, the origin of zygomorphy is being studied by comparing the function of CYC-like genes in species with zygomorphic flowers with their function in species with radially symmetrical flowers.

Population genetic structure in European populations of Spiranthes romanzoffiana set in the context of other genetic studies on orchids

Spiranthes romanzoffiana Cham. is restricted in Europe to the British Isles, where it is recognised as a conservation priority species due to frequent extirpation of populations along with no evidence of seed set; vegetative reproduction has been invoked as the sole means of perpetuation and dispersal. To investigate the reproductive ecology of this species, 17 populations have been sampled for chloroplast microsatellites and amplified fragment length polymorphisms (AFLPs). These markers revealed a previously unsuspected genetic-geographic split in the species, which correlates with differences in patterns of within-population variation. Northern populations were fixed for one chloroplast haplotype but showed high levels of AFLP genotypic diversity consistent with sexual reproduction (proportion of genotypes distinguishable, PD = 0.98). More southerly populations showed fixed differences from the northern populations in their chloroplast haplotype and for 10 AFLP markers. They harboured only 12 unique multilocus genotypes among 113 individuals from six populations (PD = 0.11). These genotypes differed mostly by single bands, and none by more than 4/138 loci, with identical multilocus genotypes occurring in widely separated populations. This uniformity in southern populations is consistent with agamospermous or autogamous reproduction, and/or an extreme population bottleneck. Finally, the observed patterns of population differentiation in S. romanzoffiana are compared with other studies of orchids, revealing a wide range of values that belie recent contrasting published generalisations that claim that orchids show either higher, or lower, levels of population differentiation than other plant families.