Four DEF-like MADS box genes displayed distinct floral morphogenetic roles in Phalaenopsis orchid

Research advances on the gene regulation of floral development and color in orchids

Orchidaceae is one of the largest monocotyledon families and contributes significantly to worldwide biodiversity, with value in the fields of landscaping, medicine, and ecology. The diverse phenotypes and vibrant colors of orchid floral organs make them excellent research objects for investigating flower development and pigmentation. In recent years, a number of orchid genomes have been published, laying the molecular foundation for revealing flower development and color presentation. In this article, we review transcription factors, the structural genes responsible for the floral pigment synthesis pathways, the molecular mechanisms of flower morphogenesis, and the potential relationship between flower type and flower color. This study provides a theoretical reference for the research on molecular mechanisms related to flower morphogenesis and color presentation, genetic improvement, and new variety creation in orchids.

Genome-wide identification of YABBY genes in three Cymbidium species and expression patterns in C. ensifolium (Orchidaceae)

Members of the YABBY gene family play significant roles in lamina development in cotyledons, floral organs, and other lateral organs. The Orchidaceae family is one of the largest angiosperm groups. Some YABBYs have been reported in Orchidaceae. However, the function of YABBY genes in Cymbidium is currently unknown. In this study, 24 YABBY genes were identified in Cymbidium ensifolium, C. goeringii, and C. sinense. We analyzed the conserved domains and motifs, the phylogenetic relationships, chromosome distribution, collinear correlation, and cis-elements of these three species. We also analyzed expression patterns of C. ensifolium and C. goeringii. Phylogenetic relationships analysis indicated that 24 YABBY genes were clustered in four groups, INO, CRC/DL, YAB2, and YAB3/FIL. For most YABBY genes, the zinc finger domain was located near the N-terminus and the helix-loop-helix domain (YABBY domain) near the C-terminus. Chromosomal location analysis results suggested that only C. goeringii YABBY has tandem repeat genes. Almost all the YABBY genes displayed corresponding one-to-one relationships in the syntenic relationships analysis. Cis-elements analysis indicated that most elements were clustered in light-responsive elements, followed by MeJA-responsive elements. Expression patterns showed that YAB2 genes have high expression in floral organs. RT-qPCR analysis showed high expression of CeYAB3 in lip, petal, and in the gynostemium. CeCRC and CeYAB2.2 were highly expressed in gynostemium. These findings provide valuable information of YABBY genes in Cymbidium species and the function in Orchidaceae.

Advances and prospects of orchid research and industrialization

Orchidaceae is one of the largest, most diverse families in angiosperms with significant ecological and economical values. Orchids have long fascinated scientists by their complex life histories, exquisite floral morphology and pollination syndromes that exhibit exclusive specializations, more than any other plants on Earth. These intrinsic factors together with human influences also make it a keystone group in biodiversity conservation. The advent of sequencing technologies and transgenic techniques represents a quantum leap in orchid research, enabling molecular approaches to be employed to resolve the historically interesting puzzles in orchid basic and applied biology. To date, 16 different orchid genomes covering four subfamilies (Apostasioideae, Vanilloideae, Epidendroideae, and Orchidoideae) have been released. These genome projects have given rise to massive data that greatly empowers the studies pertaining to key innovations and evolutionary mechanisms for the breadth of orchid species. The extensive exploration of transcriptomics, comparative genomics, and recent advances in gene engineering have linked important traits of orchids with a multiplicity of gene families and their regulating networks, providing great potential for genetic enhancement and improvement. In this review, we summarize the progress and achievement in fundamental research and industrialized application of orchids with a particular focus on molecular tools, and make future prospects of orchid molecular breeding and post-genomic research, providing a comprehensive assemblage of state of the art knowledge in orchid research and industrialization.

A spatiotemporal atlas of organogenesis in the development of orchid flowers

Development of floral organs exhibits complex molecular mechanisms involving the co-regulation of many genes specialized and precisely functioning in various tissues and developing stages. Advance in spatial transcriptome technologies allows for quantitative measurement of spatially localized gene abundance making it possible to bridge complex scenario of flower organogenesis with genome-wide molecular phenotypes. Here, we apply the 10× Visium technology in the study of the formation of floral organs through development in an orchid plant, Phalaenopsis Big Chili. Cell-types of early floral development including inflorescence meristems, primordia of floral organs and identity determined tissues, are recognized based on spatial expression distribution of thousands of genes in high resolution. In addition, meristematic cells on the basal position of floral organs are found to continuously function in multiple developmental stages after organ initiation. Particularly, the development of anther, which primordium starts from a single spot to multiple differentiated cell-types in later stages including pollinium and other vegetative tissues, is revealed by well-known MADS-box genes and many other downstream regulators. The spatial transcriptome analyses provide comprehensive information of gene activity for understanding the molecular architecture of flower organogenesis and for future genomic and genetic studies of specific cell-types.

Molecular genetic insights into orchid reproductive development

Orchids are members of the Orchidaceae, one of the largest families of flowering plants, and occupy a wide range of ecological habitats with highly specialized reproductive features. They exhibit unique developmental characteristics, such as generation of storage organs during flowering and spectacular floral morphological features, which contribute to their reproductive success in different habitats in response to various environmental cues. Here we review current understanding of the molecular genetic basis of orchid reproductive development, including flowering time control, floral patterning and flower color, with a focus on the orchid genes that have been functionally validated in plants. Furthermore, we summarize recent progress in annotating orchid genomes, and discuss how integration of high-quality orchid genome sequences with other advanced tools, such as the ever-improving multi-omics approaches and genome editing technologies as well as orchid-specific technical platforms, could open up new avenues to elucidate the molecular genetic basis of highly specialized reproductive organs and strategies in orchids.

High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids

Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker–trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids.

The Genetic and Hormonal Inducers of Continuous Flowering in Orchids: An Emerging View

Orchids are the flowers of magnetic beauty. Vivid and attractive flowers with magnificent shapes make them the king of the floriculture industry. However, the long-awaited flowering is a drawback to their market success, and therefore, flowering time regulation is the key to studies about orchid flower development. Although there are some rare orchids with a continuous flowering pattern, the molecular regulatory mechanisms are yet to be elucidated to find applicable solutions to other orchid species. Multiple regulatory pathways, such as photoperiod, vernalization, circadian clock, temperature and hormonal pathways are thought to signalize flower timing using a group of floral integrators. This mini review, thus, organizes the current knowledge of floral time regulators to suggest future perspectives on the continuous flowering mechanism that may help to plan functional studies to induce flowering revolution in precious orchid species.

The Cymbidium genome reveals the evolution of unique morphological traits

The marvelously diverse Orchidaceae constitutes the largest family of angiosperms. The genus Cymbidium in Orchidaceae is well known for its unique vegetation, floral morphology, and flower scent traits. Here, a chromosome-scale assembly of the genome of Cymbidium ensifolium (Jianlan) is presented. Comparative genomic analysis showed that C. ensifolium has experienced two whole-genome duplication (WGD) events, the most recent of which was shared by all orchids, while the older event was the τ event shared by most monocots. The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation, and flower shape mutations in C. ensifolium were shown to be associated with the abnormal expression of MADS-box genes. The most abundant floral scent components identified included methyl jasmonate, acacia alcohol and linalool, and the genes involved in the floral scent component network of C. ensifolium were determined. Furthermore, the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves, while the increased expression of MADS-box genes in leaves led to perianth-like leaves. Our results provide fundamental insights into orchid evolution and diversification.

The ancestral duplicated DL/CRC orthologs, PeDL1 and PeDL2, function in orchid reproductive organ innovation

Orchid gynostemium, the fused organ of the androecium and gynoecium, and ovule development are unique developmental processes. Two DROOPING LEAF/CRABS CLAW (DL/CRC) genes, PeDL1 and PeDL2, were identified from the Phalaenopsis orchid genome and functionally characterized. Phylogenetic analysis indicated that the most recent common ancestor of orchids contained the duplicated DL/CRC-like genes. Temporal and spatial expression analysis indicated that PeDL genes are specifically expressed in the gynostemium and at the early stages of ovule development. Both PeDLs could partially complement an Arabidopsis crc-1 mutant. Virus-induced gene silencing (VIGS) of PeDL1 and PeDL2 affected the number of protuberant ovule initials differentiated from the placenta. Transient overexpression of PeDL1 in Phalaenopsis orchids caused abnormal development of ovule and stigmatic cavity of gynostemium. PeDL1, but not PeDL2, could form a heterodimer with Phalaenopsis equestris CINCINNATA 8 (PeCIN8). Paralogous retention and subsequent divergence of the gene sequences of PeDL1 and PeDL2 in P. equestris might result in the differentiation of function and protein behaviors. These results reveal that the ancestral duplicated DL/CRC-like genes play important roles in orchid reproductive organ innovation.

Asymmetric expression patterns of B- and C-class MADS-box genes correspond to the asymmetrically specified androecial identities of Canna indica

Canna indica is a common ornamental plant with asymmetric flowers having colourful petaloid staminodes. The only fertile stamen comprises a one-theca anther and a petaloid appendage and represents the lowest stamen number in the order Zingiberales. The molecular mechanism for the asymmetric androecial petaloidy remains poorly understood. Here, we studied the identity specification in Canna stamen. We observed four types of abnormal flower in terms of androecium identity transformation and analysed the corresponding floral symmetry changes. We further tested the expression patterns of B- and C-class MADS-box genes using in situ hybridization in normal Canna stamen. Homeotic conversions in the androecium were accompanied by floral symmetry changes, and the asymmetric stamen is key in contributing to the floral asymmetry. Both B- and C-class genes exhibited higher expression levels in the anther primordium than in other androecial parts. This asymmetric expression pattern precisely corresponded to the asymmetric identities of the Canna androecium. We identified C. indica as a model species for studying androecial organ identity and floral symmetry synthetically in Zingiberales. We hypothesized that homeotic genes specify floral organ identity in a putative dose-dependent manner. The results add to the current understanding of organ identity-related floral symmetry.

Extending the Toolkit for Beauty: Differential Co-Expression of DROOPING LEAF-Like and Class B MADS-Box Genes during Phalaenopsis Flower Development

The molecular basis of orchid flower development is accomplished through a specific regulatory program in which the class B MADS-box AP3/DEF genes play a central role. In particular, the differential expression of four class B AP3/DEF genes is responsible for specification of organ identities in the orchid perianth. Other MADS-box genes (AGL6 and SEP-like) enrich the molecular program underpinning the orchid perianth development, resulting in the expansion of the original “orchid code” in an even more complex gene regulatory network. To identify candidates that could interact with the AP3/DEF genes in orchids, we conducted an in silico differential expression analysis in wild-type and peloric Phalaenopsis. The results suggest that a YABBY DL-like gene could be involved in the molecular program leading to the development of the orchid perianth, particularly the labellum. Two YABBY DL/CRC homologs are present in the genome of Phalaenopsis equestris, PeDL1 and PeDL2, and both express two alternative isoforms. Quantitative real-time PCR analyses revealed that both genes are expressed in column and ovary. In addition, PeDL2 is more strongly expressed the labellum than in the other tepals of wild-type flowers. This pattern is similar to that of the AP3/DEF genes PeMADS3/4 and opposite to that of PeMADS2/5. In peloric mutant Phalaenopsis, where labellum-like structures substitute the lateral inner tepals, PeDL2 is expressed at similar levels of the PeMADS2-5 genes, suggesting the involvement of PeDL2 in the development of the labellum, together with the PeMADS2-PeMADS5 genes. Although the yeast two-hybrid analysis did not reveal the ability of PeDL2 to bind the PeMADS2-PeMADS5 proteins directly, the existence of regulatory interactions is suggested by the presence of CArG-boxes and other MADS-box transcription factor binding sites within the putative promoter of the orchid DL2 gene.

Comparative transcriptomic analyses of normal and peloric mutant flowers in Cymbidium goeringii Rchb.f identifies differentially expressed genes associated with floral development

Cymbidium geringii has high ornamental and economic importance. Its traits, including flower shape, size, and color, are highly sought by orchid breeders. Gaining insights into the molecular basis of C. geringi flower development would accelerate genetic improvement of other orchids. Methods and Results: Here, C. goeringii RNA was purified from normal and peloric mutant flowers, and cDNA libraries constructed for Illumina sequencing. We generated 329,156,782 clean reads, integrated them, and then assembled into 236,811 unigenes averaging 595 bp long. A total of 11,992 differentially expressed genes s, of which 6119 were upregulated and 5873 downregulated, were uncovered in peloric mutant flower buds relative to normal flower buds. Kyoto Encyclopedia of Genes and Genomes enrichment assessments posited that these differentially expressed genes are associated with "Photosynthesis", "Linoleic acid metabolism", as well as "Plant hormone signal transduction" cascades. The DEGs were designated to 12 remarkably enriched GO terms, and 16 cell wall associated GO terms. The expression level of 16 determined genes were verified using RT-qPCR. Conclusions: Our gene expression data may be used to study the regulatory mechanism of flower organ development in C. geringi.

Transcriptome sequencing and metabolite profiling analyses provide comprehensive insight into molecular mechanisms of flower development in Dendrobium officinale (Orchidaceae)

This research provides comprehensive insight into the molecular networks and molecular mechanisms underlying D. officinale flower development. Flowers are complex reproductive organs and play a crucial role in plant propagation, while also providing sustenance for insects and natural bioactive metabolites for humans. However, knowledge about gene regulation and floral metabolomes in flowers is limited. In this study, we used an important orchid species (Dendrobium officinale), whose flowers can be used to make herbal tea, to perform transcriptome sequencing and metabolic profiling of early- and medium-stage flower buds, as well as opened flowers, to provide comprehensive insight into the molecular mechanisms underlying flower development. A total of 8019 differentially expressed genes (DEGs) and 239 differentiated metabolites were found. The transcription factors that were identified and analyzed belong exclusively to the MIKC-type MADS-box proteins and auxin responsive factors that are known to be involved in flower development. The expression of genes involved in chlorophyll and carotenoid biosynthesis strongly matched the metabolite accumulation patterns. The genes related to flavonoid and polysaccharide biosynthesis were active during flower development. Interestingly, indole-3-acetic acid and abscisic acid, whose trend of accumulation was inverse during flower development, may play an important role in this process. Collectively, the identification of DEGs and differentiated metabolites could help to illustrate the regulatory networks and molecular mechanisms important for flower development in this orchid.

Genome-Wide Identification of YABBY Genes in Orchidaceae and Their Expression Patterns in Phalaenopsis Orchid

The plant YABBY transcription factors are key regulators in the lamina development of lateral organs. Orchid is one of the largest families in angiosperm and known for their unique floral morphology, reproductive biology, and diversified lifestyles. However, nothing is known about the role of YABBY genes in orchids, although biologists have never lost their fascination with orchids. In this study, a total of 54 YABBY genes, including 15 genes in CRC/DL, eight in INO, 17 in YAB2, and 14 in FIL clade, were identified from the eight orchid species. A sequence analysis showed that all protein sequences encoded by these YABBY genes share the highly conserved C2C2 zinc-finger domain and YABBY domain (a helix-loop-helix motif). A gene structure analysis showed that the number of exons is highly conserved in the same clades. The genes in YAB2 clade have six exons, and genes in CRC/DL, INO, and FIL have six or seven exons. A phylogenetic analysis showed all 54 orchid YABBY genes could be classified into four major clades, including CRC/DL, INO, FIL, and YAB2. Many of orchid species maintain more than one member in CRC/DL, FIL, and YAB2 clades, implying functional differentiation among these genes, which is supported by sequence diversification and differential expression. An expression analysis of PhalaenopsisYABBY genes revealed that members in the CRC/DL clade have concentrated expressions in the early floral development stage and gynostemium, the fused male and female reproductive organs. The expression of PeINO is consistent with the biological role it played in ovule integument morphogenesis. Transcripts of members in the FIL clade could be obviously detected at the early developmental stage of the flowers. The expression of three genes, PeYAB2,PeYAB3, and PeYAB4, in the YAB2 clade could be revealed both in vegetative and reproductive tissues, and PeYAB4 was transcribed at a relatively higher level than that of PeYAB2 and PeYAB3. Together, this comprehensive analysis provides the basic information for understanding the function of the YABBY gene in Orchidaceae.

Evolution and development of three highly specialized floral structures of bee-pollinated Phalaenopsis species

Background

Variation in shape and size of many floral organs is related to pollinators. Evolution of such organs is driven by duplication and modification of MADS-box and MYB transcription factors. We applied a combination of micro-morphological (SEM and micro 3D-CT scanning) and molecular techniques (transcriptome and RT-PCR analysis) to understand the evolution and development of the callus, stelidia and mentum, three highly specialized floral structures of orchids involved in pollination. Early stage and mature tissues were collected from flowers of the bee-pollinated Phalaenopsis equestris and Phalaenopsis pulcherrima, two species that differ in floral morphology: P. equestris has a large callus but short stelidia and no mentum, whereas P. pulcherrima has a small callus, but long stelidia and a pronounced mentum.

Results

Our results show the stelidia develop from early primordial stages, whereas the callus and mentum develop later. In combination, the micro 3D-CT scan analysis and gene expression analyses show that the callus is of mixed petaloid-staminodial origin, the stelidia of staminodial origin, and the mentum of mixed sepaloid-petaloid-staminodial origin. SEP clade 1 copies are expressed in the larger callus of P. equestris, whereas AP3 clade 1 and AGL6 clade 1 copies are expressed in the pronounced mentum and long stelidia of P. pulcherrima. AP3 clade 4, PI-, AGL6 clade 2 and PCF clade 1 copies might have a balancing role in callus and gynostemium development. There appears to be a trade-off between DIV clade 2 expression with SEP clade 1 expression in the callus, on the one hand, and with AP3 clade 1 and AGL6 clade 1 expression in the stelidia and mentum on the other.

Conclusions

We detected differential growth and expression of MADS box AP3/PI-like, AGL6-like and SEP-like, and MYB DIV-like gene copies in the callus, stelidia and mentum of two species of Phalaenopsis, of which these floral structures are very differently shaped and sized. Our study provides a first glimpse of the evolutionary developmental mechanisms driving adaptation of Phalaenopsis flowers to different pollinators by providing combined micro-morphological and molecular evidence for a possible sepaloid–petaloid–staminodial origin of the orchid mentum.

Expression regulation of MALATE SYNTHASE involved in glyoxylate cycle during protocorm development in Phalaenopsis aphrodite (Orchidaceae)

Orchid (Orchidaceae) is one of the largest families in angiosperms and presents exceptional diversity in lifestyle. Their unique reproductive characteristics of orchid are attracted by scientist for centuries. One of the synapomorphies of orchid plants is that their seeds do not contain endosperm. Lipids are used as major energy storage in orchid seeds. However, regulation and mobilization of lipid usage during early seedling (protocorm) stage of orchid is not understood. In this study, we compared transcriptomes from developing Phalaenopsis aphrodite protocorms grown on 1/2-strength MS medium with sucrose. The expression of P. aphrodite MALATE SYNTHASE (PaMLS), involved in the glyoxylate cycle, was significantly decreased from 4 days after incubation (DAI) to 7 DAI. On real-time RT-PCR, both P. aphrodite ISOCITRATE LYASE (PaICL) and PaMLS were down-regulated during protocorm development and suppressed by sucrose treatment. In addition, several genes encoding transcription factors regulating PaMLS expression were identified. A gene encoding homeobox transcription factor (named PaHB5) was involved in positive regulation of PaMLS. This study showed that sucrose regulates the glyoxylate cycle during orchid protocorm development in asymbiotic germination and provides new insights into the transcription factors involved in the regulation of malate synthase expression.

Transcriptome Analysis Reveals Clues into leaf-like flower mutant in Chinese orchid Cymbidium ensifolium

The floral morphology of Cymbidium ensifolium, a well-known orchid in China, has increasingly attracted horticultural and commercial attention. However, the molecular mechanisms that regulate flower development defects in C. ensifolium mutants are poorly understood. In this work, we examined a domesticated variety of C. ensifolium named 'CuiYuMuDan', or leaf-like flower mutant, which lacks typical characteristics of orchid floral organs but continues to produce sepal-to leaf-like structures along the inflorescence. We used comparative transcriptome analysis to identify 6234 genes that are differentially expressed between mutant and wild-type flowers. The majority of these differentially expressed genes are involved in membrane-building, anabolism regulation, and plant hormone signal transduction, implying that in the leaf-like mutant these processes play roles in the development of flower defects. In addition, we identified 152 differentially expressed transcription factors, including the bHLH, MYB, MIKC, and WRKY gene families. Moreover, we found 20 differentially expressed genes that are commonly involved in flower development, including MADS-box genes, CLAVATA3 (CLV3), WUSCHEL (WUS), and PERIANTHIA (PAN). Among them, floral homeotic genes were further investigated by phylogenetic analysis and expression validation, which displayed distinctive spatial expression patterns and significant changes between the wild type and the mutant. This is the first report on the C. ensifolium leaf-like flower mutant transcriptome. Our results shed light on the molecular regulation of orchid flower development, and may improve our understanding of floral patterning regulation and advance molecular breeding of Chinese orchids.

New insight into the molecular mechanism of colour differentiation among floral segments in orchids

An unbalanced pigment distribution among the sepal and petal segments results in various colour patterns of orchid flowers. Here, we explored this type of mechanism of colour pattern formation in flowers of the Cattleya hybrid 'KOVA'. Our study showed that pigment accumulation displayed obvious spatiotemporal specificity in the flowers and was likely regulated by three R2R3-MYB transcription factors. Before flowering, RcPAP1 was specifically expressed in the epichile to activate the anthocyanin biosynthesis pathway, which caused substantial cyanin accumulation and resulted in a purple-red colour. After flowering, the expression of RcPAP2 resulted in a low level of cyanin accumulation in the perianths and a pale pink colour, whereas RcPCP1 was expressed only in the hypochile, where it promoted α-carotene and lutein accumulation and resulted in a yellow colour. Additionally, we propose that the spatiotemporal expression of different combinations of AP3- and AGL6-like genes might participate in KOVA flower colour pattern formation.

PeERF1, a SHINE-Like Transcription Factor, Is Involved in Nanoridge Development on Lip Epidermis of Phalaenopsis Flowers

Phalaenopsis orchids have a spectacular floral morphology with a highly evolved lip that offers a landing platform for pollinators. The typical morphological orchid lip features are essential for the special pollination mechanism of Phalaenopsis flowers. Previously, we found that in the lip, a member of the AP2/EREBP protein family was highly expressed. Here, we further confirmed its high expression and characterized its function during lip development. Phylogenetic analysis showed that AP2/EREBP belongs to the Va2 subgroup of ERF transcription factors. We named it PeERF1. We found that PeERF1 was only expressed at stage 5, as flowers opened. This coincided with both thickening of the cuticle and development of nanoridges. We performed knockdown expression of PeERF1 using CymMV-based virus-induced gene silencing in either the AP2 conserved domain, producing PeERF1_AP2-silenced plants, or the SHN specific domain, producing PeERF1_SHN-silenced plants. Using cryo-SEM, we found that the number of nanoridges was reduced only in the PeERF1_AP2-silenced group. This change was found on both the abaxial and adaxial surfaces of the central lip lobe. Expression of PeERF1 was reduced significantly in PeERF1_AP2-silenced plants. In cutin biosynthesis genes, expression of both PeCYP86A2 and PeDCR was significantly decreased in both groups. The expression of PeCYP77A4 was reduced significantly only in the PeERF1_AP2-silenced plants. Although PeGPAT expression was reduced in both silenced plants, but to a lesser degree. The expression of PeERF1 was significantly reduced in the petal-like lip of a big-lip variant. PeCYP77A4 and PeGPAT in the lip were also reduced, but PeDCR was not. Furthermore, heterologous overexpression of PeERF1 in the genus Arabidopsis produced leaves that were shiny on the adaxial surface. Taken together, our results show that in Phalaenopsis orchids PeERF1 plays an important role in formation of nanoridges during lip epidermis development.

Dissecting the Function of MADS-Box Transcription Factors in Orchid Reproductive Development

The orchid family (Orchidaceae) represents the second largest angiosperm family, having over 900 genera and 27,000 species in almost all over the world. Orchids have evolved a myriad of intriguing ways in order to survive extreme weather conditions, acquire nutrients, and attract pollinators for reproduction. The family of MADS-box transcriptional factors have been shown to be involved in the control of many developmental processes and responses to environmental stresses in eukaryotes. Several findings in different orchid species have elucidated that MADS-box genes play critical roles in the orchid growth and development. An in-depth understanding of their ecological adaptation will help to generate more interest among breeders and produce novel varieties for the floriculture industry. In this review, we summarize recent findings of MADS-box transcription factors in regulating various growth and developmental processes in orchids, in particular, the floral transition and floral patterning. We further discuss the prospects for the future directions in light of new genome resources and gene editing technologies that could be applied in orchid research and breeding.

Molecular mechanism underlying pseudopeloria in Habenaria radiata (Orchidaceae)

Habenaria radiata (Orchidaceae) has two whorls of perianth, comprising three greenish sepals, two white petals and one lip (labellum). By contrast, the pseudopeloric (with a decreased degree of zygomorphy) mutant cultivar of H. radiata, 'Hishou', has changes in the identities of the dorsal sepal to a petaloid organ and the two ventral sepals to lip-like organs. Here, we isolated four DEFICIENS-like and two AGL6-like genes from H. radiata, and characterized their expression. Most of these genes revealed similar expression patterns in the wild type and in the 'Hishou' cultivar, except HrDEF-C3. The HrDEF-C3 gene was expressed in petals and lip in the wild type but was ectopically expressed in sepal, petals, lip, leaf, root and bulb in 'Hishou'. Sequence analysis of the HrDEF-C3 loci revealed that the 'Hishou' genome harbored two types of HrDEF-C3 genes: one identical to wild-type HrDEF-C3 and the other carrying a retrotransposon insertion in its promoter. Genetic linkage analysis of the progeny derived from an intraspecific cross between 'Hishou' and the wild type demonstrated that the mutant pseudopeloric trait was dominantly inherited and was linked to the HrDEF-C3 gene carrying the retrotransposon. These results indicate that the pseudopeloric phenotype is caused by retrotransposon insertion in the HrDEF-C3 promoter, resulting in the ectopic expression of HrDEF-C3. As the expression of HrAGL6-C2 was limited to lateral sepals and lip, the overlapping expression of HrDEF-C3 and HrAGL6-C2 is likely to be responsible for the sepal to lip-like identity in the lateral sepals of the 'Hishou' cultivar.

Identification and expression profiling of selected MADS-box family genes in Dendrobium officinale

Dendrobium officinale, a herb with highly medicinal and ornamental value, is widely distributed in China. MADS-box genes encode transcription factors that regulate various growth and developmental processes in plants, particular in flowering. However, the MADS-box genes in D. officinale are largely unknown. In our study, expression profiling analyses of selected MADS-box genes in D. officinale were performed. In total, 16 DnMADS-box genes with full-length ORF were identified and named according to their phylogenetic relationships with model plants. The transient expression of eight selected MADS-box genes in the epidermal cells of tobacco leaves showed that these DnMADS-box proteins localized to the nucleus. Tissue-specific expression analysis pointed out eight flower-specific expressed MADS-box genes in D. officinale. Furthermore, expression patterns of DnMADS-box genes were investigated during the floral transition process. DnMADS3, DnMADS8 and DnMADS22 were significantly up-regulated in the reproductive phase compared with the vegetative phase, suggesting putative roles of these DnMADS-box genes in flowering. Our data showed that the expressions of MADS-box genes in D. officinale were controlled by diverse exogenous phytohormones. Together, these findings will facilitate further studies of MADS-box genes in Orchids and broaden our understanding of the genetics of flowering.

Floral Induction and Flower Development of Orchids

Orchids comprise one of the largest, most highly evolved angiosperm families, and form an extremely peculiar group of plants. Various orchids are available through traditional breeding and micro-propagation since they are valuable as potted plants and/or cut flowers in horticultural markets. The flowering of orchids is generally influenced by environmental signals such as temperature and endogenous developmental programs controlled by genetic factors as is usual in many flowering plant species. The process of floral transition is connected to the flower developmental programs that include floral meristem maintenance and floral organ specification. Thanks to advances in molecular and genetic technologies, the understanding of the molecular mechanisms underlying orchid floral transition and flower developmental processes have been widened, especially in several commercially important orchids such as Phalaenopsis, Dendrobium and Oncidium. In this review, we consolidate recent progress in research on the floral transition and flower development of orchids emphasizing representative genes and genetic networks, and also introduce a few successful cases of manipulation of orchid flowering/flower development through the application of molecular breeding or biotechnology tools.

Transcriptome-Wide Analysis Reveals the Origin of Peloria in Chinese Cymbidium (Cymbidium sinense)

An orchid flower exhibits a zygomorphic corolla with a well-differentiated labellum. In Cymbidium sinense, many varieties with peloric or pseudopeloric flowers have been bred during centuries of domestication. However, little is known about the molecular basis controlling orchid floral zygomorphy and the origin of these varieties. Here, we studied the floral morphogenesis of C. sinense and transcriptome-wide enriched differentially expressed genes among different varieties. The floral zygomorphy of C. sinense is established in the early developmental process. Out of 27 MIKCC-MADS factors, we found two homeotic MADS genes whose expression was down-regulated in peloric varieties but up-regulated in pseudopeloric varieties. CsAP3-2 expressed in the inner floral organs co-operates with a labellum-specific factor CsAGL6-2, asymmetrically promoting the differentiation of inner tepals. Interestingly, we detected exon deletions on CsAP3-2 in peloric varieties, indicating that loss of B-function results in the origin of peloria. Additional petaloid structures developed when we ectopically expressed these genes in Arabidopsis, suggesting their roles in floral morphogenesis. These findings indicate that the interplay among MADS factors would be crucial for orchid floral zygomorphy, and mutations in these factors may have maintained during artificial selection.

Distinguishing Orchid Species by DNA Barcoding: Increasing the Resolution of Population Studies in Plant Biology

Increasing the resolution of population studies in plant biology is one of the leading frontiers for omics sciences. One of the most pervasive challenges in molecular phylogenetics is the incongruence between phylogenies obtained using different data sets such as individual genes [like ribulose bisphosphate carboxylase large chain (rbcL) and maturase K (matK)] and intergenic spacers (IGS) [like nuclear ribosomal internal transcribed spacer 1 (nrITS 1) and 2 (nrITS 2), and chloroplast IGS between transfer RNA for leucine and phenylalanine (cp trnL-trnF IGS)]. To solve this challenge, we have screened the four well-established candidate gene sequences (i.e., rbcL, matK, trnL-trnF IGS, and 18S-ITS1-5.8S-ITS2-28S nrDNA) of 65 Indian orchid species. We also have included 31 different species of Dendrobium to identify the suitable locus for resolving the phylogeny-related problem below the taxonomic rank of genus. The Consortium for the Barcode of Life has recommended the locus rbcL and matK for barcoding of all land plants, including orchids. However, in this study, matK and rbcL (species resolving capacity 52% and 48%, respectively) were found to work above the taxonomic limit of genus, and thus cannot be considered a suitable tool to resolve closely related species of Dendrobium, whereas, we found that the locus 18S-ITS1-5.8S-ITS2-28S nrDNA is the best choice with the highest species resolving ability (95.23%) and the highest mean Kimura 2-parameter distance (254 for intergeneric and 144 for intrageneric) for phylogeny construction, and thus have been taken as the most promising single-locus barcode for orchids.

B and E MADS-box genes determine the perianth formation in Cymbidium goeringii Rchb.f

Cymbidium goeringii Rchb.f. is an important ornamental plant with a striking well-differentiated lip. Its complex floral architecture presents an exciting opportunity to examine perianth development. In flowering plants, class A, B and E floral homeotic genes play key roles in the specification of perianth identity. In this study, we used a cDNA library of wild-type C. goeringii flower buds for transcriptome sequencing. Eighteen candidate class A, B and E genes (including AP1/FUL-, AP2-, DEF-, GLO-, SEP- and AGL6-like genes) were identified. Quantitative real time polymerase chain reaction (qRT-PCR) results showed that CgDEF1, CgSEP2 and CgAGL6-1 were strongly detected only in the sepals and petals and were significantly downregulated in the lips. CgDEF3, CgDEF4 and CgAGL6-3 were highly expressed in the lips and lip-like petals but were only minimally detected in the sepals. Yeast two-hybrid analysis indicated that CgDEF1 and CgGLO formed a heterodimer. CgAGL6-1/CgSEP2 and CgDEF1 formed higher-order protein complexes with the assistance of the CgGLO protein, and both CgAGL6-1 and CgSEP2 formed a heterodimer. CgDEF3/CgDEF4 could interact independently with CgGLO and CgAGL6-3, respectively, while CgDEF3 and CgDEF4 also formed heterodimers with the assistance of the CgGLO. Based on a comprehensive analysis relating these gene expression patterns to protein interaction profiles, the mechanism of sepal/petal/lip determination was studied in C. goeringii. Furthermore, a hypothesis explaining the sepal/petal/lip determination of C. goeringii is proposed. The lip-quartet (CgDEF3/CgDEF4/CgAGL6-3/CgGLO) promoted lip formation, whereas the sepal/petal-quartet (CgDEF1/CgAGL6-1/CgSEP2/CgGLO) promoted sepal/petal formation. These results enrich the current knowledge regarding the mechanism and pathways of perianth formation in orchids.

De novo transcriptome analysis in Dendrobium and identification of critical genes associated with flowering

Artificial control of flowering time is pivotal for the ornamental value of orchids including the genus Dendrobium. Although various flowering pathways have been revealed in model plants, little information is available on the genetic regualtion of flowering in Dendrobium. To identify the critical genes associated with flowering, transcriptomes from four organs (leaf, root, stem and flower) of D. officinale were analyzed in our study. In total, 2645 flower-specific transcripts were identified. Functional annotation and classification suggested that several metabolic pathways, including four sugar-related pathways and two fatty acid-related pathways, were enriched. A total of 24 flowering-related transcripts were identified in D. officinale according to the similarities to their homologous genes from Arabidopsis, suggesting that most classical flowering pathways existed in D. officinale. Furthermore, phylogenetic analysis suggested that the FLOWERING LOCUS T homologs in orchids are highly conserved during evolution process. In addition, expression changes in nine randomly-selected critical flowering-related transcripts between the vegetative stage and reproductive stage were quantified by qRT-PCR analysis. Our study provided a number of candidate genes and sequence resources for investigating the mechanisms underlying the flowering process of the Dendrobium genus.

The Apostasia genome and the evolution of orchids

WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification.

Around 10 per cent of flowering plant species are orchids, with a broad diversity in both morphology and lifestyle. Apostasia is one of the earliest-diverging genera of Orchidaceae. To study the evolution and diversity of Orchidaceae, Zhong-Jian Liu, Yves Van de Peer and colleagues sequenced the genome of Apostasia shenzhenica, a self-pollinating species found in southeast China. The authors also report improved genomes for two species of Epidendroideae, Phalaenopsis equestris and Dendrobium catenatum, as well as transcriptome analysis of representatives of subfamilies of Orchidaceae. Their analyses provide insights into orchid origins, genome evolution, adaptation and diversification.

Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth^1,2,3. Here we report the draft genome sequence of Apostasia shenzhenica⁴, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.

Genome-wide identification and characterization of TCP genes involved in ovule development of Phalaenopsis equestris

TEOSINTE-BRANCHED/CYCLOIDEA/PCF (TCP) proteins are plant-specific transcription factors known to have a role in multiple aspects of plant growth and development at the cellular, organ and tissue levels. However, there has been no related study of TCPs in orchids. Here we identified 23 TCP genes from the genome sequence of Phalaenopsis equestris Phylogenetic analysis distinguished two homology classes of PeTCP transcription factor families: classes I and II. Class II was further divided into two subclasses, CIN and CYC/TB1. Spatial and temporal expression analysis showed that PePCF10 was predominantly expressed in ovules at early developmental stages and PeCIN8 had high expression at late developmental stages in ovules, with overlapping expression at day 16 after pollination. Subcellular localization and protein-protein interaction analyses revealed that PePCF10 and PeCIN8 could form homodimers and localize in the nucleus. However, PePCF10 and PeCIN8 could not form heterodimers. In transgenic Arabidopsis thaliana plants (overexpression and SRDX, a super repression motif derived from the EAR-motif of the repression domain of tobacco ETHYLENE-RESPONSIVE ELEMENT-BINDING FACTOR 3 and SUPERMAN, dominantly repressed), the two genes helped regulate cell proliferation. Together, these results suggest that PePCF10 and PeCIN8 play important roles in orchid ovule development by modulating cell division.

De novo transcriptome sequencing and comparative analysis to discover genes related to floral development in Cymbidium faberi Rolfe

Cymbidium faberi is a traditional orchid flower in China that is highly appreciated for its fragrant aroma from its zygomorphic flowers. One bottleneck of the commercial production of C. faberi is the long vegetative growth phase of the orchid and the difficulty of the regulation of its flowering time. Moreover, its flower size, shape and color are often targeting traits for orchid breeders. Understanding the molecular mechanisms of floral development in C. faberi will ultimately benefit the genetic improvement of this orchid plant. The goal of this study is to identify potential genes and regulatory networks related to the floral development in C. faberi by using transcriptome sequencing, de novo assembly and computational analyses. The vegetative and flower buds of C. faberi were sampled for such comparisons. The RNA-seq yielded about 189,300 contigs that were assembled into 172,959 unigenes. Furthermore, a total of 13,484 differentially expressed unigenes (DEGs) were identified between the vegetative and flower buds. There were 7683 down-regulated and 5801 up-regulated DEGs in the flower buds compared to those in the vegetative buds, among which 3430 and 6556 DEGs were specifically enriched in the flower or vegetative buds, respectively. A total of 173 DEGs orthologous to known genes associated with the floral organ development, floral symmetry and flowering time were identified, including 12 TCP transcription factors, 34 MADS-box genes and 28 flowering time related genes. Furthermore, expression levels of ten genes potentially involved in floral development and flowering time were verified by quantitative real-time PCR. The identified DEGs will facilitate the functional genetic studies for further understanding the flower development of C. faberi.

The genome and transcriptome of Phalaenopsis yield insights into floral organ development and flowering regulation

The Phalaenopsis orchid is an important potted flower of high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802,’ a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal that the key role of PhAGL6b in the regulation of labellum organ development involves alternative splicing in the big lip mutant. Petal or sepal overexpressing PhAGL6b leads to the conversion into a lip-like structure. We also discovered that the gibberellin pathway that regulates the expression of flowering time genes during the reproductive phase change is induced by cool temperature. Our work thus depicted a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

Functional characterization of duplicated B-class MADS-box genes in Japanese gentian

The heterodimer formation between B-class MADS-box proteins of GsAP3a and GsPI2 proteins plays a core role for petal formation in Japanese gentian plants. We previously isolated six B-class MADS-box genes (GsAP3a, GsAP3b, GsTM6, GsPI1, GsPI2, and GsPI3) from Japanese gentian (Gentiana scabra). To study the roles of these MADS-box genes in determining floral organ identities, we investigated protein-protein interactions among them and produced transgenic Arabidopsis and gentian plants overexpressing GsPI2 alone or in combination with GsAP3a or GsTM6. Yeast two-hybrid and bimolecular fluorescence complementation analyses revealed that among the GsPI proteins, GsPI2 interacted with both GsAP3a and GsTM6, and that these heterodimers were localized to the nuclei. The heterologous expression of GsPI2 partially converted sepals into petaloid organs in transgenic Arabidopsis, and this petaloid conversion phenomenon was accelerated by combined expression with GsAP3a but not with GsTM6. In contrast, there were no differences in morphology between vector-control plants and transgenic Arabidopsis plants expressing GsAP3a or GsTM6 alone. Transgenic gentian ectopically expressing GsPI2 produced an elongated tubular structure that consisted of an elongated petaloid organ in the first whorl and stunted inner floral organs. These results imply that the heterodimer formation between GsPI2 and GsAP3a plays a core role in determining petal and stamen identities in Japanese gentian, but other B-function genes might be important for the complete development of petal organs.

Proteomic insights into floral biology

The flower is the most important biological structure for ensuring angiosperms reproductive success. Not only does the flower contain critical reproductive organs, but the wide variation in morphology, color, and scent has evolved to entice specialized pollinators, and arguably mankind in many cases, to ensure the successful propagation of its species. Recent proteomic approaches have identified protein candidates related to these flower traits, which has shed light on a number of previously unknown mechanisms underlying these traits. This review article provides a comprehensive overview of the latest advances in proteomic research in floral biology according to the order of flower structure, from corolla to male and female reproductive organs. It summarizes mainstream proteomic methods for plant research and recent improvements on two dimensional gel electrophoresis and gel-free workflows for both peptide level and protein level analysis. The recent advances in sequencing technologies provide a new paradigm for the ever-increasing genome and transcriptome information on many organisms. It is now possible to integrate genomic and transcriptomic data with proteomic results for large-scale protein characterization, so that a global understanding of the complex molecular networks in flower biology can be readily achieved. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.

Transcriptome-wide analysis of the MADS-box gene family in the orchid Erycina pusilla

Orchids exhibit a range of unique flower shapes and are a valuable ornamental crop. MADS-box transcription factors are key regulatory components in flower initiation and development. Changing the flower shape and flowering time can increase the value of the orchid in the ornamental horticulture industry. In this study, 28 MADS-box genes were identified from the transcriptome database of the model orchid Erycina pusilla. The full-length genomic sequences of these MADS-box genes were obtained from BAC clones. Of these, 27 were MIKC-type EpMADS (two truncated forms) and one was a type I EpMADS. Eleven EpMADS genes contained introns longer than 10 kb. Phylogenetic analysis classified the 24 MIKC(c) genes into nine subfamilies. Three specific protein motifs, AG, FUL and SVP, were identified and used to classify three subfamilies. The expression profile of each EpMADS gene correlated with its putative function. The phylogenetic analysis was highly correlated with the protein domain identification and gene expression results. Spatial expression of EpMADS6, EpMADS12 and EpMADS15 was strongly detected in the inflorescence meristem, floral bud and seed via in situ hybridization. The subcellular localization of the 28 EpMADS proteins was also investigated. Although EpMADS27 lacks a complete MADS-box domain, EpMADS27-YFP was localized in the nucleus. This characterization of the orchid MADS-box family genes provides useful information for both orchid breeding and studies of flowering and evolution.

Digital Gene Expression Analysis Based on De Novo Transcriptome Assembly Reveals New Genes Associated with Floral Organ Differentiation of the Orchid Plant Cymbidium ensifolium

Cymbidium ensifolium belongs to the genus Cymbidium of the orchid family. Owing to its spectacular flower morphology, C. ensifolium has considerable ecological and cultural value. However, limited genetic data is available for this non-model plant, and the molecular mechanism underlying floral organ identity is still poorly understood. In this study, we characterize the floral transcriptome of C. ensifolium and present, for the first time, extensive sequence and transcript abundance data of individual floral organs. After sequencing, over 10 Gb clean sequence data were generated and assembled into 111,892 unigenes with an average length of 932.03 base pairs, including 1,227 clusters and 110,665 singletons. Assembled sequences were annotated with gene descriptions, gene ontology, clusters of orthologous group terms, the Kyoto Encyclopedia of Genes and Genomes, and the plant transcription factor database. From these annotations, 131 flowering-associated unigenes, 61 CONSTANS-LIKE (COL) unigenes and 90 floral homeotic genes were identified. In addition, four digital gene expression libraries were constructed for the sepal, petal, labellum and gynostemium, and 1,058 genes corresponding to individual floral organ development were identified. Among them, eight MADS-box genes were further investigated by full-length cDNA sequence analysis and expression validation, which revealed two APETALA1/AGL9-like MADS-box genes preferentially expressed in the sepal and petal, two AGAMOUS-like genes particularly restricted to the gynostemium, and four DEF-like genes distinctively expressed in different floral organs. The spatial expression of these genes varied distinctly in different floral mutant corresponding to different floral morphogenesis, which validated the specialized roles of them in floral patterning and further supported the effectiveness of our in silico analysis. This dataset generated in our study provides new insights into the molecular mechanisms underlying floral patterning of Cymbidium and supports a valuable resource for molecular breeding of the orchid plant.

The C-Terminal Sequence and PI motif of the Orchid (Oncidium Gower Ramsey) PISTILLATA (PI) Ortholog Determine its Ability to Bind AP3 Orthologs and Enter the Nucleus to Regulate Downstream Genes Controlling Petal and Stamen Formation

This study focused on the investigation of the effects of the PI motif and C-terminus of the Oncidium Gower Ramsey MADS box gene 8 (OMADS8), a PISTILLATA (PI) ortholog, on floral organ formation. 35S::OMADS8 completely rescued and 35S::OMADS8-PI (with the PI motif deleted) partially rescued petal/stamen formation, whereas these deficiencies were not rescued by 35S::OMADS8-C (C-terminal 29 amino acids deleted) in pi-1 mutants. OMADS8 could interact with Arabidopsis APETALA3 (AP3) and enter the nucleus. The nuclear entry efficiency was reduced for OMADS8-PI/AP3 and OMADS8-C/AP3. OMADS8 could also interact with OMADS5/OMADS9 (the Oncidium AP3 ortholog) and enter the nucleus with an efficiency only slightly affected by the deletion of the C-terminal sequence or PI motif. However, the stability of the OMADS8/OMADS5 and OMADS8/OMADS9 complexes was significantly reduced by deletion of the C-terminal sequence or PI motif. Further analysis indicated that the expression of genes downstream of AP3/PI (BNQ1/BNQ2/GNC/At4g30270) was compensated by 35S::OMADS8 and 35S::OMADS8-PI to a level similar to wild-type plants but was not affected by 35S::OMADS8-C in the pi-1 mutants. A similar FRET (fluorescence resonance energy transfer) efficiency was observed for Arabidopsis AGAMOUS (AG) and the Oncidium AG ortholog OMADS4 for OMADS8, OMADS8-PI and OMADS8-C. These results indicated that the OMADS8 PI motif and C-terminus were valuable for the interaction of OMADS8 with the AP3 orthologs to form higher order heterotetrameric complexes that regulated petal/stamen formation in both Oncidium orchids and transgenic Arabidopsis. However, the C-terminal sequence and PI motif were dispensable for the interaction of OMADS8 with the AG orthologs.

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.

Three R2R3-MYB transcription factors regulate distinct floral pigmentation patterning in Phalaenopsis spp

Orchidaceae are well known for their fascinating floral morphologic features, specialized pollination, and distinctive ecological strategies. With their long-lasting flowers of various colors and pigmentation patterning, Phalaenopsis spp. have become important ornamental plants worldwide. In this study, we identified three R2R3-MYB transcription factors PeMYB2, PeMYB11, and PeMYB12. Their expression profiles were concomitant with red color formation in Phalaenopsis spp. flowers. Transient assay of overexpression of three PeMYBs verified that PeMYB2 resulted in anthocyanin accumulation, and these PeMYBs could activate the expression of three downstream structural genes Phalaenopsis spp. Flavanone 3-hydroxylase5, Phalaenopsis spp. Dihydroflavonol 4-reductase1, and Phalaenopsis spp. Anthocyanidin synthase3. In addition, these three PeMYBs participated in the distinct pigmentation patterning in a single flower, which was revealed by virus-induced gene silencing. In the sepals/petals, silencing of PeMYB2, PeMYB11, and PeMYB12 resulted in the loss of the full-red pigmentation, red spots, and venation patterns, respectively. Moreover, different pigmentation patterning was regulated by PeMYBs in the sepals/petals and lip. PeMYB11 was responsive to the red spots in the callus of the lip, and PeMYB12 participated in the full pigmentation in the central lobe of the lip. The differential pigmentation patterning was validated by RNA in situ hybridization. Additional assessment was performed in six Phalaenopsis spp. cultivars with different color patterns. The combined expression of these three PeMYBs in different ratios leads to a wealth of complicated floral pigmentation patterning in Phalaenopsis spp.

"The usual suspects"- analysis of transcriptome sequences reveals deviating B gene activity in C. vulgaris bud bloomers

BACKGROUND

The production of heather (Calluna vulgaris) in Germany is highly dependent on cultivars with mutated flower morphology, the so-called diplocalyx bud bloomers. So far, this unique flower type of C. vulgaris has not been reported in any other plant species. The flowers are characterised by an extremely extended flower attractiveness, since the flower buds remain closed throughout the complete flowering season. The flowers of C. vulgaris bud bloomers are male sterile, because the stamens are absent. Furthermore, petals are converted into sepals. Therefore the diplocalyx bud bloomer flowers consist of two whorls of sepals directly followed by the gynoecium.

RESULTS

A broad comparison was undertaken to identify genes differentially expressed in the bud flowering phenotype and in the wild type of C. vulgaris. Transcriptome sequence reads were generated using 454 sequencing of two flower type specific cDNA libraries. In total, 360,000 sequence reads were obtained, assembled to 12,200 contigs, functionally mapped, and annotated. Transcript abundances were compared and 365 differentially expressed genes detected. Among these differentially expressed genes, Calluna vulgaris PISTILLATA (CvPI) which is the orthologue of the Arabidopsis B gene PISTILLATA (PI) was considered as the most promising candidate gene. Quantitative Reverse Transcription Polymerase Chain Reaction (qRT PCR) was performed to analyse the gene expression levels of two C. vulgaris B genes CvPI and Calluna vulgaris APETALA 3 (CvAP3) in both flower types. CvAP3 which is the orthologue of the Arabidopsis B gene APETALA 3 (AP3) turned out to be ectopically expressed in sepals of wild type and bud bloomer flowers. CvPI expression was proven to be reduced in the bud blooming flowers.

CONCLUSIONS

Differential expression patterns of the B-class genes CvAP3 and CvPI were identified to cause the characteristic morphology of C. vulgaris flowers leading to the following hypotheses: ectopic expression of CvAP3 is a convincing explanation for the formation of a completely petaloid perianth in both flower types. In C. vulgaris, CvPI is essential for determination of petal and stamen identity. The characteristic transition of petals into sepals potentially depends on the observed deficiency of CvPI and CvAP3 expression in bud blooming flowers.

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.

The genome sequence of the orchid Phalaenopsis equestris

Orchidaceae, renowned for its spectacular flowers and other reproductive and ecological adaptations, is one of the most diverse plant families. Here we present the genome sequence of the tropical epiphytic orchid Phalaenopsis equestris, a frequently used parent species for orchid breeding. P. equestris is the first plant with crassulacean acid metabolism (CAM) for which the genome has been sequenced. Our assembled genome contains 29,431 predicted protein-coding genes. We find that contigs likely to be underassembled, owing to heterozygosity, are enriched for genes that might be involved in self-incompatibility pathways. We find evidence for an orchid-specific paleopolyploidy event that preceded the radiation of most orchid clades, and our results suggest that gene duplication might have contributed to the evolution of CAM photosynthesis in P. equestris. Finally, we find expanded and diversified families of MADS-box C/D-class, B-class AP3 and AGL6-class genes, which might contribute to the highly specialized morphology of orchid flowers.

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.

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.

Analysis of the APETALA3- and PISTILLATA-like genes in Hedyosmum orientale (Chloranthaceae) provides insight into the evolution of the floral homeotic B-function in angiosperms

BACKGROUND AND AIMS

According to the floral ABC model, B-function genes appear to play a key role in the origin and diversification of the perianth during the evolution of angiosperms. The basal angiosperm Hedyosmum orientale (Chloranthaceae) has unisexual inflorescences associated with a seemingly primitive reproductive morphology and a reduced perianth structure in female flowers. The aim of this study was to investigate the nature of the perianth and the evolutionary state of the B-function programme in this species.

METHODS

A series of experiments were conducted to characterize B-gene homologues isolated from H. orientale, including scanning electron microscopy to observe the development of floral organs, phylogenetic analysis to reconstruct gene evolutionary history, reverse transcription-PCR, quantitative real-time PCR and in situ hybridization to identify gene expression patterns, the yeast two-hybrid assay to explore protein dimerization affinities, and transgenic analyses in Arabidopsis thaliana to determine activities of the encoded proteins.

KEY RESULTS

The expression of HoAP3 genes was restricted to stamens, whereas HoPI genes were broadly expressed in all floral organs. HoAP3 was able to partially restore the stamen but not petal identity in Arabidopsis ap3-3 mutants. In contrast, HoPI could rescue aspects of both stamen and petal development in Arabidopsis pi-1 mutants. When the complete C-terminal sequence of HoPI was deleted, however, no or weak transgenic phenotypes were observed and homodimerization capability was completely abolished.

CONCLUSIONS

The results suggest that Hedyosmum AP3-like genes have an ancestral function in specifying male reproductive organs, and that the activity of the encoded PI-like proteins is highly conserved between Hedyosmum and Arabidopsis. Moreover, there is evidence that the C-terminal region is important for the function of HoPI. Our findings indicate that the development of the proposed perianth in Hedyosmum does not rely on the B homeotic function.

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.