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In order to construct a flowering model suited to orchids, the ABCDE model needs to be modified to explain the fact that orchids lack a stamen whorl. This kind of gene expression pattern is rather peculiar and has not been described in previous studies.

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More in-depth research needs to be conducted in order to understand the mechanism of pollinia pattern formation in orchids. Mutants with polymorphic flower phenotypes provide useful tools in the investigation of transcription factor functions. For reasons as yet unknown, the two lateral petals in the orchid flower sometimes become lip-like due to a peloric mutation Figure 5A , for more peloric phenotypes see Figure S5 in File S1.

The peloric mutation transforms the bilateral symmetric orchid flower into radial symmetric structure by the formation of three lips in the petal whorl. The peloric mutant is often associated with defective development of the pollinia and column. Compared to the wild-type, expression of genes involved in DNA methylation and chromatin remodeling is increased in peloric mutants [ 55 ], suggesting that the peloric phenotype may be the result of epigenetic effects.

In order to identify genes that are co-expressed in the lip structure and the genes responsible for peloric transformation, we compared the expression profiles of the petal and lip of flowers from wild-type and a peloric mutant of another moth orchid, P. Comparative profiling of wild-type and peloric flowers allowed genes involved in morphological, topological and peloric development to be grouped for more detailed studies Figure 5B.

Differential genes responsible for morphological differentiation can be identified by comparing petals of wild type to the peloric mutant Figure 5C. Thirty genes that may be responsible for topological arrangement of the second whorl were deduced from comparing profiling of petal to lip whether in the wild type or in the mutant Figure 5C.

The Venn diagram shows the number of genes differentially expressed in the petal and lip in the wild-type and peloric mutant Figure 5C. A total of genes exhibited differential expression levels in the petal and lip in the wild type. Among these genes, genes that did not show a change between the peloric petal and peloric lip were postulated to be genes responsible for morphological differentiation.

The remaining 30 genes that were differentially expressed between the petal and lip in the wild-type or peloric mutant, were postulated to be responsible for the topological arrangement of the second whorl Figure 5C.

The PCA plot Figure 5D revealed that peloric petals formed clusters with the lips by the genes input was projected onto the first component. Large group of genes in lipid metabolism, secondary metabolism, cytochrome P, transport activity and hormone metabolism may be responsible for the unique color and shape of lip. A group of MADS box transcription factors were also included. Clustering analyses of the morphology-related genes showed that the expression profile of the peloric petal is much more similar to that of the lip from wild-type or peloric mutant than to that of the petal Figure 5F , indicating the significance of this group of genes in the orchid lip development.

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This is suggested by the Principal Component Analysis PCA with high loading scores and provides a potential transcriptional activation network for future studies. A Phenotypes of wild-type and peloric mutants of Phalaenopsis equestris. B Proposed model of mechanism of peloric formation. D Principal component analysis PCA of genes shown in C that are differentially expressed in petal or lip tissues.

F Genes clustering analysis of genes in C that are differentially expressed in petal and lip tissues. Thirty of the genes that were postulated to have topological effects Figure 5C , genes for several enzymes such as phenylalanine ammonia-lyase PATC and tyrosine decarboxylase PATC and PATC that are involved in amino acid metabolism appeared to be expressed at higher levels in the lip than in the petal.

In contrast, a putative zinc finger protein gene PATC was expressed at a higher level in the petal than in the lip.

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Genes for leucine-rich repeat transmembrane protein kinase PATC and anther-specific proline-rich protein PATC showed the same trend in their expression patterns. These genes seemed to maintain their spatial expression pattern regardless of the morphological changes in the peloric petal. These results are consistent with our hypothesis that these transcription factors play essential roles in regulating floral identity. Amy: P. The factors that are involved in the determination of bilateral symmetry of orchid flowers have not been reported.

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Whether there is an as yet unidentified orchid CYC homologous gene or specialized orchid transcription factor that regulates the bilateral symmetry of orchid flower remains to be clarified. Using a microarray, we conducted a large-scale investigation of the expression profiles of functional genes that encode transcription factors in P. Genes specifically expressed in the floral organs were analyzed for their potential roles in floral organ identity. Several major conclusions can be drawn from our studies. First, PaAGL , which was expressed specifically in the orchid lip, may play an essential role in lip formation.

Third, clusters of genes involved in the morphological differentiation of the lip were further confirmed by a comparison of expression profiles between flowers of wild-type and a peloric mutant. Taken together, our results led to the proposal of a modified ABCDE model for orchids that accounts for mechanisms of flower morphorgenesis unique to orchids, and suggest that new classes of transcription factors have evolved to control the formation of floral organs in orchids.

Supporting figures and tables. Figure S1.


Performance check of orchid specialized microarray with scatter plot. Table S1. Top 20 genes differentially expressed in specific tissues. Figure S2. Quantitative PCR validation of genes differentially expressed in specific tissues. Table S2. Genes from the microarray clustering assay that were validated by quantitative PCR. Table S3. List of primers used for quantitative PCR analysis.

Figure S3. Table S4. Figure S4. Subcellular localization of MADS box genes according to particle bombardment. Figure S5.

Peloric flowers of orchids. Phalaenopsis aphrodite was kindly provided by Dr. The authors wish to express special thanks to members of the core labs at Academia Sinica for assistance: Miss Shu-Jen Chou for microarray experiments, Miss Shu-Chen Shen for confocal microscope experiment, Miss Lin-Yun Kuang for particle bombardment experiments. Finally, we are grateful to Miss Miranda Loney for English editing of this manuscript.

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Click through the PLOS taxonomy to find articles in your field. Abstract Previously we developed genomic resources for orchids, including transcriptomic analyses using next-generation sequencing techniques and construction of a web-based orchid genomic database. Introduction Sexual propagation is an important physiological event for both animals and plants.

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DNA microarray fabrication Probes for the orchid microarray were designed against transcriptome contigs of Phalaenopsis aphrodite from the Orchidstria database [ 32 ]. Array data analysis Tissues such as leaves, roots, flower buds, open flower and germinating seeds Figure 1A were repeated in triplicate in microarray experiments. Download: PPT. Figure 1. Gene clustering analyses of tissue-specific expression patterns in Phalaenopsis orchid. Flower-specific transcription factors in P.

Subcellular localization MADS box factors The subcellular localization of several Phalaenopsis MADS box genes was examined by particle bombardment of green fluorescence protein fusion constructs into the orchid petal. Differential expression of MADS box genes The morphological variation in the arrangement of floral organs in orchid flowers is unique among the angiosperms Figure 3A. Figure 3. Comparative models of flower development in actnomorphic and zygomorphic angiosperms including morphological variation and distribution of transcription factors.

Figure 4. Quantitative PCR validation of orchid transcription factors with floral organ-specific expression patterns. Comparative expression analysis of wild-type and peloric mutant flowers Mutants with polymorphic flower phenotypes provide useful tools in the investigation of transcription factor functions. Figure 5. Gene classification from comparative analysis of expression profiles of wild-type and peloric mutants.

Figure 6.