Cool-night temperature induces spike emergence and affects photosynthetic efficiency and metabolizable carbohydrate and organic acid pools in Phalaenopsis aphrodite

Temperature-Regulated Flowering Locus T-Like Gene Coordinates the Spike Initiation in Phalaenopsis Orchid

Phalaenopsis aphrodite can be induced to initiate spike growth and flowering by exposure to low ambient temperatures. However, the factors and mechanisms responsible for spike initiation in P. aphrodite remain largely unknown. In this study, we show that a repressor Flowing Locus T-like (FTL) gene, FTL, can act as a negative regulator of spike initiation in P. aphrodite. The mRNA transcripts of PaFTL are consistently high during high ambient temperature, thereby preventing premature spike initiation. However, during low ambient temperature, PaFTL expression falls while FT expression increases, allowing for spike initiation. Knock-down of PaFTL expression through virus-inducing gene silencing promoted spike initiation at 30/28°C. Moreover, PaFTL interacts with FLOWERING LOCUS D in a similar manner to FT to regulate downstream flowering initiation genes. Transgenic P. aphrodite plants exhibiting high expression of PaFTL do not undergo spike initiation, even when exposed to low ambient temperatures. These findings shed light on the flowering mechanisms in Phalaenopsis and provide new insights into how perennial plants govern spike initiation in response to temperature cues.

Overexpressing plant ferredoxin-like protein enhances photosynthetic efficiency and carbohydrates accumulation in Phalaenopsis

Crassulacean acid metabolism (CAM) is one of three major models of carbon dioxide assimilation pathway with better water-use efficiency and slower photosynthetic efficiency in photosynthesis. Previous studies indicated that the gene of sweet pepper plant ferredoxin-like protein (PFLP) shows high homology to the ferredoxin-1(Fd-1) family that belongs to photosynthetic type Fd and involves in photosystem I. It is speculated that overexpressing pflp in the transgenic plant may enhance photosynthetic efficiency through the electron transport chain (ETC). To reveal the function of PFLP in photosynthetic efficiency, pflp transgenic Phalaenopsis, a CAM plant, was generated to analyze photosynthetic markers. Transgenic plants exhibited 1.2-folds of electron transport rate than that of wild type (WT), and higher CO2 assimilation rates up to 1.6 and 1.5-folds samples at 4 pm and 10 pm respectively. Enzyme activity of phosphoenolpyruvate carboxylase (PEPC) was increased to 5.9-folds in Phase III, and NAD+-linked malic enzyme (NAD+-ME) activity increased 1.4-folds in Phase IV in transgenic plants. The photosynthesis products were analyzed between transgenic plants and WT. Soluble sugars contents such as glucose, fructose, and sucrose were found to significantly increase to 1.2, 1.8, and 1.3-folds higher in transgenic plants. The starch grains were also accumulated up to 1.4-folds in transgenic plants than that of WT. These results indicated that overexpressing pflp in transgenic plants increases carbohydrates accumulation by enhancing electron transport flow during photosynthesis. This is the first evidence for the PFLP function in CAM plants. Taken altogether, we suggest that pflp is an applicable gene for agriculture application that enhances electron transport chain efficiency during photosynthesis.

Bioclimatic controls of CO2 assimilation near range limits of the CAM succulent tree Aloidendron dichotomum

Aloidendron dichotomum appears to be undergoing the early stages of a range shift in response to anthropogenic climate change in south-western Africa. High mortality has been recorded in warmer populations, while population expansions have been recorded in cooler poleward parts of its range. This study aimed to determine the key environmental controls on A. dichotomum photosynthesis in areas of population expansion, to inform the potential attribution of directional population expansion to anthropogenic warming. Nocturnal acid accumulation and CO2 assimilation were measured in individuals growing under a range of temperature and watering treatments in a greenhouse experiment. In addition, nocturnal acid accumulation and phosphoenolpyruvate carboxylase activity were quantified in two wild populations at the most southerly and south-easterly range extents. Multiple lines of evidence confirmed that A. dichotomum performs Crassulacean acid metabolism. Total nocturnal acid accumulation was highest at night-time temperatures of ~21.5 °C, regardless of soil water availability, and night-time CO2 assimilation rates increased with leaf temperature, suggesting a causal link to the cool southern range limit. Leaf acidity at the start of the dark period was highly predictive of nocturnal acid accumulation in all individuals, implicating light availability during the day as an important determinant of nocturnal acid accumulation.

Transcriptome Analysis Reveals Endogenous Hormone Changes during Spike Development in Phalaenopsis

Phalaenopsis orchids are popular worldwide due to their high ornamental and economic value; the spike and inflorescence formation of their flowers could be efficiently controlled under proper conditions. In this study, transcriptomic profiles and endogenous hormone changes were investigated to better understand the spike formation of Phalaenopsis. Morphological observations revealed four spike initiation statuses (i.e., S0: the status refers to axillary buds remaining dormant in the leaf axils; S1: the status refers to the 0.5 cm-long initial spike; S2: the status refers to the 1 cm-long spike; S3: the status refers to the 3 cm-long spike) during the process of spike development, while anatomical observations revealed four related statuses of inflorescence primordium differentiation. A total of 4080 differentially expressed genes were identified based on pairwise comparisons of the transcriptomic data obtained from the S0 to S3 samples; high levels of differential gene expression were mostly observed in S1 vs. S2, followed by S0 vs. S1. Then, the contents of 12 endogenous hormones (e.g., irindole-3-acetic acid (IAA), salicylic acid (SA), abscisic acid (ABA), gibberellins, and cytokinins) were measured. The results showed that the ABA content was decreased from S0 to S1, while the gibberellic acid 1 (GA1) content exhibited an opposite trend, indicating the reduction in ABA levels combined with the increase in GA1 levels in S0 promoted the axillary bud dormancy breaking, preparing for the following spike initiation. The GA20 oxidase and ABA 8'-hydroxylase genes, which are involved in endogenous hormone metabolism and signaling pathways, displayed similar expression patterns, suggesting they were probably the key genes participating in the GA and ABA regulation. Taken together, the findings of this study indicate that GA and ABA may be the key endogenous hormones breaking the dormancy and promoting the germination of axillary buds in Phalaenopsis.

Molecular Characterization and Expression Profile of PaCOL1, a CONSTANS-like Gene in Phalaenopsis Orchid

CONSTANS (CO) and CONSTANS-like (COL) genes play important roles in coalescing signals from photoperiod and temperature pathways. However, the mechanism of CO and COLs involved in regulating the developmental stage transition and photoperiod/temperature senescing remains unclear. In this study, we identified a COL ortholog gene from the Taiwan native orchid Phalaenopsis aphrodite. The Phalaenopsis aphrodite CONSTANS-like 1 (PaCOL1) belongs to the B-box protein family and functions in the nucleus and cytosol. Expression profile analysis of Phalaenopsis aphrodite revealed that PaCOL1 was significantly expressed in leaves, but its accumulation was repressed during environmental temperature shifts. We found a differential profile for PaCOL1 accumulation, with peak accumulation at late afternoon and at the middle of the night. Arabidopsis with PaCOL1 overexpression showed earlier flowering under short-day (SD) conditions (8 h/23 °C light and 16 h/23 °C dark) but similar flowering time under long-day (LD) conditions (16 h/23 °C light and 8 h/23 °C dark). Transcriptome sequencing revealed several genes upregulated in PaCOL1-overexpressing Arabidopsis plants that were previously involved in flowering regulation of the photoperiod pathway. Yeast two-hybrid (Y2H) analysis and bimolecular fluorescence complementation (BiFC) analysis revealed that PaCOL1 could interact with a crucial clock-associated regulator, AtCCA1, and a flowering repressor, AtFLC. Furthermore, expressing PaCOL1 in cca1.lhy partially reversed the mutant flowering time under photoperiod treatment, which confirms the role of PaCOL1 function in the rhythmic associated factors for modulating flowering.

Spike Activator 1, Encoding a bHLH, Mediates Axillary Bud Development and Spike Initiation in Phalaenopsis aphrodite

Double-spikes Phalaenopsis orchids have greater market value than those with single-spike. In this study, a gene designated as Spike Activator 1 (SPK1), which encodes a basic helix-loop-helix (bHLH) transcription factor, was isolated and characterized from Phalaenopsis aphrodite (moth orchid). SPK1 was highly expressed in the meristematic tissues. In the axillary bud, SPK1 was highly upregulated by a moderately low temperature of 20 °C but downregulated by a spike inhibition temperature of 30 °C. SPK1 protein is localized in the nucleus. Another bHLH, bHLH35, which is also highly expressed in young tissues in the same way as SPK1 was also identified. In contrast to SPK1, bHLH35 transcripts are downregulated at 20 °C but upregulated at 30 °C. Bimolecular florescence complementation assay and yeast two-hybrid assays indicated that SPK1 interacts with bHLH35 and forms a heterodimer. Virus-induced gene silencing (VIGS) showed that 7 out of 15 vector control plants produced double spikes but that only 1 out of 15 VIGS-spk1 plants produced double spikes. RT-qPCR results indicated that VIGS-spk1 downregulated gene expression levels of SPK1, FT, CYCB, and EXPA8. Overall, we propose that SPK1 plays an essential role in early axillary bud development and spike initiation of P. aphrodite.

Night Temperature Affects the Growth, Metabolism, and Photosynthetic Gene Expression in Astragalus membranaceus and Codonopsis lanceolata Plug Seedlings

Astragalus membranaceus and Codonopsis lanceolata are two important medical herbs used in traditional Oriental medicine for preventing cancer, obesity, and inflammation. Night temperature is an important factor that influences the plug seedling quality. However, little research has focused on how the night temperature affects the growth and development of plug seedlings of these two medicinal species. In this study, uniform plug seedlings were cultivated in three environmentally controlled chambers for four weeks under three sets of day/night temperatures (25/10 °C, 25/15 °C, or 25/20 °C), the same relative humidity (75%), photoperiod (12 h), and light intensity (150 μmol·m-2·s-1 PPFD) provided by white LEDs. The results showed that night temperature had a marked influence on the growth and development of both species. The night temperature of 15 °C notably enhanced the quality of plug seedlings evidenced by the increased shoot, root, and leaf dry weights, stem diameter, and Dickson's quality index. Moreover, a night temperature of 15 °C also stimulated and increased contents of primary and secondary metabolites, including soluble sugar, starch, total phenols and flavonoids. Furthermore, the 15 °C night temperature increased the chlorophyll content and stomatal conductance and decreased the hydrogen peroxide content. Analysis of the gene expression showed that granule-bound starch synthase (GBSS), ribulose bisphosphate carboxylase large chain (RBCL), and ferredoxin (FDX) were up-regulated when the night temperature was 15 °C. Taken together, the results suggested that 15 °C is the optimal night temperature for the growth and development of plug seedlings of A. membranaceus and C. lanceolata.

Isolation a Homogalacturonan from the Outer Seed Coat of Shaddock (Citrus grandis Osbeck)

An acidic mucilage was isolated from the outer-layer seed coat of shaddock (Citrus grandis Osbeck) by water extraction at room temperature, and purified by DE-52 anion-exchange chromatography using 0.26 – 0.37 M NaCl. This purified mucilage was almost entirely composed of galacturonic acid residues. Glycosyl-linkage analysis showed that the backbone was 1→4 linked. Fourier Transform Infrared Spectroscopic analysis and determination of the degree of methylation further revealed that the mucilage was a low-degree (11.94%) esterified homogalacturonan. Size exclusion chromatography showed that the major molecular weight distribution of 610.9 kDa.

Continuous high and low temperature induced a decrease of photosynthetic activity and changes in the diurnal fluctuations of organic acids in Opuntia streptacantha

Opuntia plants grow naturally in areas where temperatures are extreme and highly variable in the day during the entire year. These plants survive through different adaptations to respond to adverse environmental conditions. Despite this capability, it is unknown how CAM photosynthetic activity and growth in Opuntia plantlets is affected by constant heat or cold. Therefore, the main objective of this research was to evaluate the short-term effect of high (40°C) and low (4°C) continuous temperatures on the photosynthetic efficiency, the organic acid content (malic acid) and the relative growth rate (RGR) in seven-month-old Opuntia streptacantha plantlets during 5, 10, and 15 days. Chlorophyll fluorescence analysis allowed us to determine that high temperatures negatively impact the photosynthetic efficiency of O. streptacantha plantlets, which exhibited the lowest values of maximum quantum efficiency of the photosystem II (Fv/Fm = 52%, Fv/F0 = 85%), operational quantum yield of PS (ΦPSII = 65%) and relative electron transport rate (rETR = 65%), as well as highest values of basal fluorescence (F0 = 226%) during 15 days of treatment. Similarly, low temperatures decreased Fv/Fm (16%), Fv/F0 (50%), ΦPSII and rETR (16%). High temperatures also decreased nocturnal acidification in approximately 34-50%, whereas low temperatures increased it by 30-36%. Additionally, both continuous temperatures affected drastically diurnal consumption of malic acid, which was related to a significant RGR inhibition, where the specific photosynthetic structure area component was the most affected. Our results allowed determining that, despite the high tolerance to extreme temperatures described for Opuntia plants, young individuals of O. streptacantha suffered photosynthetic impairment that led to the inhibition of their growth. Thus, the main findings reported in this study can help to predict the potential impact of climatic change on the establishment and survival of succulent species of arid and semiarid regions of Mexico.

Constitutive expression of a plant ferredoxin-like protein (pflp) enhances capacity of photosynthetic carbon assimilation in rice (Oryza sativa)

The plant ferredoxin-like protein (PFLP) gene, cloned from sweet peppers predicted as an electron carrier in photosynthesis, shows high homology to the Fd-I sequence of Arabidopsis thaliana, Lycopersicon esculentum, Oryza sativa and Spinacia oleracea. Most of pflp related studies focused on anti-pathogenic effects, while less understanding for the effects in photosynthesis with physiological aspects, such as photosynthesis rate, and levels of carbohydrate metabolites. This project focuses on the effects of pflp overexpression on photosynthesis by physiological evaluations of carbon assimilation with significant higher levels of carbohydrates with higher photosynthesis efficiency. In this report, two independent transgenic lines of rice plants (designated as pflp-1 and pflp-2) were generated from non-transgenic TNG67 rice plant (WT). Both transgenic pflp rice plants exhibited enhanced photosynthesis efficiency, and gas exchange rates of photosynthesis were 1.3- and 1.2-fold higher for pflp-1 and pflp-2 than WT respectively. Significantly higher electron transport rates of pflp rice plants were observed. Moreover, photosynthetic products, such as fructose, glucose, sucrose and starch contents of pflp transgenic lines were increased accordingly. Molecular evidences of carbohydrate metabolism related genes activities (osHXK5, osHXK6, osAGPL3, osAGPS2α, osSPS, ospFBPase, oscFBPase, and osSBPase) in transgenic lines were higher than those of WT. For performance of crop production, 1000-grain weight for pflp-1 and pflp-2 rice plants were 52.9 and 41.1 g that were both significantly higher than 31.6 g for WT, and panicles weights were 1.4- and 1.2-fold higher than WT. Panicle number, tiller number per plants for pflp rice plants were all significantly higher compared with those of WT where there was no significant difference observed between two pflp rice plants. Taken altogether; this study demonstrated that constitutive pflp expression can improve rice production by enhancing the capacity of photosynthetic carbon assimilation.

Plant Physiological, Morphological and Yield-Related Responses to Night Temperature Changes across Different Species and Plant Functional Types

Land surface temperature over the past decades has shown a faster warming trend during the night than during the day. Extremely low night temperatures have occurred frequently due to the influence of land-sea thermal difference, topography and climate change. This asymmetric night temperature change is expected to affect plant ecophysiology and growth, as the plant carbon consumption processes could be affected more than the assimilation processes because photosynthesis in most plants occurs during the daytime whereas plant respiration occurs throughout the day. The effects of high night temperature (HNT) and low night temperature (LNT) on plant ecophysiological and growing processes and how the effects vary among different plant functional types (PFTs) have not been analyzed extensively. In this meta-analysis, we examined the effect of HNT and LNT on plant physiology and growth across different PFTs and experimental settings. Plant species were grouped according to their photosynthetic pathways (C3, C4, and CAM), growth forms (herbaceous, woody), and economic purposes (crop, non-crop). We found that HNT and LNT both had a negative effect on plant yield, but the effect of HNT on plant yield was primarily related to a reduction in biomass allocation to reproduction organs and the effect of LNT on plant yield was more related to a negative effect on total biomass. Leaf growth was stimulated at HNT and suppressed at LNT. HNT accelerated plants ecophysiological processes, including photosynthesis and dark respiration, while LNT slowed these processes. Overall, the results showed that the effects of night temperature on plant physiology and growth varied between HNT and LNT, among the response variables and PFTs, and depended on the magnitude of temperature change and experimental design. These findings suggest complexities and challenges in seeking general patterns of terrestrial plant growth in HNT and LNT. The PFT specific responses of plants are critical for obtaining credible predictions of the changes in crop production, plant community structure, vegetation dynamics, biodiversity, and ecosystem functioning of terrestrial biomes when asymmetric night temperature change continues.

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 Phalaenopsis aphrodite Flowering Genes PaFT1 and PaFD

We show that the key flowering regulators encoded by Phalaenopsis aphrodite FLOWERING LOCUS T1 (PaFT1) and PaFD share high sequence homologies to these from long-day flowering Arabidopsis and short-day flowering rice. Interestingly, PaFT1 is specifically up-regulated during flowering inductive cooling treatment but is not subjected to control by photoperiod in P. aphrodite. Phloem or shoot apex-specific expression of PaFT1 restores the late flowering of Arabidopsis ft mutants. Moreover, PaFT1 can suppress the delayed flowering caused by SHORT VEGATATIVE PHASE (SVP) overexpression as well as an active FRIGIDA (FRI) allele, indicating the functional conservation of flowering regulatory circuit in different plant species. PaFT1 promoter:GUS in Arabidopsis showed similar staining pattern to that of Arabidopsis FT in the leaves and guard cells but different in the shoot apex. A genomic clone or heat shock-inducible expression of PaFT1 is sufficient to the partial complementation of the ft mutants. Remarkably, ectopic PaFT1 expression also triggers precocious heading in rice. To further demonstrate the functional conservation of the flowering regulators, we show that PaFD, a bZIP transcription factor involved in flowering promotion, interacts with PaFT1, and PaFD partially complemented Arabidopsis fd mutants. Transgenic rice expressing PaFD also flowered early with increased expression of rice homologues of APETALA1 (AP1). Consistently, PaFT1 knock-down Phalaenopsis plants generated by virus-induced gene silencing exhibit delayed spiking. These studies suggest functional conservation of FT and FD genes, which may have evolved and integrated into distinct regulatory circuits in monopodial orchids, Arabidopsis and rice that promote flowering under their own inductive conditions.

Genomic analyses of the CAM plant pineapple

The innovation of crassulacean acid metabolism (CAM) photosynthesis in arid and/or low CO2 conditions is a remarkable case of adaptation in flowering plants. As the most important crop that utilizes CAM photosynthesis, the genetic and genomic resources of pineapple have been developed over many years. Genetic diversity studies using various types of DNA markers led to the reclassification of the two genera Ananas and Pseudananas and nine species into one genus Ananas and two species, A. comosus and A. macrodontes with five botanical varieties in A. comosus. Five genetic maps have been constructed using F1 or F2 populations, and high-density genetic maps generated by genotype sequencing are essential resources for sequencing and assembling the pineapple genome and for marker-assisted selection. There are abundant expression sequence tag resources but limited genomic sequences in pineapple. Genes involved in the CAM pathway has been analysed in several CAM plants but only a few of them are from pineapple. A reference genome of pineapple is being generated and will accelerate genetic and genomic research in this major CAM crop. This reference genome of pineapple provides the foundation for studying the origin and regulatory mechanism of CAM photosynthesis, and the opportunity to evaluate the classification of Ananas species and botanical cultivars.

A novel in vitro protocol for inducing direct somatic embryogenesis in Phalaenopsis aphrodite without taking explants

An alternative in vitro protocol for embryo induction directly from intact living seedlings of Phalaenopsis aphrodite subspecies formosana was established in this study. Without the supplementation of plant growth regulators (PGRs), no embryos were obtained from all the seedlings when cultured on the solid medium. In contrast, embryos formed from the seedlings on the 2-layer medium and the 2-step culture system without the use of PGRs. It was found that the age of the seedlings affected embryo induction. The 2-month-old seedlings typically had higher embryogenic responses when compared with the 4-month-old seedlings in the 2-layer medium or 2-step system. For the 2-month-old seedlings, 1 mg/L TDZ resulted in the highest number of embryos at the distal site of the shoot. However, on the leaves' surface, 0.5 mg/L TDZ induced the highest number of embryos. When the 2-month-old seedlings were cultured using the 2-step method at 1 mg/L of TDZ, the highest embryogenic response was obtained, with an average of 44 embryos formed on each seedling. These adventitious embryos were able to convert into plantlets in a PGR-free 1/2 MS medium, and the plantlets had normal morphology and growth.

Transcriptome-wide characterization of miRNA-directed and non-miRNA-directed endonucleolytic cleavage using Degradome analysis under low ambient temperature in Phalaenopsis aphrodite subsp. formosana

Plant microRNAs (miRNAs) regulate gene expression through post-transcriptional gene silencing. Phalaenopsis aphrodite subsp. formosana is an orchid species native to Taiwan, which has high economic value and a high frequency of floral polymorphism. To date, few studies have focused on the regulatory roles of miRNAs and functional small RNAs (sRNAs) in orchids although understanding the regulation of flower development and flowering time is potentially important. Here, we combined analyses of the transcriptome, sRNAs and the degradome to identify sRNA-directed transcript cleavages in Phalaenopsis. Degradome analysis provided large-scale evidence of conserved and novel miRNA-directed cleavage of target transcripts, and 46 abundant sRNA groups and their target transcripts were identified. Low temperature-responsive sRNAs were validated with normalized reads from an sRNA library and quantitative stem-loop reverse transcription-PCR (RT-PCR) analysis. According to gene ontology (GO) categorization, target transcripts of the novel miRNAs and sRNAs are functionally involved in metabolic processes or responses to stress. One particular homologous gene, Allcontig28452, which encodes digalactosyldiacylglycerol synthase 2 (DGD2), was found to be targeted by natural antisense transcripts (NATs) unique to Phalaenopsis. In summary, comprehensive analyses of the transcriptome, sRNAs and degradome using deep sequencing technology provided a useful platform for investigating miRNA-directed and non-miRNA-directed endonucleolytic cleavage in a non-model plant, the orchid Phalaenopsis.

Research on orchid biology and biotechnology

Orchidaceae constitute one of the largest families of angiosperms. They are one of the most ecological and evolutionary significant plants and have successfully colonized almost every habitat on earth. Because of the significance of plant biology, market needs and the current level of breeding technologies, basic research into orchid biology and the application of biotechnology in the orchid industry are continually endearing scientists to orchids in Taiwan. In this introductory review, we give an overview of the research activities in orchid biology and biotechnology, including the status of genomics, transformation technology, flowering regulation, molecular regulatory mechanisms of floral development, scent production and color presentation. This information will provide a broad scope for study of orchid biology and serve as a starting point for uncovering the mysteries of orchid evolution.

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.

Low night temperature acclimation of Phalaenopsis

The capability of Phalaenopsis to acclimate its photosynthetic capacity and metabolic activity to cool night temperature conditions is crucial for improving orchid production in terms of efficient greenhouse heating. The extent to which Phalaenopsis possesses acclimation potential and the mechanistic background of the metabolic processes involved, have, however, not been studied before. Plants were subjected to a direct and gradual shift from a day to night temperature regime of 28/28-28/16°C, the cold stress and cold acclimation treatment, respectively. In comparison with the cold stress treatment, the cold acclimation treatment led to a higher malate accumulation and a reduction in leaf net CO(2) uptake. Consistently, the contribution of respiratory CO(2) recycling to nocturnal malate synthesis was calculated to be 23.5 and 47.0% for the cold stress and cold acclimation treatment, respectively. Moreover, the lower levels of starch measured in the cold acclimated leaves confirmed the suggested enhanced respiratory CO(2) recycling, implying that Phalaenopsis CAM operation evolved towards CAM idling. It is, however, plausible that this adjustment was not an effect of the low night temperature per se but a consequence of cool-root induced drought stress. Apart from that, at the start of the photoperiod, membrane stability showed a depression which was directly counteracted by an increased generation of glucose, fructose and sucrose. From these observations, it can be concluded that the observed plasticity in CAM operation and metabolic flexibility may be recognized as important steps in the low night temperature acclimation of Phalaenopsis.

Sequencing-based approaches reveal low ambient temperature-responsive and tissue-specific microRNAs in phalaenopsis orchid

Plant small RNAs (smRNAs) are short, non-coding RNA molecules that mediate RNA silencing and regulate a group of genes involved in plant development and responses to environmental stimuli. Low temperature is necessary to initiate stalk development in the orchid Phalaenopsis aphrodite subsp. formosana. To identify smRNAs in Phalaenopsis responding to low temperatures, a smRNA profiling analysis using high-throughput sequencing technology was performed. Subsequent bioinformatic analysis was applied to categorize the miRNAs identified. A total of 37,533,509 smRNA reads yielded 11,129 independent orchid miRNA sequences, representing 329 known miRNA families identified in other plant species. Because the genomic resources available for Phalaenopsis are limited, a transcriptomic database was established using deep sequencing data sets to identify miRNAs precursors and their target transcripts. Comparing small RNAs and the transcriptomic database, 14 putative miRNA precursors of 10 miRNA families were identified, as were hundreds of putative targets. Comparing sequencing data and smRNA northern hybridization results identified miR156, miR162, miR528 and miR535 as low temperature-induced miRNAs. In addition, tissue-specific expression of these miRNAs was investigated. It was concluded that miR156 and miR172 may be components of a regulatory pathway mediating transition from the vegetative to the reproductive phase in Phalaenopsis. The smRNA and transcriptomic databases could be the foundations for further research aimed at elucidating the control of the flowering time in orchids.