Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy.

To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy.

Phylogenetic analysis and character evolution of tribe Arethuseae (Orchidaceae) reveal a new genus Mengzia.

Delimitation of the tribe Arethuseae has varied considerably since it was first defined. The relationships within Arethuseae, particularly within the subtribe Arethusinae, remain poorly elucidated. In this study, we reconstructed the phylogeny of Arethuseae, using six plastid markers (matK, ycf1, rbcL rpoc1, rpl32-trnL and trnL-F) from 83 taxa. The ancestral state reconstruction of 11 selected morphological characters was also conducted to identify synapomorphies and assess potential evolutionary transitions. Morphological character comparision between the distinct species Bletilla foliosa and other species are conducted. Our results unequivocally supported the monophyly of Arethuseae, which included highly supported clades and a clear synapomorphy of non-trichome-like lamellae. Furthermore, B. foliosa formed a separate clade in the subtribe Arethusinae, instead of clustering with the other Bletilla species in the subtribe Coelogyninae. The morphological characters comparision further showed that the B. foliosa clade could be distinguished from other genera in Arethuseae by multiple characters, including presence of lateral inflorescence, three lamellae with trichome-like apex and four pollinia. In light of these molecular and morphological evidences, we propose Mengzia as a new genus to accommodate B. foliosa and accordingly provide descriptions of this new genus and combination.

Author Correction: The Apostasia genome and the evolution of orchids.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An assessment of the Chinese medicinal Dendrobium industry: Supply, demand and sustainability.

ETHNOPHARMACOLOGICAL RELEVANCE: A high proportion of species native to China from the genus Dendrobium (Orchidaceae) have been used as folk medicine for more than 2300 years. The fresh or dried stem of many Dendrobium species are regarded as "superior grade" tonic in Traditional Chinese Medicine (TCM), for their traditional properties of nourishing the kidney, moisturizing the lung, benefiting the stomach, promoting the production of body fluids and clearing heat. AIM OF THE STUDY: This review aims to provide comprehensive and updated information on the diversity of Dendrobium species used in TCM and the development of the Dendrobium industry. The supply and demand of the Chinese medicinal Dendrobium are investigated. Moreover, we discuss the problems the industry faces and the relationship between the cultivation and species conservation. MATERIALS AND METHODS: The available information on many Dendrobium species (especially D. officinale) was collected from the electronic databases (using Pubmed, CNKI, Baidu scholar, Google scholar and Web of Science). We also obtained information from communication with specialists with profound knowledge in related research field and industry practitioners. Information was also obtained from website of the Forestry Bureau or relevant government departments, online databases, books, Ph.D. dissertations and M.Sc. theses. RESULTS: Approximately 41 species in genus Dendrobium have been recorded in TCM. The development of the Dendrobium industry could be divided into three phases: (a) the wild-collection phase, (b) the massive commercial artificial-sheltered cultivation phase and (c) the diversified ecologically-friendly cultivation phase. The development of seedlings production technology, the improvement of substrates and the integration of cultivation technology support the rapid increase of Dendrobium herbs in the Chinese TCM market. Doubts around the quality and efficacy of product in artificial-sheltered cultivation, the lack of product standards and the low level of product development have limited the utilization for TCM and hampered the development of the Dendrobium industry. Both the artificial-sheltered cultivation and ecologically-friendly cultivation contribute to the conservation of Dendrobium species, through the use seedlings derived from seeds of sexual reproduction rather than meristematic-based clonal propagation. CONCLUSIONS: This review summarizes the species and cultivation history of medicinal herbs in the Dendrobium. The review can help inform future scientific research towards the TCM in Dendrobium, including mycorrhizal technology and microorganism fertilizer, pharmacological studies, the directed cultivation of varieties and diversified product. It is suggested that Dendrobium cultivation has a great potential to link the commercial TCM industry together with initiatives of biodiversity conservation.

[Research progress on molecular mechanism of Dendrobium officinale and its active components to metabolic syndrome].

Metabolic syndrome,a kind of clinical syndrome marked by the presence of symptoms such as hyperglycemia,dyslipidemia and hypertension,has an increasing incidence and comes to be present in younger people. More importantly,prolonged maintenance of this condition can significantly increase the incidence of chronic diseases such as diabetes,cardiovascular disease and cancer.However,the formation mechanism of metabolic syndrome is very complex and has not been fully studied and revealed. Dendrobium officinale is a traditional medicine and food substance with multiple physiological functions. In recent years,D. officinale has attracted much attention from the scholars both at home and abroad due to its functions such as improving blood lipid,lowering blood pressure and regulating blood sugar. However,there is no systematic review on the current studies about D. officinale in intervening metabolic syndrome and its underlying molecular mechanism. In this paper,the biological activity of the main active components,and the research or application status of D. officinale extract in the recent years were reviewed. Then,we analyzed the digestion,absorption and the safety and toxicity of D. officinale and its active components in the body. Finally,we summarized the effects of D. officinale and its active components on metabolic syndrome in animals and human bodies,and discussed its possible molecular mechanisms at the cellular level. This paper provides solid theoretical guidance and reliable molecular basis for further research and advanced development of D. officinale and its active components,especially for its oncoming clinical application.

Morphological Type Identification of Self-Incompatibility in Dendrobium and Its Phylogenetic Evolution Pattern.

Self-incompatibility (SI) is a type of reproductive barrier within plant species and is one of the mechanisms for the formation and maintenance of the high diversity and adaptation of angiosperm species. Approximately 40% of flowering plants are SI species, while only 10% of orchid species are self-incompatible. Intriguingly, as one of the largest genera in Orchidaceae, 72% of Dendrobium species are self-incompatible, accounting for nearly half of the reported SI species in orchids, suggesting that SI contributes to the high diversity of orchid species. However, few studies investigating SI in Dendrobium have been published. This study aimed to address the following questions: (1) How many SI phenotypes are in Dendrobium, and what are they? (2) What is their distribution pattern in the Dendrobium phylogenetic tree? We investigated the flowering time, the capsule set rate, and the pollen tube growth from the representative species of Dendrobium after artificial pollination and analysed their distribution in the Asian Dendrobium clade phylogenetic tree. The number of SI phenotypes exceeded our expectations. The SI type of Dendrobium chrysanthum was the primary type in the Dendrobium SI species. We speculate that there are many different SI determinants in Dendrobium that have evolved recently and might be specific to Dendrobium or Orchidaceae. Overall, this work provides new insights and a comprehensive understanding of Dendrobium SI.

[Original materials of traditional Chinese medicinal names of "Jinchai" and "Jinchai Shihu" based on vegetative morphology].

"Jinchai Shihu" were called Jinchai and recoded in "Taishang Zhouhou Yujingfang" of Tang Dynasty, which first clearly documented the name of Shihu in complex Dendrobium medicines and were condiered as superior medicinal articles. Morphological features are one of the naming principles for Chinese medicines. In this paper, botanical origin plants under the names of "Jinchai" and "Jinchai Shihu" were investigated. Based on documents from the local Chronicles and historical accounts, the Chinese characters of Jinchai have the distinctive features of gold color and two hair clasps. Moreover, the hair clasps are usually cylindrical in shape with uniform thickness in middle and upper part, and tapers off to the foot. And its bottom part style is simple and head part is complex. Thus we speculated the herbal "Jinchai" and "Jinchai Shihu" should have similar morphologic features as Chinese characters of Jinchai, including golden color and hairpin shape of stems without braches, short and solid sterm. After comparing the dried vegetative morphology of 10 common medicinal Dendrobium species, we suggested that of Dendrobium flexicaule matches well with the morphological features from historical herbal records.

[Herbal textual research on relationship between Chinese medicine"Shihu" (Dendrobium spp.) and "Tiepi Shihu" (D. catenatum)].

Dendrobium species on the ancient Chinese herbal texts were investigated in this paper, including their dscriptions of original species, producing areas and quality. Our results indicated that the major producing areas were Lu'an, Anhui province and Wenzhou, Taizhou, Zhejiang province. In addition, the sweet flavor, short, thin and solid stems were standing for good quality. Based on the stable producing areas and quality descriptions, D. catenatum (D. officinale) ("Tiepi Shihu") and D. houshanense were high quality medicinal Dendrobium species ("Shihu" ) in ancient China. Besides, there were 3 scientific names for "Tiepi Shihu", including D. candidum, D. officinale, D. catenatum. After textual investigation, We suggest that D. catenatum should be its scientific name, and D. officinale was synonyms published later. However, the name "D. officinale" could be reserved as it is much more popular used in publication and commodities. Moreover, its Chinese name should be "Tiepi Shihu".

The Apostasia genome and the evolution of orchids.

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. Here we report the draft genome sequence of Apostasia shenzhenica, 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.

[Breakthrough in key science and technologies in Dendrobium catenatum industry].

In view of the significant difficulties of propagation, planting and simple product in Dendrobium catenatum(D. officinale)industry development, a series of research were carried out. Genome study showed that D. catenatum is a specie of diploid with 38 chromosomes and 28 910 protein-coding genes. It was identified that specific genes accumulated in different organs at the transcriptome level. We got an insight into the gene regulation mechanism of the loss of the endospermous seed, the wide ecological adaptability and the synthesis of polysaccharides, which provided a theoretical basis for genetic engineering breeding and development and utilization of active pharmaceutical ingredients. The rapid propagation system was established for applying to industrialized production by overcoming breeding problems on seed setting and sprouting, which laid a foundation for artificial cultivation of D. catenatum. And in order to give a clear explanation of genetic variation of important economic traits, we built up the breeding system. Since special varieties of D. catenatum were bred, it helped solve the problem of trait segregation of seedling progeny and support the improvement of D. catenatum industry. The regulation of dynamic variation of target compounds, together with the mechanism of nutrient uptake, was revealed. The breakthrough of key technologies including culture substrates, light regulation and precisely collection was carried out. Several cultivation modes like facility cultivation, original ecological cultivation, cliff epiphytic cultivation, stereoscopic cultivation and potting cultivation were set up. Above all, the goal of cultivating D. catenatum as well as producing good D. catenatum will be achieved.

Lack of S-RNase-Based Gametophytic Self-Incompatibility in Orchids Suggests That This System Evolved after the Monocot-Eudicot Split.

Self-incompatibility (SI) is found in approximately 40% of flowering plant species and at least 100 families. Although orchids belong to the largest angiosperm family, only 10% of orchid species present SI and have gametophytic SI (GSI). Furthermore, a majority (72%) of Dendrobium species, which constitute one of the largest Orchidaceae genera, show SI and have GSI. However, nothing is known about the molecular mechanism of GSI. The S-determinants of GSI have been well characterized at the molecular level in Solanaceae, Rosaceae, and Plantaginaceae, which use an S-ribonuclease (S-RNase)-based system. Here, we investigate the hypothesis that Orchidaceae uses a similar S-RNase to those described in Rosaceae, Solanaceae, and Plantaginaceae SI species. In this study, two SI species (Dendrobium longicornu and D. chrysanthum) were identified using fluorescence microscopy. Then, the S-RNase- and SLF-interacting SKP1-like1 (SSK1)-like genes present in their transcriptomes and the genomes of Phalaenopsis equestris, D. catenatum, Vanilla shenzhenica, and Apostasia shenzhenica were investigated. Sequence, phylogenetic, and tissue-specific expression analyses revealed that none of the genes identified was an S-determinant, suggesting that Orchidaceae might have a novel SI mechanism. The results also suggested that RNase-based GSI might have evolved after the split of monocotyledons (monocots) and dicotyledons (dicots) but before the split of Asteridae and Rosidae. This is also the first study to investigate S-RNase-based GSI in monocots. However, studies on gene identification, differential expression, and segregation analyses in controlled crosses are needed to further evaluate the genes with high expression levels in GSI tissues.

De novo transcriptome assembly databases for the butterfly orchid Phalaenopsis equestris.

Orchids are renowned for their spectacular flowers and ecological adaptations. After the sequencing of the genome of the tropical epiphytic orchid Phalaenopsis equestris, we combined Illumina HiSeq2000 for RNA-Seq and Trinity for de novo assembly to characterize the transcriptomes for 11 diverse P. equestris tissues representing the root, stem, leaf, flower buds, column, lip, petal, sepal and three developmental stages of seeds. Our aims were to contribute to a better understanding of the molecular mechanisms driving the analysed tissue characteristics and to enrich the available data for P. equestris. Here, we present three databases. The first dataset is the RNA-Seq raw reads, which can be used to execute new experiments with different analysis approaches. The other two datasets allow different types of searches for candidate homologues. The second dataset includes the sets of assembled unigenes and predicted coding sequences and proteins, enabling a sequence-based search. The third dataset consists of the annotation results of the aligned unigenes versus the Nonredundant (Nr) protein database, Kyoto Encyclopaedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups (COG) databases with low e-values, enabling a name-based search.

Seasonal variation in the mating system of a selfing annual with large floral displays.

BACKGROUND AND AIMS: Flowering plants display considerable variation in mating system, specifically the relative frequency of cross- and self-fertilization. The majority of estimates of outcrossing rate do not account for temporal variation, particularly during the flowering season. Here, we investigated seasonal variation in mating and fertility in Incarvillea sinensis (Bignoniaceae), an annual with showy, insect-pollinated, 'one-day' flowers capable of delayed selfing. We examined the influence of several biotic and abiotic environmental factors on day-to-day variation in fruit set, seed set and patterns of mating. METHODS: We recorded daily flower number and pollinator abundance in nine 3 × 3-m patches in a population at Mu Us Sand land, Inner Mongolia, China. From marked flowers we collected data on daily fruit and seed set and estimated outcrossing rate and biparental inbreeding using six microsatellite loci and 172 open-pollinated families throughout the flowering period. KEY RESULTS: Flower density increased significantly over most of the 50-d flowering season, but was associated with a decline in levels of pollinator service by bees, particularly on windy days. Fruit and seed set declined over time, especially during the latter third of the flowering period. Multilocus estimates of outcrossing rate were obtained using two methods (the programs MLTR and BORICE) and both indicated high selfing rates of ∼80 %. There was evidence for a significant increase in levels of selfing as the flowering season progressed and pollinator visitation declined. Biparental inbreeding also declined significantly as the flowering season progressed. CONCLUSIONS: Temporal variation in outcrossing rates may be a common feature of the mating biology of annual, insect-pollinated plants of harsh environments but our study is the first to examine seasonal mating-system dynamics in this context. Despite having large flowers and showy floral displays, I. sinensis attracted relatively few pollinators. Delayed selfing by corolla dragging largely explains the occurrence of mixed mating in I. sinensis, and this mode of self-fertilization probably functions to promote reproductive assurance when pollinator service is limited by windy environmental conditions and competition from co-occurring flowering plants.

The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution.

Orchids make up about 10% of all seed plant species, have great economical value, and are of specific scientific interest because of their renowned flowers and ecological adaptations. Here, we report the first draft genome sequence of a lithophytic orchid, Dendrobium catenatum. We predict 28,910 protein-coding genes, and find evidence of a whole genome duplication shared with Phalaenopsis. We observed the expansion of many resistance-related genes, suggesting a powerful immune system responsible for adaptation to a wide range of ecological niches. We also discovered extensive duplication of genes involved in glucomannan synthase activities, likely related to the synthesis of medicinal polysaccharides. Expansion of MADS-box gene clades ANR1, StMADS11, and MIKC(*), involved in the regulation of development and growth, suggests that these expansions are associated with the astonishing diversity of plant architecture in the genus Dendrobium. On the contrary, members of the type I MADS box gene family are missing, which might explain the loss of the endospermous seed. The findings reported here will be important for future studies into polysaccharide synthesis, adaptations to diverse environments and flower architecture of Orchidaceae.

[Investigation of original materials under traditonal Chinese medicine names of "Jinchai" and "Jinchai Shihu"].

To clear from botanical view the original materials under the traditional Chinese medicine names of "Jinchai", "Jinchai Shihu" within the genus Dendrobium of the family Orchidaceae. Combined of different methods including study of historical records from the local chronicles and historical accounts of past event in Hubei, Sichuan, Chongqing, Henan and Shaanxi provinces, interviewing face to face with the old traditional Chinese workers and folk doctors in 20 downtowns and countrysides, such as, Laohekou, Lichuan, Fangxian, Xixia, Neixiang, and Ankang, and collecting a few plants of "Jinchai" for taxonomic identification. The traditional Chinese medicine names of "Jinchai", "Jinchai Shihu" were widely used by the local people from the eastern Chongqing, western Hubei, northeasten Sichuan, southeastern Shaanxi, western Henan. Those two names were frequently found in the local Chronicles and historical accounts of past event, even in the local daily life such as folk songs and stories. The botanical identification results showed that a endemic species of D. flexicaule is the original materials of the traditional Chinese medicine names "Jinchai" and "Jinchai Shihu", and this species are also called "Longtoujin", "Renzijin", "Huanzijin" and "Longtoufengweijin" by the local people. The dried artifactitious specimens of D. flexicaule are traditionally named as "Jinerhuan". The botanic resource plants of the traditional Chinese medicine names of "Jinchai", "Jinchai Shihu" are the endemic species of D. flexicaule that is distributed mainly in central areas of China including eastern Chongqing, western Hubei, northeasten Sichuan, southeastern Shaanxi, and western Henan, rather than D. nobile as referring in both Chinese and English version of Flora of China, and in official recorded serious versions of The Chinese Pharmacopoeia since 1977. In order to avoid confusion in the traditional Chinese medicine dendrobiums industry, the Chinese name of D. nobile is suggested as "Biancao Shihu", which characterized one stem feature of this species, and the traditional Chinese medicine names "Jinchai" or "JinchaiShihu" is suggested to refer to the species D. flexicaule.

Distinct subcellular localization and potential role of LINE1-ORF1P in meiotic oocytes.

LINE-1 is an autonomous non-LTR retrotransposon in mammalian genomes and encodes ORF1P and ORF2P. ORF2P has been clearly identified as the enzyme supplier needed in LINE-1 retrotransposition. However, the role of ORF1P is not well explored. In this study, we employed loss/gain-of-function approach to investigate the role of LINE1-ORF1P in mouse oocyte meiotic maturation. During mouse oocyte development, ORF1P was observed in cytoplasm as well as in nucleus at germinal vesicle (GV) stage while was localized on the spindle after germinal vesicle breakdown (GVBD). Depletion of ORF1P caused oocyte arrest at the GV stage as well as down-regulation of CDC2 and CYCLIN B1, components of the maturation-promoting factor (MPF). Further analysis demonstrated ORF1P depletion triggered DNA damage response and most of the oocytes presented altered chromatin configuration. In addition, SMAD4 showed nuclear foci signal after Orf1p dsRNA injection. ORF1P overexpression held the oocyte development at MI stage and the chromosome alignment and spindle organization were severely affected. We also found that ORF1P could form DCP1A body-like foci structure in both cytoplasm and nucleus after heat shock. Taken together, accurate regulation of ORF1P plays an essential role in mouse oocyte meiotic maturation.

Reticulate evolution and sea-level fluctuations together drove species diversification of slipper orchids (Paphiopedilum) in South-East Asia.

South-East Asia covers four of the world's biodiversity hotspots, showing high species diversity and endemism. Owing to the successive expansion and contraction of distribution and the fragmentation by geographical barriers, the tropical flora greatly diversified in this region during the Tertiary, but the evolutionary tempo and mode of species diversity remain poorly investigated. Paphiopedilum, the largest genus of slipper orchids comprising nearly 100 species, is mainly distributed in South-East Asia, providing an ideal system for exploring how plant species diversity was shaped in this region. Here, we investigated the evolutionary history of this genus with eight cpDNA regions and four low-copy nuclear genes. Discordance between gene trees and network analysis indicates that reticulate evolution occurred in the genus. Ancestral area reconstruction suggests that vicariance and long-distance dispersal together led to its current distribution. Diversification rate variation was detected and strongly correlated with the species diversity in subg. Paphiopedilum (~80 species). The shift of speciation rate in subg. Paphiopedilum was coincident with sea-level fluctuations in the late Cenozoic, which could have provided ecological opportunities for speciation and created bridges or barriers for gene flow. Moreover, some other factors (e.g. sympatric distribution, incomplete reproductive barriers and clonal propagation) might also be advantageous for the formation and reproduction of hybrid species. In conclusion, our study suggests that the interplay of reticulate evolution and sea-level fluctuations has promoted the diversification of the genus Paphiopedilum and sheds light into the evolution of Orchidaceae and the historical processes of plant species diversification in South-East Asia.

PLK4 is essential for meiotic resumption in mouse oocytes.

Polo-like kinase (PLK) 4 is a unique member of the PLK family that plays vital roles in centriole biogenesis during mitosis. The localization of PLK4 on centrioles must be precisely regulated during mitosis to ensure correct centriole duplication. However, little is known about the function of PLK4 in mammalian oocyte meiosis. We addressed this question by examining the expression and localization of PLK4 in mouse oocytes and using RNA interference and protein overexpression to investigate its function in meiosis. PLK4 expression peaked at the germinal vesicle breakdown (GVBD) stage, and the protein was localized in the cytoplasm throughout meiotic maturation. Depletion of PLK4 caused meiotic arrest at the GV stage and suppressed CYCLINB1 and CDC2 activities. Moreover, PLK4 depletion prevented the de-phosphorylation of CDC2-Tyr15 in nucleus and induced a decrease in the level of the CDC25C protein. PLK1 overexpression failed to rescue GV-stage arrest in PLK4-depleted oocytes, whereas overexpressing PLK4 resulted in normal GVBD in oocytes in which PLK1 activity was inhibited. In addition, PLK4 overexpression did not cause abnormal spindle formation or affect extrusion of the first polar body. These results illustrate the fact that PLK4 is essential for meiotic resumption but may not influence spindle formation in mouse oocytes during meiotic maturation.