Yi-Bo Luo

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.

Comparison of hypoglycemic and antioxidative effects of polysaccharides from four different Dendrobium species

Four polysaccharides from Dendrobium huoshanense (DHP), D. officinale (DOP), D. nobile (DNP) and D. chrysotoxum (DCP), which had obvious differences in intrinsic viscosities and monosaccharide compositions, were extracted to compare their hypoglycemic and antioxidative activities in alloxan-induced diabetic mice by oral administration. The analysis of fasting blood glucose, glycosylated serum protein and serum insulin levels showed that DHP, DOP and DNP, but not DCP, possessed significant hypoglycemic effect with the decreasing order of DHP>DNP>DOP. Histopathological observation confirmed the capability of DHP, DOP and DNP to intervene the damage in pancreas tissues. The determination of superoxide dismutase, catalase, malonaldehyde and L-glutathione levels in the liver and kidney displayed that DHP, DOP and DNP had protective effects against alloxan-induced oxidative damage and the effect of DHP ranked first. These results suggested that there were significant differences in hypoglycemic and antioxidative activities between four Dendrobium polysaccharides, which may be contributed to their physicochemical properties.

Studies of Mycorrhizal Fungi of Chinese Orchids and Their Role in Orchid Conservation in China—A Review

China has over 1,200 species of native orchids in nearly 173 genera. About one fourth of native species are of horticultural merit. Some species are of Chinese medicinal value. In fact, the demand on orchid species with high Chinese medicinal values such as Gastrodia elata, Dendrobium offcinale, along with demands on species of cultural importance, such as those in the genus of Cymbidium, is a major factor causing wild populations to diminish and in some cases, drive wild populations to the brink of extinction. These market demands have also driven studies on the role of mycorrhizal fungi in orchid seed germination, seedling and adult growth, and reproduction. Most of these mycorrhizal studies of Chinese orchids, however, are published in Chinese, some in medical journals, and thus overlooked by the mainstream orchid mycorrhizal publications. Yet some of these studies contained interesting discoveries on the nature of the mycorrhizal relationships between orchids and fungi. We present a review of some of these neglected publications. The most important discovery comes from the mycorrhizal studies on G. elata, in which the researchers concluded that those fungi species required to stimulate seed germination are different from those that facilitate the growth of G. elata beyond seedling stages. In addition, presence of the mycorrhizal fungi associated with vegetative growth of post-seedling G. elata hindered the germination of seeds. These phenomena were unreported prior to these studies. Furthermore, orchid mycorrhizal studies in China differ from the mainstream orchid studies in that many epiphytic species (in the genus of Dendrobium, as medicinal herbs) were investigated as well as terrestrial orchids (mostly in the genus Cymbidium, as traditional horticultural species). The different responses between epiphytic and terrestrial orchid seeds to fungi derived from roots suggest that epiphytic orchids may have a more general mycorrhizal relationship with fungi than do terrestrial orchid species during the seed germination stage. To date, orchid mycorrhizal research in China has had a strongly commercial purpose. We suggest that this continuing research on orchid mycorrhizal relationships are a solid foundation for further research that includes more rare and endangered taxa, and more in-situ studies to assist conservation and restoration of the endangered orchids. Knowledge on the identities and roles of mycorrhizal fungi of orchids holds one of the keys to successful restoration and sustainable use of Chinese orchids.

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.

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

BACKGROUND AND AIMS The Platanthera clade dominates the North American orchid flora and is well represented in eastern Asia. It has also generated some classic studies of speciation in Platanthera sections Platanthera and Limnorchis. However, it has proved rich in taxonomic controversy and near-monotypic genera. The clade is reviewed via a new molecular phylogenetic analysis and those results are combined with brief reconsideration of morphology in the group, aiming to rationalize the species into a smaller number of larger monophyletic genera and sections. METHODS Nuclear ribosomal internal transcribed spacer (ITS) sequences were obtained from 86 accessions of 35 named taxa, supplemented from GenBank with five accessions encompassing a further two named taxa. KEY RESULTS Using Pseudorchis as outgroup, and scoring indels, the data matrix generated 30 most-parsimonious trees that differed in the placement of two major groups plus two closely related species. Several other internal nodes also attracted only indifferent statistical support. Nonetheless, by combining implicit assessment of morphological divergence with explicit assessment of molecular divergence (when available), nine former genera can be rationalized into four revised genera by sinking the monotypic Amerorchis, together with Aceratorchis and Chondradenia (neither yet sequenced), into Galearis, and by amalgamating Piperia, Diphylax and the monotypic Tsaiorchis into the former Platanthera section Platanthera. After further species sampling, this section will require sub-division into at least three sections. The present nomenclatural adjustments prompt five new combinations. CONCLUSIONS Resolution of major groups should facilitate future species-level research on the Platanthera clade. Recent evidence suggests that ITS sequence divergence characterizes most species other than the P. bifolia group. The floral differences that distinguished Piperia, Diphylax and Tsaiorchis from Platanthera, and Aceratorchis and Chondradenia from Galearis, reflect various forms of heterochrony (notably paedomorphosis); this affected both the perianth and the gynostemium, and may have proved adaptive in montane habitats. Floral reduction was combined with lateral expansion of the root tubers in Piperia and Diphylax (including Tsaiorchis), whereas root tubers were minimized in the putative (but currently poorly supported) Neolindleya-Galearis clade. Allopolyploidy and/or autogamy strongly influenced speciation in Platanthera section Limnorchis and perhaps also Neolindleya. Reproductive biology remains an important driver of evolution in the clade, though plant-pollinator specificity and distinctness of the species boundaries have often been exaggerated.

Reproductive success of non-rewarding Cypripedium japonicum benefits from low spatial dispersion pattern and asynchronous flowering

BACKGROUND AND AIMS Outcrossing animal-pollinated plants, particularly non-rewarding species, often experience pollinator limitation to reproduction. Pollinator visitation is affected by various factors, and it is hypothesized that reproduction in non-rewarding plants would benefit from low spatial flower abundance and asynchronous flowering. In order to test this hypothesis, the influence of spatial pattern and flowering phenology on male and female reproductive success (RS) was investigated in a non-rewarding orchid, Cypripedium japonicum, in central China over two flowering seasons. METHODS The probabilities of intrafloral self-pollination and geitonogamy caused by pollinator behaviours were estimated from field observations. Pollinator limitation was evaluated by hand-pollination experiments. RS was surveyed in different spatial flower dispersal patterns and local flower densities. The effects of flowering phenological traits on RS were assessed by univariate and multivariate regression analyses. KEY RESULTS Hand-pollination experiments revealed that fruit production was strongly pollen limited throughout the entire reproductive season - over two seasons, 74.3 % of individuals set fruit following hand pollination, but only 5.2-7.7 % did so under natural conditions. Intrafloral self-pollination and geitonogamy within the potential clones might be rare. Both male and female fitness were substantially lower in clustered plants than in those growing singly. An increase in local conspecific flower density significantly and negatively influenced male RS, but had no effect on female RS. Phenotypic selection analysis indicated that individuals flowering earlier have the greatest probability of RS. Over 85 % of sampled flowering individuals had a flowering synchrony value >0.7; however, highly synchronous flowering was not advantageous for RS, as indicated by the negative directional selection differentials and gradients, and by the positive quadratic selection gradients. CONCLUSIONS These results support the hypothesis that, as a consequence of density-dependent selection, low spatio-temporal flower abundance is advantageous for attracting pollinators and for reproduction in natural populations of non-rewarding C. japonicum.

Maternal factors required for oocyte developmental competence in mice: Transcriptome analysis of non-surrounded nucleolus (NSN) and surrounded nucleolus (SN) oocytes

During mouse antral follicle development, the oocyte chromatin gradually transforms from a less condensed state with no Hoechst-positive rim surrounding the nucleolus (NSN) to a fully condensed chromatin state with a Hoechst-positive rim surrounding the nucleolus (SN). Compared with SN oocytes, NSN oocytes display a higher gene transcription activity and a lower rate of meiosis resumption (G2/M transition), and they are mostly arrested at the two-cell stage after in vitro fertilization. To explore the differences between NSN and SN oocytes, and the maternal factors required for oocyte developmental competence, we compared the whole-transcriptome profiles between NSN and SN oocytes. First, we found that the NSN and SN oocytes were different in their metabolic pathways. In the phosphatidylinositol signaling pathway, the SN oocytes tend to produce diacylglycerol, whereas the NSN oocytes tend to produce phosphatidylinositol (3,4,5)-trisphosphate. For energy production, the SN oocytes and NSN oocytes differed in the gluconeogenesis and in the synthesis processes. Second, we also found that the key genes associated with oocyte meiosis and/or preimplantation embryo development were differently expressed in the NSN and SN oocytes. Our results illustrate that during the NSN-SN transition, the oocytes change their metabolic activities and accumulate maternal factors for further oocyte maturation and post-fertilization embryo development.

Pollination by deceit in Paphiopedilum barbigerum (Orchidaceae): a staminode exploits the innate colour preferences of hoverflies (Syrphidae)

Paphiopedilum barbigerum T. Tang et F. T. Wang, a slipper orchid native to southwest China and northern Vietnam, produces deceptive flowers that are self-compatible but incapable of mechanical self-pollination (autogamy). The flowers are visited by females of Allograpta javana and Episyrphus balteatus (Syrphidae) that disperse the orchids massulate pollen onto the receptive stigmas. Measurements of insect bodies and floral architecture show that the physical dimensions of these two fly species correlate with the relative positions of the receptive stigma and dehiscent anthers of P. barbigerum. These hoverflies land on the slippery centralised wart located on the shiny yellow staminode and then fall backwards through the labellum entrance. They are temporarily trapped in the inflated chamber composed of the interconnected labellum and column. The attractive staminode of P. barbigerum strongly reflects the colour yellow (500-560 nm), a colour preferred innately by most pollen-eating members of the Syrphidae. No scent molecules were detected using GC mass spectrometry analysis, showing that the primary attractant in this system is visual, not olfactory. Pollination-by-deceit in P. barbigerum is contrasted with its congener, P. dianthum, a brood site mimic that is pollinated by ovipositing females of E. balteatus. As the natural rate of fruit set in P. barbigerum (mean 26.3% pooled over three seasons) is lower than that of P. dianthum (mean 58.5% over two seasons), the evolution of false brood sites in some Paphiopedilum spp. should be selectively advantageous as they may provide an increase in the attention and return rates of dependable pollinators to flowers that always lack a reward.

Evolution and biogeography of the slipper orchids: Eocene vicariance of the conduplicate genera in the Old and New World Tropics.

Intercontinental disjunctions between tropical regions, which harbor two-thirds of the flowering plants, have drawn great interest from biologists and biogeographers. Most previous studies on these distribution patterns focused on woody plants, and paid little attention to herbs. The Orchidaceae is one of the largest families of angiosperms, with a herbaceous habit and a high species diversity in the Tropics. Here we investigate the evolutionary and biogeographical history of the slipper orchids, which represents a monophyletic subfamily (Cypripedioideae) of the orchid family and comprises five genera that are disjunctly distributed in tropical to temperate regions. A relatively well-resolved and highly supported phylogeny of slipper orchids was reconstructed based on sequence analyses of six maternally inherited chloroplast and two low-copy nuclear genes (LFY and ACO). We found that the genus Cypripedium with a wide distribution in the northern temperate and subtropical zones diverged first, followed by Selenipedium endemic to South America, and finally conduplicate-leaved genera in the Tropics. Mexipedium and Phragmipedium from the neotropics are most closely related, and form a clade sister to Paphiopedilum from tropical Asia. According to molecular clock estimates, the genus Selenipedium originated in Palaeocene, while the most recent common ancestor of conduplicate-leaved slipper orchids could be dated back to the Eocene. Ancestral area reconstruction indicates that vicariance is responsible for the disjunct distribution of conduplicate slipper orchids in palaeotropical and neotropical regions. Our study sheds some light on mechanisms underlying generic and species diversification in the orchid family and tropical disjunctions of herbaceous plant groups. In addition, we suggest that the biogeographical study should sample both regional endemics and their widespread relatives.

Potential Challenges of Climate Change to Orchid Conservation in a Wild Orchid Hotspot in Southwestern China

Southwestern China including Guangxi Province is one of nine world hotspots for orchid. Warming in the region in the past century was around 0.5°C, slightly lower than the global average of 0.7°C, while rainfall has remained the same. It is projected that the warming trend will continue for the next two centuries, while precipitation will increase slightly, and soil moisture level will decrease. We identify a number of threats due to climate changes to orchid community in the Yachang Orchid Nature Reserve in Guangxi (hereafter refer to as Yachang Reserve), a good representative of the region. Firstly, decreased soil moisture is likely to have a negative effect on growth and survival of orchids, especially terrestrial and saprophytic ones. Sixty eight (50%) orchid species in the Yachang Reserve are in this category. Secondly, the greater majority of the orchids in Yachang Reserve (72%) have populations on or close to the limestone mountain tops. These populations are likely to shrink or even become extinct as the warming continues because they have no higher places to which they are able to migrate. Natural poleward migration is unlikely for these populations because of the complex terrain, small size of the reserve and human-dominated surroundings. Species with narrow distributions (14%) and/or small population sizes (46%) will be the most vulnerable. In addition, populations represent the southern limit of the species (24%) are also prone to local extinction. Thirdly, extreme rainfall events are projected to occur more frequently, which can exacerbate erosion. This may impact orchid populations that grow on steep cliffs. Fifty seven species (42%) of the orchids in Yachang have cliff populations. Fourthly, the majority of orchid species have specialized insect pollination systems. It is unknown whether the change or lack of change in plant phenology will be in synchrony with the potential phenological shifts of their pollinators. Fifty four (40%) orchid species in Yachang Reserve flower in the spring and are potentially subject to this threat. Finally, mycorrhizal fungi are vital for seed germination for all orchids and important for post-seedling growth for some species. Yet there is a lack of knowledge of the nature of mycorrhiza on all orchids in the region, and little is known on the responses of these vital symbiotic relationships to temperature and soil moisture. Overall, 15% of the orchid species and a quarter of the genera bear high risk of population reduction or local extinction under the current projection of climate change. While studies on predicting and documenting the consequences of climate change on biodiversity are increasing, few identified the actual mechanisms through which climate change will affect individual species. Our study provides a unique perspective by identifying specific threats to a plant community.