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

Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth 1-3 . Here we report the draft genome sequence of Apostasia shenzhenica 4 , 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 thirdgeneration 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.

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.

CeF3, CeF3:Tb3+, and CeF3:Tb3+/LaF3 (core/shell) nanoparticles were prepared by the polyol method and characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), X-ray photoelectron spectra (XPS), UV−vis absorption spectra, photoluminescence (PL) spectra, and lifetimes. The results of XRD indicate that the obtained CeF3, CeF3:Tb3+, and CeF3:Tb3+/LaF3 (core/shell) nanoparticles crystallized well at 200 °C in diethylene glycol (DEG) with a hexagonal structure. The TEM images illustrate that the CeF3 and CeF3:Tb3+ nanoparticles are spherical with a mean diameter of 7 nm. The growth of the LaF3 shell around the CeF3:Tb3+ core nanoparticles resulted in an increase of the average size (11 nm) of the nanopaticles as well as in a broadening of their size distribution. These nanocrystals can be well-dispersed in ethanol to form clear colloidal solutions. The colloidal solutions of CeF3 and CeF3:Tb3+ show the characteristic emission of Ce3+ 5d−4f (320 nm) and Tb3+ 5D4−7FJ (J = 6−3, with 5D4−7F5 green emission at 542 nm as the strongest one) transitions, respectively. The emission intensity and lifetime of the CeF3:Tb3+/LaF3 (core/shell) nanoparticles increased with respect to those of CeF3:Tb3+ core particles. This indicates that a significant amount of nonradiative centers existing on the surface of CeF3:Tb3+ nanoparticles can be eliminated by the shielding effect of LaF3 shells. Finally, the energy transfer from Ce3+ to Tb3+ was investigated in CeF3:Tb3+ nanoparticles in detail.

Leaf nitrogen (N) and phosphorus (P) concentrations constrain photosynthetic and metabolic processes, growth and the productivity of plants. Their stoichiometry and scaling relationships regulate the allocation of N and P from subcellular to organism, and even ecosystem levels, and are crucial to the modelling of plant growth and nutrient cycles in terrestrial ecosystems. Prior work has revealed a general biogeographic pattern of leaf N and P stoichiometric relationships and shown that leaf N scales roughly as two-thirds the power of P. However, determining whether and how leaf N and P stoichiometries, especially their scaling exponents, change with functional groups and environmental conditions requires further verification. In this study, we compiled a global data set and documented the global leaf N and P concentrations and the N:P ratios by functional group, climate zone and continent. The global overall mean leaf N and P concentrations were 18.9 mg g −1 and 1.2 mg g −1 , respectively, with significantly higher concentrations in herbaceous than woody plants (21.72 mg g −1 vs. 18.22 mg g −1 for N; and 1.64 mg g −1 vs. 1.10 mg g −1 for P). Both leaf N and P showed higher concentrations at high latitudes than low latitudes. Among six continents, Europe had the highest N and P concentrations (20.79 and 1.54 mg g −1 ) and Oceania had the smallest values (10.01 and 0.46 mg g −1 ). These numerical values may be used as a basis for the comparison of other individual studies. Further, we found that the scaling exponent varied significantly across different functional groups, latitudinal zones, ecoregions and sites. The exponents of herbaceous and woody plants were 0.659 and 0.705, respectively, with significant latitudinal patterns decreasing from tropical to temperate to boreal zones. At sites with a sample size ≥10, the values fluctuated from 0.366 to 1.928, with an average of 0.841. Several factors including the intrinsic attributes of different life forms, P-related growth rates and relative nutrient availability of soils likely account for the inconstant exponents of leaf N vs. P scaling relationships.

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.

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.

We present results of the correlation analysis of distributions of the presence/absence of short nucleotide subsequences of different length ('n-mers', n = 5-20) in more than 1500 microbial and virus genomes, together with five genomes of multicellular organisms (including human). We calculate whether a given n-mer is present or absent (frequency of presence) in a given genome, which is not the usually calculated number of appearances of n-mers in one or more genomes (frequency of appearance). For organisms that are not close relatives of each other, the presence/absence of different 7-20mers in their genomes are not correlated. For close biological relatives, somecorrelation of the presence of n-mers in this range appears, but is not as strong as expected. Suppressed correlations among the n-mers present in different genomes leads to the possibility of using random sets of n-mers (with appropriately chosen n) to discriminate genomes of different organisms and possibly individual genomes of the same species including human with a low probability of error.