Structural adaptations of two sympatric epiphytic orchids (Orchidaceae) to a cloudy forest environment in rocky outcrops of Southeast Brazil

The survival of plants in epiphytic environments depends on vegetative adaptations capable to defraud different stresses. Based on the structural diversity of the Orchidaceae, the current study has the objective of relating the anatomical structure of Dichaea cogniauxiana and Epidendrum secundum with the distinct environments where they live. It was expected that, despite structural similarities as strategies for resource acquisition, some peculiar variations related to the distinct light microenvironments (inside or in the edge of the nebular forest, near to "campo rupestre" area) might be found. Leaves and roots of both species were collected in a nebular forest located at a "campo rupestre" area at Serra da Piedade, Brazil), in January and February 2005. D. cogniauxiana is adhered to trunks, in sites with high atmospheric humidity and shaded, while E. secundum is located at the edge of the nebular forest, in more luminous sites. The leaves of E. secundum had thicker cuticle and higher number of stomata per area than those of D. cogniauxiana, characteristics coherent with their distinct pattern of exhibition to sun light. The suprastomatic chambers formed by the thicker cuticle may function as a barrier of resistance to water evaporation. The succulence of the leaves of E. secundum propitiates organic acids storage at night, and the storage of starch may be involved in PEP-carboxylase metabolism, both propitiating CAM mechanism. Roots with larger number of cell layers of the velamen, and specialized thick walled cortical cells (both in E. secundum) help water absorption and indicate better adaptation to an environment with intense solar radiation and a probable higher water deficit. The remarkable cell wall thickening of E. secundum exodermis can confer more efficient protection against the excess of transpiration at the border of the nebular forest. On the other hand, besides D. cogniauxiana be epiphyte, it is in a low position - in a shaded environment and with high relative humidity. Its thin thickened velamen permits the entrance of the low available light, and photosynthesis, producing oxygen and helping to avoid hypoxia condition. As features registered for D. cogniauxiana and E. secundum roots, we can depict the velamen, distinct exodermis and endodermis, and specialized thick walled cortical cells as characteristic of epiphytic plants.

Comparative anatomy of the floral elaiophore in representatives of the newly re-circumscribed Gomesa and Oncidium clades (Orchidaceae: Oncidiinae)

BACKGROUND AND AIMS

Recently, molecular approaches have been used to investigate the phylogeny of Oncidiinae. This has resulted in the transfer of taxa previously considered to be species of Oncidium Sw. into Gomesa R. Br. and the re-circumscription of both genera. In this study, the structure of the floral elaiophore (oil gland) is described and compared for Gomesa echinata (Barb. Rodr.) M.W. Chase & N.H. Williams, G. ranifera (Lindl.) M.W. Chase & N.H. Williams, Oncidium amazonicum (Schltr.) M.W. Chase & N.H. Williams and O. oxyceras (Königer & J.G. Weinm.) M.W. Chase & N.H. Williams in order to determine whether phylogenetic revision is supported by differences in its anatomy.

METHODS

The floral elaiophore structure was examined and compared at three developmental stages (closed bud, first day of anthesis and final stage of anthesis) for all four species using light microscopy, fluorescence microscopy, scanning electron microscopy, transmission electron microscopy and histochemistry.

KEY RESULTS

In all species investigated, the floral elaiophore occurs on the labellar callus and is of the epithelial type, comprising cuboidal to palisade-like, secretory epidermal cells and a layer of sub-epidermal cells, both tissues enclosing ground parenchyma supplied with collateral vascular bundles and containing idioblasts, often with raphides or phenolic contents. A bi-layered cuticle comprising an outer, lamellate and an inner, reticulate layer is present, and sub-cuticular accumulation of secreted material results in distension of the cuticle. Secretion-filled cavities are present at anthesis in the elaiophore cell walls and, in most species, the outer, tangential walls of the elaiophore have small, peg-like projections that protrude into the cytoplasm. In all taxa examined, the elaiophore organelle complement, especially the smooth endoplasmic reticulum (SER), is typical of lipid-secreting cells.

CONCLUSIONS

In terms of location, morphology, anatomy and ultrastructure, the floral elaiophores of both Gomesa and Oncidium species examined are very similar, and distinction between these genera is not possible based on elaiophore features alone. Furthermore, many of these elaiophore characters are shared with representatives of other clades of Oncidiinae, including the Ornithocephalus clade. Consequently, elaiophores are considered homoplasious and of limited value in investigating the phylogeny of this subtribe.

Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids

BACKGROUND

Sexually deceptive orchids of the genus Ophrys mimic the mating signals of their pollinator females to attract males as pollinators. This mode of pollination is highly specific and leads to strong reproductive isolation between species. This study aims to identify candidate genes responsible for pollinator attraction and reproductive isolation between three closely related species, O. exaltata, O. sphegodes and O. garganica. Floral traits such as odour, colour and morphology are necessary for successful pollinator attraction. In particular, different odour hydrocarbon profiles have been linked to differences in specific pollinator attraction among these species. Therefore, the identification of genes involved in these traits is important for understanding the molecular basis of pollinator attraction by sexually deceptive orchids.

RESULTS

We have created floral reference transcriptomes and proteomes for these three Ophrys species using a combination of next-generation sequencing (454 and Solexa), Sanger sequencing, and shotgun proteomics (tandem mass spectrometry). In total, 121 917 unique transcripts and 3531 proteins were identified. This represents the first orchid proteome and transcriptome from the orchid subfamily Orchidoideae. Proteome data revealed proteins corresponding to 2644 transcripts and 887 proteins not observed in the transcriptome. Candidate genes for hydrocarbon and anthocyanin biosynthesis were represented by 156 and 61 unique transcripts in 20 and 7 genes classes, respectively. Moreover, transcription factors putatively involved in the regulation of flower odour, colour and morphology were annotated, including Myb, MADS and TCP factors.

CONCLUSION

Our comprehensive data set generated by combining transcriptome and proteome technologies allowed identification of candidate genes for pollinator attraction and reproductive isolation among sexually deceptive orchids. This includes genes for hydrocarbon and anthocyanin biosynthesis and regulation, and the development of floral morphology. These data will serve as an invaluable resource for research in orchid floral biology, enabling studies into the molecular mechanisms of pollinator attraction and speciation.

Complete chloroplast genome of the genus Cymbidium: lights into the species identification, phylogenetic implications and population genetic analyses

BACKGROUND

Cymbidium orchids, including some 50 species, are the famous flowers, and they possess high commercial value in the floricultural industry. Furthermore, the values of different orchids are great differences. However, species identification is very difficult. To a certain degree, chloroplast DNA sequence data are a versatile tool for species identification and phylogenetic implications in plants. Different chloroplast loci have been utilized for evaluating phylogenetic relationships at each classification level among plant species, including at the interspecies and intraspecies levels. However, there is no evidence that a short sequence can distinguish all plant species from each other in order to infer phylogenetic relationships. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution.

RESULTS

The complete nucleotide sequences of eight individuals from a total of five Cymbidium species' chloroplast (cp) genomes were determined using Illumina sequencing technology of the total DNA via a combination of de novo and reference-guided assembly. The length of the Cymbidium cp genome is about 155 kb. The cp genomes contain 123 unique genes, and the IR regions contain 24 duplicates. Although the genomes, including genome structure, gene order and orientation, are similar to those of other orchids, they are not evolutionarily conservative. The cp genome of Cymbidium evolved moderately with more than 3% sequence divergence, which could provide enough information for phylogeny. Rapidly evolving chloroplast genome regions were identified and 11 new divergence hotspot regions were disclosed for further phylogenetic study and species identification in Orchidaceae.

CONCLUSIONS

Phylogenomic analyses were conducted using 10 complete chloroplast genomes from seven orchid species. These data accurately identified the individuals and established the phylogenetic relationships between the species. The results reveal that phylogenomics based on organelle genome sequencing lights the species identification-organelle-scale "barcodes", and is also an effective approach for studying whole populations and phylogenetic characteristics of Cymbidium.

A new molecular phylogeny and a new genus, Pendulorchis, of the Aerides-Vanda alliance (Orchidaceae: Epidendroideae)

BACKGROUND

The Aerides-Vanda alliance is a complex group in the subtribe Aeridinae (subfamily Epidendroideae, Orchidaceae). Some phylogenetic systems of this alliance have been previously proposed based on molecular and morphological analyses. However, several taxonomic problems within this alliance as well as between it and its allies remain unsolved.

METHODOLOGY/PRINCIPAL FINDINGS

We utilized ITS and five plastid DNA regions in this phylogenetic analysis. Consensus trees strongly indicate that the Aerides-Vanda alliance is monophyletic, and the 14 genera of this alliance can be grouped into the following clades with 14 subclades: 1. Aerides, comprising two subclades: Rhynchostylis and Aerides; 2. Ascocentropsis; 3. Papilionanthe; 4. Vanda, comprising five subclades: Neofinetia, Christensonia, Seidenfadenia, Ascocentrum, and Vanda-Trudelia, in which Vanda and Trudelia form a subclade; 5. Tsiorchis, comprising three subclades: Chenorchis, Tsiorchis, and two species of Ascocentrum; 6. Paraholcoglossum; and 7. Holcoglossum. Among the 14 genera, only Ascocentrum is triphyletic: two species of the Ascocentrum subclade, an independent subclade Ascocentrum subclade in the Tsiorchis clade; the Ascocentrum subclade in the Vanda clade; and one species in the Holcoglossum clade. The Vanda and Trudelia species belong to the same subclade. The molecular conclusion is consistent with their morphological characteristics.

CONCLUSIONS

We elucidate the relationship among the 14 genera of the Aerides-Vanda alliance. Our phylogenetic results reveal that the Aerides-Vanda alliance is monophyletic, but it can be divided into 14 genera. The data prove that Ascocentrum is triphyletic. Plants with elongate-terete leaves and small flowers should be treated as a new genus, Pendulorchis. Saccolabium himalaicum (Ascocentrum himalaicum) should be transferred to Pendulorchis. Ascocentrum pumilum, endemic to Taiwan, should be transferred to Holcoglossum. A new combination, Holcoglossum pumilum, was also established. Trudelia should not be recognized as an independent genus. Two new species, Pendulorchis gaoligongensis and Holcoglossum singchianum, were described as well.

OrchidBase 2.0: comprehensive collection of Orchidaceae floral transcriptomes

Both floral development and evolutionary trends of orchid flowers have long attracted the interest of biologists. However, expressed sequences derived from the flowers of other orchid subfamilies are still scarce except for a few species in Epidendroideae. In order to broadly increase our scope of Orchidaceae genetic information, we updated the OrchidBase to version 2.0 which has 1,562,071 newly added floral non-redundant transcribed sequences (unigenes) collected comprehensively from 10 orchid species across five subfamilies of Orchidaceae. A total of 662,671,362 reads were obtained by using next-generation sequencing (NGS) Solexa Illumina sequencers. After assembly, on average 156,207 unigenes were generated for each species. The average length of a unigene is 347 bp. We made a detailed annotation including general information, relative expression level, gene ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway mapping and gene network prediction. The online resources for putative annotation can be searched either by text or by using BLAST, and the results can be explored on the website and downloaded. We have re-designed the user interface in the new version. Users can enter the Phalaenopsis transcriptome or Orchidaceae floral transcriptome to browse or search the unigenes. OrchidBase 2.0 is freely available at http://orchidbase.itps.ncku.edu.tw/.

Orchidstra: an integrated orchid functional genomics database

A specialized orchid database, named Orchidstra (URL: http://orchidstra.abrc.sinica.edu.tw), has been constructed to collect, annotate and share genomic information for orchid functional genomics studies. The Orchidaceae is a large family of Angiosperms that exhibits extraordinary biodiversity in terms of both the number of species and their distribution worldwide. Orchids exhibit many unique biological features; however, investigation of these traits is currently constrained due to the limited availability of genomic information. Transcriptome information for five orchid species and one commercial hybrid has been included in the Orchidstra database. Altogether, these comprise >380,000 non-redundant orchid transcript sequences, of which >110,000 are protein-coding genes. Sequences from the transcriptome shotgun assembly (TSA) were obtained either from output reads from next-generation sequencing technologies assembled into contigs, or from conventional cDNA library approaches. An annotation pipeline using Gene Ontology, KEGG and Pfam was built to assign gene descriptions and functional annotation to protein-coding genes. Deep sequencing of small RNA was also performed for Phalaenopsis aphrodite to search for microRNAs (miRNAs), extending the information archived for this species to miRNA annotation, precursors and putative target genes. The P. aphrodite transcriptome information was further used to design probes for an oligonucleotide microarray, and expression profiling analysis was carried out. The intensities of hybridized probes derived from microarray assays of various tissues were incorporated into the database as part of the functional evidence. In the future, the content of the Orchidstra database will be expanded with transcriptome data and genomic information from more orchid species.

Monophyly or paraphyly--the taxonomy of Holcoglossum (Aeridinae: Orchidaceae)

Recently, there have been a lot of intense debates about the acceptance/rejection of paraphyletic groups in biological classification. On the one hand, evolutionary classification states that similarity and common descent are two criteria for biological classification and paraphyletic groups are natural units of biological classification. On the other hand, cladistic classification considers that common descent is the only criterion in biological classification and monophyly should be strictly adhered to. Holcoglossum is used herein as a case to illustrate this problem. Although Holcoglossum is a small orchid genus of less than 20 species, there is little consensus about its generic circumscription since it was established, which leads to confusion in taxonomic treatments in the Aerides-Vanda group. Based on the analyses of molecular and morphological evidence, our results suggest that the clade comprising Holcoglossum s.s., Ascolabium, Penkimia and Ascocentrum himalaicum is strongly supported as a monophyly, and that the three taxa are nested within different subclades of Holcoglossum s.s. Thus, it is reasonable to recognize a monophyletic circumscription of Holcoglossum, which is also well supported by some vegetative and floral characters. The Holcoglossum s.l. would facilitate a better understanding of pollinator-driven floral divergence and vegetative stasis than a paraphyletic and narrowly defined genus.

Stelis zootrophionoides (Orchidaceae: Pleurothallidinae), a new species from Mexico

Background

Stelis (Orchidaceae) encompasses approximately 1100 species of epiphytic orchids distributed throughout the Neotropics, with the highest diversity in Andean South America. Sixty-two species were recorded previously in Mexico.

Methods

We formally describe here Stelis zootrophionoides as a new species from Chiapas, Mexico. To determine its systematic position, we conducted a morphological comparison with other members of Pleurothallidinae and a phylogenetic analysis of nucleotide sequences from the plastid matK/trnK and trnL/trnF regions, as well as the nuclear ribosomal ITS region for 52 species of Pleurothallidinae. Sequences of 49 species were downloaded from GenBank and those of three species, including the new taxon, were newly generated for this work. The new species is described and illustrated; notes on its ecological preferences and a comparison with closely related species are presented.

Conclusions

The new species, known only from one location and apparently restricted to the cloud forest in the central highlands of Chiapas, Mexico, is considered a rare species. This small epiphyte is unique among the Mexican species of Stelis by the combination of dark purple flowers with the distal third of the dorsal sepal adhered to the apices of the lateral sepals, which are partially united into a bifid synsepal, leaving two lateral window-like openings, and sagittate labellum. Stelis jalapensis, known from southern Mexico and Guatemala, also has the apices of the sepals adhered to each other, but it is distinguished by its larger flowers with lanceolate, acute dorsal sepal, completely fused lateral sepals (i.e. the synsepal is not bifid), and oblong-elliptic labellum. The phylogenetic analysis shows that S. zootrophionoides is closely related to other Mexican Stelis and corroborates previous suggestions that fused sepal apices have arisen independently in different lineages of Pleurothallidinae.

Germination failure is not a critical stage of reproductive isolation between three congeneric orchid species

PREMISE OF THE STUDY

In food-deceptive orchid species, postmating reproductive barriers (fruit set and embryo mortality) have been shown to be more important for reproductive isolation than premating barriers (pollinator isolation). However, currently there is very little knowledge about whether germination failure acts as a reproductive barrier in hybridizing orchid species.

METHODS

In this study, we investigated germination and protocorm development of pure and hybrid seeds of three species of the orchid genus Dactylorhiza. To test the hypothesis that germination failure contributed to total reproductive isolation, reproductive barriers based on germination were combined with already available data on early acting barriers (fruit set and embryo mortality) to calculate the relative and absolute contributions of these barriers to reproductive isolation.

KEY RESULTS

Protocorms were formed in all crosses, indicating that both hybrid and pure seeds were able to germinate and grow into protocorms. Also, the number of protocorms per seed packet was not significantly different between hybrid and pure seeds. High fruit set, high seed viability, and substantial seed germination resulted in very low reproductive isolation (average RI = 0.05). In two of six interspecific crosses, hybrids performed even better than the intraspecific crosses.

CONCLUSIONS

Very weak postmating reproductive barriers were observed between our study species and may explain the frequent occurrence of first-generation hybrids in mixed Dactylorhiza populations. Germination failure, which is regarded as one of the most important bottlenecks in the orchid life cycle, was not important for reproductive isolation.

Minority cytotypes in European populations of the Gymnadenia conopsea complex (Orchidaceae) greatly increase intraspecific and intrapopulation diversity

BACKGROUND AND AIMS

Patterns of ploidy variation among and within populations can provide valuable insights into the evolutionary mechanisms shaping the dynamics of plant systems showing ploidy diversity. Whereas data on majority ploidies are, by definition, often sufficiently extensive, much less is known about the incidence and evolutionary role of minority cytotypes.

METHODS

Ploidy and proportions of endoreplicated genome were determined using DAPI (4',6-diamidino-2-phenylindole) flow cytometry in 6150 Gymnadenia plants (fragrant orchids) collected from 141 populations in 17 European countries. All widely recognized European species, and several taxa of less certain taxonomic status were sampled within Gymnadenia conopsea sensu lato.

KEY RESULTS

Most Gymnadenia populations were taxonomically and/or ploidy heterogeneous. Two majority (2x and 4x) and three minority (3x, 5x and 6x) cytotypes were identified. Evolution largely proceeded at the diploid level, whereas tetraploids were much more geographically and taxonomically restricted. Although minority ploidies constituted <2 % of the individuals sampled, they were found in 35 % of populations across the entire area investigated. The amount of nuclear DNA, together with the level of progressively partial endoreplication, separated all Gymnadenia species currently widely recognized in Europe.

CONCLUSIONS

Despite their low frequency, minority cytotypes substantially increase intraspecific and intrapopulation ploidy diversity estimates for fragrant orchids. The cytogenetic structure of Gymnadenia populations is remarkably dynamic and shaped by multiple evolutionary mechanisms, including both the ongoing production of unreduced gametes and heteroploid hybridization. Overall, it is likely that the level of ploidy heterogeneity experienced by most plant species/populations is currently underestimated; intensive sampling is necessary to obtain a holistic picture.

Mycorrhizal diversity and specificity in Lecanorchis (Orchidaceae)

Lecanorchis is a nonphotosynthetic plant genus in Vanilloideae, Orchidaceae. Because of the distribution of many Lecanorchis taxa in various climate conditions, we hypothesized that mycorrhizal diversity and specificity are different among the different taxa of Lecanorchis. In the present study, identities of mycorrhizal fungi were examined for 90 individuals of 10 Lecanorchis taxa at 26 sites from Niigata to Okinawa Prefectures in Japan. Phylogenetic analyses of Lecanorchis taxa based on the internal transcribed spacer (ITS) region of the nuclear ribosomal RNA gene (rDNA) divided the examined Lecanorchis taxa into three groups, groups A, B, and C. ITS rDNA sequences suggested that fungi associating with Lecanorchis were ectomycorrhiza-forming fungi in Lactarius, Russula, Atheliaceae, and Sebacina, with Lactarius and Russula dominant. Our results suggested some degree of mycorrhizal specialization among Lecanorchis taxa. Interestingly, the Lecanorchis group C had some specific relationships with Lactarius, whereas less specificity was found in the relationships with Russula. However, observed specificity results may be biased by geographic opportunity, and we suggest further research to assess whether Lecanorchis species are limited to the associations we observed.

The genetic basis of pollinator adaptation in a sexually deceptive orchid

In plants, pollinator adaptation is considered to be a major driving force for floral diversification and speciation. However, the genetic basis of pollinator adaptation is poorly understood. The orchid genus Ophrys mimics its pollinators' mating signals and is pollinated by male insects during mating attempts. In many species of this genus, chemical mimicry of the pollinators' pheromones, especially of alkenes with different double-bond positions, plays a key role for specific pollinator attraction. Thus, different alkenes produced in different species are probably a consequence of pollinator adaptation. In this study, we identify genes that are likely involved in alkene biosynthesis, encoding stearoyl-acyl carrier protein (ACP) desaturases (SAD), in three closely related Ophrys species, O. garganica, O. sphegodes, and O. exaltata. Combining floral odor and gene expression analyses, two SAD homologs (SAD1/2) showed significant association with the production of (Z)-9- and (Z)-12-alkenes that were abundant in O. garganica and O. sphegodes, supporting previous biochemical data. In contrast, two other newly identified homologs (SAD5/6) were significantly associated with (Z)-7-alkenes that were highly abundant only in O. exaltata. Both molecular evolutionary analyses and pollinator preference tests suggest that the alkenes associated with SAD1/2 and SAD5/6 are under pollinator-mediated divergent selection among species. The expression patterns of these genes in F₁ hybrids indicate that species-specific expression differences in SAD1/2 are likely due to cis-regulation, while changes in SAD5/6 are likely due to trans-regulation. Taken together, we report a genetic mechanism for pollinator-mediated divergent selection that drives adaptive changes in floral alkene biosynthesis involved in reproductive isolation among Ophrys species.

In plants, the extraordinary floral diversity has been suggested to be a consequence of divergent adaptation. However, the genetic basis of this process is poorly understood. In this study, we take advantage of the high specificity of plant-pollinator interactions in the sexually deceptive orchid genus Ophrys. We leverage the available, ample evidence showing that floral odors, especially alkenes, are the key factor for specific pollinator attraction in certain species of these orchids. Further, we investigate the genetic basis of pollinator adaptation. By applying an inter-disciplinary approach, including chemical ecology, gene expression analysis, population genetics, and pollinator-behavioral tests, we show that genetic changes in different copies of a biosynthetic gene are associated with the production of different floral scents and with pollinator adaptation in these orchid species. Moreover, we found that both cis- and trans-regulatory factors are likely involved in controlling gene expression of these biosynthetic gene copies. These findings support the hypothesis that adaptation is mediated by very few genetic changes with large phenotypic effects, rather than requiring a large number of co-adapted genes.

Phylogenetics of tribe Orchideae (Orchidaceae: Orchidoideae) based on combined DNA matrices: inferences regarding timing of diversification and evolution of pollination syndromes

BACKGROUND AND AIMS

Tribe Orchideae (Orchidaceae: Orchidoideae) comprises around 62 mostly terrestrial genera, which are well represented in the Northern Temperate Zone and less frequently in tropical areas of both the Old and New Worlds. Phylogenetic relationships within this tribe have been studied previously using only nuclear ribosomal DNA (nuclear ribosomal internal transcribed spacer, nrITS). However, different parts of the phylogenetic tree in these analyses were weakly supported, and integrating information from different plant genomes is clearly necessary in orchids, where reticulate evolution events are putatively common. The aims of this study were to: (1) obtain a well-supported and dated phylogenetic hypothesis for tribe Orchideae, (ii) assess appropriateness of recent nomenclatural changes in this tribe in the last decade, (3) detect possible examples of reticulate evolution and (4) analyse in a temporal context evolutionary trends for subtribe Orchidinae with special emphasis on pollination systems.

METHODS

The analyses included 118 samples, belonging to 103 species and 25 genera, for three DNA regions (nrITS, mitochondrial cox1 intron and plastid rpl16 intron). Bayesian and maximum-parsimony methods were used to construct a well-supported and dated tree. Evolutionary trends in the subtribe were analysed using Bayesian and maximum-likelihood methods of character evolution.

KEY RESULTS

The dated phylogenetic tree strongly supported the recently recircumscribed generic concepts of Bateman and collaborators. Moreover, it was found that Orchidinae have diversified in the Mediterranean basin during the last 15 million years, and one potential example of reticulate evolution in the subtribe was identified. In Orchidinae, pollination systems have shifted on numerous occasions during the last 23 million years.

CONCLUSIONS

The results indicate that ancestral Orchidinae were hymenopteran-pollinated, food-deceptive plants and that these traits have been dominant throughout the evolutionary history of the subtribe in the Mediterranean. Evidence was also obtained that the onset of sexual deception might be linked to an increase in labellum size, and the possibility is discussed that diversification in Orchidinae developed in parallel with diversification of bees and wasps from the Miocene onwards.

The comparative chloroplast genomic analysis of photosynthetic orchids and developing DNA markers to distinguish Phalaenopsis orchids

The chloroplast genome of Phalaenopsis equestris was determined and compared to those of Phalaenopsis aphrodite and Oncidium Gower Ramsey in Orchidaceae. The chloroplast genome of P. equestris is 148,959 bp, and a pair of inverted repeats (25,846 bp) separates the genome into large single-copy (85,967 bp) and small single-copy (11,300 bp) regions. The genome encodes 109 genes, including 4 rRNA, 30 tRNA and 75 protein-coding genes, but loses four ndh genes (ndhA, E, F and H) and seven other ndh genes are pseudogenes. The rate of inter-species variation between the two moth orchids was 0.74% (1107 sites) for single nucleotide substitution and 0.24% for insertions (161 sites; 1388 bp) and deletions (189 sites; 1393 bp). The IR regions have a lower rate of nucleotide substitution (3.5-5.8-fold) and indels (4.3-7.1-fold) than single-copy regions. The intergenic spacers are the most divergent, and based on the length variation of the three intergenic spacers, 11 native Phalaenopsis orchids could be successfully distinguished. The coding genes, IR junction and RNA editing sites are relatively more conserved between the two moth orchids than between those of Phalaenopsis and Oncidium spp.

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.

Symbiotic germination capability of four Epipactis species (Orchidaceae) is broader than expected from adult ecology

PREMISE OF THE STUDY

Both abiotic and biotic factors shape species distributions. Orchids produce minute seeds with few nutrient reserves, thus requiring mycorrhizal fungi for germination. Therefore, both environmental conditions and mycorrhizal fungi distribution affect their germination success, but these ecological requirements and their congruence with habitat preferences of adults remain poorly understood. We investigated the importance of these factors during germination in four forest orchid species of the genus Epipactis.

METHODS

We sowed seeds of three habitat specialists and one generalist in different forest types at sites harboring adults of at least one of these ecologically diverging species. We analyzed germination pattern and identified mycorrhizal fungi of both seedlings and adults.

KEY RESULTS

Habitat conditions had little influence on germination pattern as seedlings grew in more habitats than expected from the adults' ecology. Ectomycorrhizal fungi availability did not limit germination. Suitable mycorrhizal fungi, mostly pezizalean ascomycetes, were recruited in various forest types, though the fungal communities differed according to habitat type. Finally, orchids with divergent ecological preferences shared similar mycorrhizal fungi.

CONCLUSIONS

Limited adult distribution contrasted with successful seed germination at diverse sites and indicates existence of niche differentiation between adults and seedlings. Ecological specialization may thus be determined by factors other than mycorrhizal fungi that act later in the ontogeny, perhaps during the transition to above-ground development.

Microsatellite markers for the Chinese endangered and endemic orchid Cymbidium tortisepalum (Orchidaceae)

PREMISE OF THE STUDY

Microsatellite primers were developed in the Chinese endangered and endemic orchid, Cymbidium tortisepalum, to investigate its genetic diversity and population genetic structure, and to identify its varieties.

METHODS AND RESULTS

Using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol, 15 primer sets were identified in two wild populations. The number of alleles per locus ranged from two to six, with a mean of 3.5. The observed and expected heterozygosities varied from 0.250 to 0.917 and from 0.228 to 0.841, respectively. All of these primers successfully amplified in the congener C. goeringii, and 12 were found useful in C. faberi and C. sinense.

CONCLUSIONS

These markers will facilitate further studies on the population genetics and molecular identification of C. tortisepalum, its varieties, and other congener species.

A comparative survey of floral characters in Capanemia Barb. Rodr. (Orchidaceae: Oncidiinae)

BACKGROUND AND AIMS

Capanemia Barb. Rodr. comprises seven species that mostly inhabit the Brazilian Atlantic Rain Forest domain. The genus currently consists of two sections: Capanemia Cogn. and Planifolia Pabst, distinguished on the basis of leaf shape. We compare the floral morphology and anatomy of all species to determine whether separation into sections is supported by floral characters.

METHODS

Both fresh flowers and herbarium specimens were investigated, and column and pollinarium features, together with the presence or absence of floral rewards, recorded. Anatomical features were examined using both light microscopy and scanning electron microscopy.

KEY RESULTS AND CONCLUSIONS

With the sole exception of Capanemia therezae, all species shared a distinctive set of floral characters. Flowers were mostly white or yellowish-white and fragrant, and column wings were positioned parallel to the labellum, concealing the stigmatic cavity. Pollinaria had proportionally long tegular stipes and clavate to reniform pollinia, whereas the labellum possessed a conspicuous indument of trichomes, but was devoid of nectar or any other secretion that might function as a food-reward. Capanemia therezae, however, was exceptional in having greenish, unscented flowers with short, rounded and divergent column wings and an exposed stigmatic cavity. Its pollinaria had proportionally short tegular stipes and round pollinia, whereas the labellum lacked trichomes. Droplets of nectar were evident on the adaxial surface of the labellum, adjacent to the callus. Floral features did not support the currently accepted sectional division of Capanemia. If ongoing phylogenetic studies demonstrate that both sections are indeed monophyletic, then these taxa should be distinguished solely on the basis of foliar features.

[The orchid community in the Biosphere Reserve Sierra del Rosario, Cuba]

The Biosphere Reserve Sierra del Rosario is located in Western Cuba and two different areas can be characterized: one for tourism and forestry activities, El Taburete (ET), and the other for conservation and research, El Salón (ES). With the aim to know the effect of visitation activities on the orchid community in the Reserve, a comparative study between the disturbed area and the preserved one was undertaken. The field work, held between 2004-2005, consisted on four transects in each locality (10 x 100m, 0.1ha). For each transect, the existing orchid species (terrestrial and epiphytic), kind of phorophytes, and level of occupation were identified. Different analysis were considered: dominance-diversity, Sorensen similarity, the dominance index and the relative abundance of the most abundant species. Our results showed 27 phorophytes species, 20 species in ET (98 phorophytes), and 16 species in ES (76 phorophytes). A total of 22 genus, 26 species and 8 326 individuals of orchids were identified. In ET, 17 genus, 18 species and 5 075 individuals were found, while for ES were 15 genus, 18 species and 3 251 individuals. Both locations have a similarity of species of 57.14%. Oeceoclades maculata, an invasive species, was the most abundant. The most dominant species were Microchilus plantagineus in ES and O. maculata in ET. The dominance in ET was of 81.79%, while in ES of 69.27%. It is important to sketch management plans focused on controlling O. maculata in both areas, and the restoration of the disturbed area.

Paraholcoglossum and Tsiorchis, two new orchid genera established by molecular and morphological analyses of the Holcoglossum alliance

BACKGROUND

Holcoglossum is a small orchid genus of 12 species ranging from SW China to Thailand and NE India. Although molecular and morphological analyses have been performed to establish the phylogenetic relationships within this genus, the interspecific relations and its relations with allied genera, such as Rhynchostylis, Aerides and Vanda, remain unclear.

METHODOLOGY/PRINCIPAL FINDINGS

In addition to morphological analysis, maximum parsimony, maximum likelihood, and Bayesian inference analyses were performed based on fragments of the nuclear ITS and chloroplast trnL-F and matK genes of 31 taxa (15 Holcoglossum, 14 Aeridinae, 2 outgroups) representing all major clades of the Holcoglossum alliance. The results suggest that Holcoglossum is triphyletic, comprising three clades: the Holcoglossum clade, its sister clade, and a distant clade more closely related to Rhynchostylis, Aerides, and Vanda than to the Holcoglossum clade. The Holcoglossum clade is further divided into three subclades; the genetic distances between these three subclades also support this delimitation. The molecular conclusion is consistent with their distinct morphological characters.

CONCLUSIONS

We propose that the latter two clades comprise two new genera, Paraholcoglossum and Tsiorchis, and Holcoglossum clade divides into three sections. In addition, a new section, Holcoglossum sect. Nujiangensia, and a new species, Holcoglossum linearifolium, are proposed. Some new combinations are made, and a new scheme is provided for the classification of all species of Holcoglossum, Paraholcoglossum, and Tsiorchis.

Evidence for progenitor-derivative speciation in sexually deceptive orchids

BACKGROUND AND AIMS

Sexually deceptive orchids of the genus Ophrys use mimicry of pollinator females to attract specific pollinators. Pollinator shifts may drive speciation in Ophrys, since novel pollinators may in principle act as isolating factors immediately. It is thus possible that evolution of novel species occurs rapidly and with a progenitor-derivative pattern. The aims of this study are to compare genetic structure and diversity among widespread and geographically restricted Ophrys taxa, to test whether genetic structure is associated with specific pollinators, and to investigate whether any widespread species may have acted as a progenitor for the evolution of more restricted taxa.

METHODS

Genetic differentiation and diversity were investigated in O. leucadica and O. cinereophila, the two taxa of the Ophrys fusca sensu lato complex widespread in the Aegean, and three geographically restricted taxa from Rhodes, O. attaviria, O. parvula and O. persephonae, all differing in their specific pollinators. This was done using amplified fragment length polymorphism (AFLP) DNA fingerprinting, and sequencing of the low-copy nuclear gene LEAFY (LFY).

KEY RESULTS

All taxa were found to be separate genetic entities, with O. leucadica forming two geographic groups from the west and east of the Aegean. Genetic structure was significantly shaped by pollinators and geography, and comparison of sequence and AFLP data revealed ancestral polymorphisms shared among several taxa. Among the sampled taxa, O. leucadica harbours the greatest genetic differentiation and geographic structure, and the highest genetic diversity. Part of the genome of O. parvula, endemic to Rhodes, may be derived from O. leucadica.

CONCLUSIONS

Pollinators probably influence the genetic structure of the investigated Ophrys species. The genetic pattern identified is consistent with O. leucadica being the oldest of the sampled taxa, making O. leucadica a candidate progenitor species from which more restricted taxa such as O. parvula may have evolved.

Comparative labellar micromorphology of Zygopetalinae (Orchidaceae)

BACKGROUND AND AIMS

Molecular evidence indicates that the Neotropical sub-tribe Zygopetalinae is sister to Maxillariinae. Most members of the latter sub-tribe have deceit pollination strategies, but some species produce rewards such as nectar, pseudopollen, resin and wax, and are pollinated by a range of pollinators that include stingless bees (Meliponini), wasps and hummingbirds. By contrast, relatively little is known about the pollination of Zygopetalinae species. However, some are pollinated by fragrance-gathering, male euglossine bees or employ nectar deceit strategies. The aim of this study is to describe the labellar micromorphology of Zygopetalinae and to compare it with that of Maxillariinae sensu lato (s.l.) as part of an ongoing project to record the range of labellar characters found within the tribe Maxillarieae, and to assess whether these characters represent synapomorphies or homoplasies resulting from similar pollination pressures.

METHODS

The labella of 31 species of Zygopetalinae, including Cryptarrhena R. Br. and representatives of the Zygopetalum, Huntleya and Warrea clades, were examined using light microscopy and scanning electron microscopy, and the range of labellar characters was recorded. These characters were subsequently compared with those of Maxillariinae s.l. which formed the subject of our previous investigations.

KEY RESULTS AND CONCLUSIONS

The labellar micromorphology of Zygopetalinae is less diverse than that of Maxillariinae and does not reflect the currently accepted phylogeny of the former sub-tribe based on molecular studies. Instead, the relative uniformity in labellar micromorphology of Zygopetalinae is probably due to homoplasies resulting from similar pollinator pressures. Labellar trichomes are relatively uncommon in Zygopetalinae, but occur in certain members of both the Zygopetalum and Huntleya clades. Trichomes are unbranched, uniseriate and multicellular with rounded apices, or unbranched and unicellular, with tapering, pointed and flexuose apices. Hitherto, unicellular trichomes of this kind have been observed only for euglossophilous orchid taxa, and the adoption of a relatively limited range of pollination strategies by Zygopetalinae may have resulted in reduced investment in micromorphological labellar characters.

[Genetic differentiation in plants of the genus Cypripedium from Russia inferred from allozyme data]

Ten gene loci of nine enzyme systems (PGI, 6-PGD, NADHD, SKDH, GDH, PGM, DIA, ADH, GOT-1, and GOT-2) were analyzed in Cypripedium calceolus, C. macranthon, C. shanxiense, and C. ventricosum plants from the south of the Russian Far East. Alleles of loci 6-PGD, NADHD, GDH, ADH, GOT-1, and PGIproved to be diagnostic for C. calceolus and C. macranthon. Plants of C. shanxiense from Primorye and Sakhalin Island were monomorphic at all of the loci examined, and their allelic structure can be regarded as diagnostic for the species. The allelic structure for fragments of the C. calceolus population from the western and eastern parts of the species range differed in two loci, PGl and SKDH: alleles absent in C. calceolus plants from the western part of the range occurred at a high frequency in the plants of this species from the eastern part of the range (28 and 55 plants or 41% and 68%, respectively). These alleles were found in C. shanxiense. The genetic structure of C. shanxiense was similar to that of C. calceolus from the eastern part of the range, i.e., the region when these species are sympartic. The additional alleles in C. calceolus from the eastern part of the range might have appeared as a result of hybridization with C. shanxiense. Our results indicate that C. calceolus plants occuring on the territory of Russia form two groups that represent two different units of genetic diversity preservation. We suggest that C. x ventricosum plants in southern Primorye were formed by hybridization between C. macranthon and C. calceolus x C. shanxiense hybrids. Thus, they differ from plants inhabiting the Urals and West Siberia, which originated by hybridization between C. macranthon and C. calceolus. The population of C. x ventricosum presumably also consists of two plant groups differing in genetic structure, which should be regarded as two different units of preservation of this taxon.

Comparative anatomy of the nectary spur in selected species of Aeridinae (Orchidaceae)

BACKGROUND AND AIMS

To date, the structure of the nectary spur of Aeridinae has not been studied in detail, and data relating to the nectaries of ornithophilous orchids remain scarce. The present paper compares the structural organization of the floral nectary in a range of Aeridinae species, including both entomophilous and ornithophilous taxa.

METHODS

Nectary spurs of Ascocentrum ampullaceum (Roxb.) Schltr. var. aurantiacum Pradhan, A. curvifolium (Lindl.) Schltr., A. garayi Christenson, Papilionanthe vandarum (Rchb.f.) Garay, Schoenorchis gemmata (Lindl.) J.J. Sm., Sedirea japonica (Rchb.f.) Garay & H.R. Sweet and Stereochilus dalatensis (Guillaumin) Garay were examined by means of light microscopy, scanning electron microscopy and transmission electron microscopy.

KEY RESULTS AND CONCLUSIONS

The diverse anatomy of the nectary is described for a range of Aeridinae species. All species of Ascocentrum investigated displayed features characteristic of ornithophilous taxa. They have weakly zygomorphic, scentless, red or orange flowers, display diurnal anthesis, possess cryptic anther caps and produce nectar that is secluded in a relatively massive nectary spur. Unicellular, secretory hairs line the lumen at the middle part of the spur. Generally, however, with the exception of Papilionanthe vandarum, the nectary spurs of all entomophilous species studied here (Schoenorchis gemmata, Sedirea japonica, Stereochilus dalatensis) lack secretory trichomes. Moreover, collenchymatous secretory tissue, present only in the nectary spur of Asiatic Ascocentrum species, closely resembles that found in nectaries of certain Neotropical species that are hummingbird-pollinated and assigned to subtribes Maxillariinae Benth., Laeliinae Benth. and Oncidiinae Benth. This similarity in anatomical organization of the nectary, regardless of geographical distribution and phylogeny, indicates convergence.