Phylogenetic relationships in the orchid genus Serapias L. based on noncoding regions of the chloroplast genome

Orchidinae-205: A new genome-wide custom bait set for studying the evolution, systematics, and trade of terrestrial orchids

Terrestrial orchids are a group of genetically understudied, yet culturally and economically important plants. The Orchidinae tribe contains many species that produce edible tubers that are used for the production of traditional delicacies collectively called 'salep'. Overexploitation of wild orchids in the Eastern Mediterranean and Western Asia threatens to drive many of these species to extinction, but cost-effective tools for monitoring their trade are currently lacking. Here we present a custom bait kit for target enrichment and sequencing of 205 novel genetic markers that are tailored to phylogenomic applications in Orchidinae s.l. A subset of 31 markers capture genes putatively involved in the production of glucomannan, a water-soluble polysaccharide that gives salep its distinctive properties. We tested the kit on 73 taxa native to the area, demonstrating universally high locus recovery irrespective of species identity, that exceeds the total sequence length obtained with alternative kits currently available. Phylogenetic inference with concatenation and coalescent approaches was robust and showed high levels of support for most clades, including some which were previously unresolved. Resolution for hybridizing and recently radiated lineages remains difficult, but could be further improved by analysing multiple haplotypes and the non-exonic sequences captured by our kit, with the promise to shed new light on the evolution of enigmatic taxa with a complex speciation history. Offering a step-up from traditional barcoding and universal markers, the genome-wide custom loci targeted by Orchidinae-205 are a valuable new resource to study the evolution, systematics and trade of terrestrial orchids.

Pollination mechanism in Serapias with no pollinaria reconfiguration

Orchidaceae, one of the most numerous families in the world's flora, have evolved various pollination strategies to favour cross-pollination, such as deceptive pollination and pollinarium reconfiguration. Among the terrestrial orchids of the Mediterranean, only species belonging to the genus Serapias show a strategy defined as shelter imitation. The floral elements form a tubular structure that insects use during their resting phases. The purpose of this article was to clarify the mechanisms that guarantee pollination with particular attention to the morphological interactions between orchids and pollinators and whether pollinaria reconfiguration is necessary in the promotion of cross-pollination in Serapias. Breeding system experiments and hand-pollination treatments indicated that Serapias was highly self-compatible, shows low value of natural fruit set and is pollinator limited. Time-lapse photos showed that the pollinarium had no refolding of the stipe or caudicle after its removal from the flower. The morphology of the flower determined the attack of the pollinarium on the occiput/vertex of insect. When the insect left the flower, the pollinarium was unable to encounter the stigma. When the insect made a second visit to another flower, the pollen masses of the first pollinarium ended up on the stigma and at the same time, the insect picked up a second pollinarium. Our observations and analyses suggested that morphological interactions between flower and pollinator are crucial to the success of pollination and to prevent self-pollination and thus that pollinarium reconfiguration is unnecessary in shelter deceptive orchids, such as Serapias species, for the promotion of cross-pollination. Serapias represent a case of interactions between plant and pollinator; the formation of the tubular shape of the flower is an essential preadaptation for the development of resting site mimicry originating exclusively in Serapias among Mediterranean orchids.

Phylogeny of Chinese Allium Species in Section Daghestanica and Adaptive Evolution of Allium (Amaryllidaceae, Allioideae) Species Revealed by the Chloroplast Complete Genome

The genus Allium (Amaryllidaceae, Allioideae) is one of the largest monocotyledonous genera and it includes many economically important crops that are cultivated for consumption or medicinal uses. Recent advances in molecular phylogenetics have revolutionized our understanding of Allium taxonomy and evolution. However, the phylogenetic relationships in some Allium sections (such as the Allium section Daghestanica) and the genetic bases of adaptative evolution, remain poorly understood. Here, we newly assembled six chloroplast genomes from Chinese endemic species in Allium section Daghestanica and by combining these genomes with another 35 allied species, we performed a series of analyses including genome structure, GC content, species pairwise Ka/Ks ratios, and the SSR component, nucleotide diversity and codon usage. Positively selected genes (PSGs) were detected in the Allium lineage using the branch-site model. Comparison analysis of Bayesian and ML phylogeny on CCG (complete chloroplast genome), SCG (single copy genes) and CDS (coding DNA sequences) produced a well-resolved phylogeny of Allioideae plastid lineages, which illustrated several novel relationships with the section Daghestanica. In addition, six species in section Daghestanica showed highly conserved structures. The GC content and the GC3s content in Allioideae species exhibited lower values than studied non-Allioideae species, along with elevated pairwise Ka/Ks ratios. The rps2 gene was lost in all examined Allioideae species, and 10 genes with significant posterior probabilities for codon sites were identified in the positive selection analysis, seven of them are associated with photosynthesis. Our study uncovered a new species relationship in section Daghestanica and suggested that the selective pressure has played an important role in Allium adaptation and evolution, these results will facilitate our further understanding of evolution and adaptation of species in the genus Allium.

Functional differentiation in pollination processes among floral traits in Serapias species (Orchidaceae)

Floral displays, influencing attractiveness to insects, increase the number of pollinator visits and the efficiency of each visit in terms of pollen exchange and thus affect the plant reproductive success. Here, we conducted an in situ manipulation experiment to investigate whether the floral modifications affect reproductive success in natural orchid populations of Serapias lingua and Serapias vomeracea. We estimated male and female reproductive success of three treatment groups, disassembly of floral tube, cutting of lip, and painting of the callus surface, in terms of pollinaria removed/deposited and fruit production. Results revealed that phenotypic modification had opposite effects on reproductive success of two examine species. Indeed, reproductive success was significantly increased by the detached of the petals and sepals, and decreased, due to callus painting and lip removal, in S. lingua. On the contrary, unmanipulated plants of S. vomeracea showed significantly higher value of pollinaria removed and deposited and fruit set than manipulated ones. The differences between S. lingua and S. vomeracea agree to the different pollination strategy of examined species. S. vomeracea shows shelter imitation strategy, and thus, the disassembly of tunnel-like corolla does not allow the insects to use the flower as a refuge, while S. lingua is a sexually deceptive orchid and therefore the opening of the flower made more visible callus (visible at a greater distance) increasing the pollinators attraction. This study provides evidence that pollinators were largely sensitive to the experimental modification of the flower phenotype, which is consistent with the presence of significant selection on individual floral characters. Our experimental investigations of the effects of variation in display on pollinator visitation provide insights into the evolution of floral morphology in orchid with shelter imitation strategy.

Effects of population structure on pollen flow, clonality rates and reproductive success in fragmented Serapias lingua populations

BACKGROUND

Fragmentation of habitats by roads, railroads, fields, buildings and other human activities can affect population size, pollination success, sexual and asexual reproduction specially in plants showing pollinator limitation, such as Mediterranean orchids. In this study, we assessed pollen flow, selfing rates, vegetative reproduction and female reproductive success and their correlations with habitat characters in nine fragmented subpopulations of Serapias lingua. To improve understanding of population structure effects on plant biology, we examined genetic differentiation among populations, pollen flow, selfing rates and clonal reproduction using nuclear microsatellite markers.

RESULTS

Smaller populations showed a significant heterozygote deficit occurred at all five nuclear microsatellite loci, the coefficient of genetic differentiation among populations was 0.053 and pairwise FST was significantly correlated with the geographical distance between populations. Paternity analysis of seeds showed that most pollen flow occurred within a population and there was a positive correlation between percentage of received pollen and distance between populations. The fruit production rate varied between 5.10 % and 20.30 % and increased with increasing population size, while the percentage of viable seeds (78-85 %) did not differ significantly among populations. The extent of clonality together with the clonal and sexual reproductive strategies varied greatly among the nine populations and correlated with the habitats where they occur. The small, isolated populations tended to have high clonal diversity and low fruit production, whereas the large populations with little disturbance were prone to have reductions in clonal growth and increased sexual reproduction.

CONCLUSIONS

We found that clonality offers an advantage in small and isolated populations of S. lingua, where clones may have a greater ability to persist than sexually reproducing individuals.

Phylogeny and classification of the East Asian Amitostigma alliance (Orchidaceae: Orchideae) based on six DNA markers

BACKGROUND

Tribe Orchideae dominates the orchid flora of the temperate Northern Hemisphere but its representatives in East Asia had been subject to less intensive phylogenetic study than those in Eurasia and North America. Although this situation was improved recently by the molecular phylogenetic study of Jin et al., comparatively few species were analyzed from the species-rich and taxonomically controversial East Asian Amitostigma alliance. Here, we present a framework nrITS tree of 235 accessions of Orchideae plus an in-depth analysis of 110 representative accessions, encompassing most widely recognized species within the alliance, to elucidate their relationships.

RESULTS

We used parsimony, likelihood and Bayesian approaches to generate trees from data for two nuclear (nrITS, low-copy Xdh) and four chloroplast (matK, psbA-trnH, trnL-F, trnS-trnG) markers. Nuclear and plastid data were analyzed separately due to a few hard incongruences that most likely reflect chloroplast capture. Our results suggest key phylogenetic placements for Sirindhornia and Brachycorythis, and confirm previous assertions that the Amitostigma alliance is monophyletic and sister to the Eurasian plus European clades of subtribe Orchidinae. Seven robust clades are evident within the alliance, but none corresponds precisely with any of the traditional genera; the smaller and more morphologically distinct genera Tsaiorchis, Hemipilia, Neottianthe and Hemipiliopsis are monophyletic but each is nested within a polyphyletic plexus of species attributed to either Ponerorchis or the most plesiomorphic genus, Amitostigma. Two early-divergent clades that escaped analysis by Jin et al. undermine their attempt to circumscribe an expanded monophyletic genus Ponerorchis.

CONCLUSIONS

We provide a new framework on the complex phylogenetic relationships between Amitostigma and other genera traditionally included in its alliance; based on which, we combine the entire Amitostigma alliance into a morphologically and molecularly circumscribed Amitostigma sensu latissimo that also contains seven molecularly circumscribed sections. Our molecular trees imply unusually high levels of morphological homoplasy, but these will need to be quantified via a future group-wide review of the alliance based on living plants if morphology is to be fully integrated into our classification.

Eugenol synthase genes in floral scent variation in Gymnadenia species

Floral signaling, especially through floral scent, is often highly complex, and little is known about the molecular mechanisms and evolutionary causes of this complexity. In this study, we focused on the evolution of "floral scent genes" and the associated changes in their functions in three closely related orchid species of the genus Gymnadenia. We developed a benchmark repertoire of 2,571 expressed sequence tags (ESTs) in Gymnadenia odoratissima. For the functional characterization and evolutionary analysis, we focused on eugenol synthase, as eugenol is a widespread and important scent compound. We obtained complete coding complementary DNAs (cDNAs) of two copies of putative eugenol synthase genes in each of the three species. The proteins encoded by these cDNAs were characterized by expression and testing for activity in Escherichia coli. While G. odoratissima and Gymnadenia conopsea enzymes were found to catalyze the formation of eugenol only, the Gymnadenia densiflora proteins synthesize eugenol, as well as a smaller amount of isoeugenol. Finally, we showed that the eugenol and isoeugenol producing gene copies of G. densiflora are evolutionarily derived from the ancestral genes of the other species producing only eugenol. The evolutionary switch from production of one to two compounds evolved under relaxed purifying selection. In conclusion, our study shows the molecular bases of eugenol and isoeugenol production and suggests that an evolutionary transition in a single gene can lead to an increased complexity in floral scent emitted by plants.

A pollinators' eye view of a shelter mimicry system

BACKGROUND AND AIMS

'Human-red' flowers are traditionally considered to be rather unpopular with bees, yet some allogamous species in the section Oncocyclus (genus Iris, Iridaceae) have evolved specialized interactions with their pollinators, a narrow taxonomic range of male solitary bees. The dark-red, tubular flowers of these irises are nectarless but provide protective shelters (i.e. a non-nutritive form of reward) primarily to male solitary bees (Apidae, Eucerini) that pollinate the flowers while looking for a shelter. An earlier study on orchids suggested that species pollinated predominantly by male solitary bees produce significantly larger amounts and larger numbers of different n-alkenes (unsaturated cuticular hydrocarbons). Whether or not this also applies to the Oncocyclus irises and whether pollinators are attracted by specific colours or scents of these flowers is unknown.

METHODS

Using Iris atropurpurea, recording of pollinator preferences for shelters with different spatial parameters was combined with analyses of floral colours (by spectrophotometry) and scents (by gas chromatography-mass spectrometry) to test the hypotheses that (a) pollinators significantly prefer floral tunnels facing the rising sun (floral heat-reward hypothesis), and that (b) flowers pollinated predominantly by male solitary bees produce significantly larger amounts and larger numbers of unsaturated cuticular hydrocarbons (n-alkenes) in their floral scent (preadaptation to sexual-deception hypothesis).

KEY RESULTS

Male bees do not significantly prefer shelters facing the rising sun or with the presence of high absolute/relative amounts and numbers of n-alkenes in the floral scent.

CONCLUSIONS

The results suggest that the flowers of I. atropurpurea probably evolved by pollinator-mediated selection acting primarily on floral colours to mimic large achromatic ('bee-black') protective shelters used preferentially by male solitary bees, and that pollinator visits are presumably not the result of an odour-based sexual stimulation or motivated by an increased morning floral heat reward in tunnels facing the rising sun.

Pre-adaptations and the evolution of pollination by sexual deception: Cope's rule of specialization revisited

Pollination by sexual deception is arguably one of the most unusual liaisons linking plants and insects, and perhaps the most illustrative example of extreme floral specialization in angiosperms. While considerable progress has been made in understanding the floral traits involved in sexual deception, less is known about how this remarkable mimicry system might have arisen, the role of pre-adaptations in promoting its evolution and its extent as a pollination mechanism outside the few groups of plants (primarily orchids) where it has been described to date. In the Euro-Mediterranean region, pollination by sexual deception is traditionally considered to be the hallmark of the orchid genus Ophrys. Here, we introduce two new cases outside of Ophrys, in plant groups dominated by generalized, shelter-mimicking species. On the basis of phylogenetic reconstructions of ancestral pollination strategies, we provide evidence for independent and bidirectional evolutionary transitions between generalized (shelter mimicry) and specialized (sexual deception) pollination strategies in three groups of flowering plants, and suggest that pseudocopulation has evolved from pre-adaptations (floral colours, shapes and odour bouquets) that selectively attract male pollinators through shelter mimicry. These findings, along with comparative analyses of floral traits (colours and scents), shed light on particular phenotypic changes that might have fuelled the parallel evolution of these extraordinary pollination strategies. Collectively, our results provide the first substantive insights into how pollination sexual deception might have evolved in the Euro-Mediterranean region, and demonstrate that even the most extreme cases of pollinator specialization can reverse to more generalized interactions, breaking 'Cope's rule of specialization'.

Complete chloroplast genome of Oncidium Gower Ramsey and evaluation of molecular markers for identification and breeding in Oncidiinae

BACKGROUND

Oncidium spp. produce commercially important orchid cut flowers. However, they are amenable to intergeneric and inter-specific crossing making phylogenetic identification very difficult. Molecular markers derived from the chloroplast genome can provide useful tools for phylogenetic resolution.

RESULTS

The complete chloroplast genome of the economically important Oncidium variety Onc. Gower Ramsey (Accession no. GQ324949) was determined using a polymerase chain reaction (PCR) and Sanger based ABI sequencing. The length of the Oncidium chloroplast genome is 146,484 bp. Genome structure, gene order and orientation are similar to Phalaenopsis, but differ from typical Poaceae, other monocots for which there are several published chloroplast (cp) genome. The Onc. Gower Ramsey chloroplast-encoded NADH dehydrogenase (ndh) genes, except ndhE, lack apparent functions. Deletion and other types of mutations were also found in the ndh genes of 15 other economically important Oncidiinae varieties, except ndhE in some species. The positions of some species in the evolution and taxonomy of Oncidiinae are difficult to identify. To identify the relationships between the 15 Oncidiinae hybrids, eight regions of the Onc. Gower Ramsey chloroplast genome were amplified by PCR for phylogenetic analysis. A total of 7042 bp derived from the eight regions could identify the relationships at the species level, which were supported by high bootstrap values. One particular 1846 bp region, derived from two PCR products (trnHGUG -psbA and trnFGAA-ndhJ) was adequate for correct phylogenetic placement of 13 of the 15 varieties (with the exception of Degarmoara Flying High and Odontoglossum Violetta von Holm). Thus the chloroplast genome provides a useful molecular marker for species identifications.

CONCLUSION

In this report, we used Phalaenopsis. aphrodite as a prototype for primer design to complete the Onc. Gower Ramsey genome sequence. Gene annotation showed that most of the ndh genes inOncidiinae, with the exception of ndhE, are non-functional. This phenomenon was observed in all of the Oncidiinae species tested. The genes and chloroplast DNA regions that would be the most useful for phylogenetic analysis were determined to be the trnHGUG-psbA and the trnFGAA-ndhJ regions. We conclude that complete chloroplast genome information is useful for plant phylogenetic and evolutionary studies in Oncidium with applications for breeding and variety identification.