Discovery of the photosynthetic relatives of the "Maltese mushroom" Cynomorium

Plastomes in the holoparasitic family Balanophoraceae: Extremely high AT content, severe gene content reduction, and two independent genetic code changes

The transition to a heterotrophic lifestyle in angiosperms is characterized by convergent evolutionary changes. Plastid genome remodeling includes dramatic functional and physical reductions with the highest degrees observed in fully heterotrophic plants. Genes related to photosynthesis are generally absent or pseudogenized, while a few genes related to other metabolic processes that take place within the plastid are almost invariably maintained. The family Balanophoraceae consists of root holoparasites that present reduced plastid genomes with an extraordinarily elevated AT content and the single genetic code change ever documented in land plant plastomes (the stop codon TAG now codes for tryptophan). Here, we studied the plastomes of Lophophytum leandri and Ombrophytum subterraneum (Balanophoraceae) that showed the remarkable absence of the gene trnE, a highly biased nucleotide composition, and an independent genetic code change (the standard stop codon TGA codes for tryptophan). This is the second genetic code change identified in land plant plastomes. Analysis of the transcriptome of Lophophytum indicated that the entire C5 pathway typical of plants is conserved despite the lack of trnE in its plastome. A hypothetical model of plastome evolution in the Balanophoraceae is presented.

Astringent drugs for bleedings and diarrhoea: The history of Cynomorium coccineum (Maltese Mushroom)

ETHNOPHARMACOLOGICAL RELEVANCE

The botanical identity of the ancient vernacular cynomorium does not correspond to the modern scientific genus while it is not clear how many species of hipocistis (Cytinus sp.) were differentiated by the ancient physicians and whether Cynomorium coccineum was subsumed. The early history of therapeutic uses related to the herbal drugs derived from these parasitic taxa is therefore not easily accessible. Cynomorium coccineum became an important pharmaceutical commodity after the Siege of Malta but its importance decreased in the 18th century and now is considered obsolete.

MATERIAL AND METHODS

We compare the morphological, ecological and therapeutic information of Cynomorium and other parasitizing plant taxa across the past 2000 years and contextualize their uses with the pharmacological properties of their principal metabolites focusing on the raise and fall of C. coccineum as a medicine.

RESULTS

The therapeutic uses of C. coccineum, the Maltese mushroom, seem to become clearly traceable since the Canon of Medicine by Avicenna. Styptic and astringent drugs such as Cynomorium, Cytinus but also gall apples and many others have been selected for their protein-linking capacity leading to the formation of a protective layer on the mucous membranes, which can be used to reduce the secretion of water and electrolytes in case of diarrhoea, dysentery and external bleedings. Whether C. coccineum is effective as a systemically applied anti-haemorrhagic drug is questionable.

CONCLUSION

It appears that the vernacular cynomorium of the ancients corresponds to an edible Orobanche sp. while it remains doubtful whether the vernacular hipocistis was next to Cytinus sp. also applied to C. coccineum as evidence of C. coccineum parasitizing Cistus sp. is scarce. The isolation of gallic acid used as a styptic and the increasing availability of chemical styptics in the 18th century together with the availability of effective alternative anti-diarrhoeic drugs with a more reliable supply very probably led to the decline of the importance of the Maltese mushroom in pharmacy during the 18th century. The effectiveness of gallic acid as a systemic anti-haemorrhagic remains uncertain.

Plants in the management of male infertility

This review attempts to collate existing data and provide the perspectives for future studies on the effects of plants on the male gonads. For many of these medicinal plants such as Lepidium meyenii, Rupus coreanus, Tribulus terrestres, Panax ginseng, Petasites japonicas, Apium graveolens, Eurycoma longifólia, Pedalium murex, Corchorus depressus, Mucuna pruriens, Astragalus membranaceus, Nigella sativa, Crataegus monogyna, Fagara tessmannii, Phaleria macrocarpa, Anacyclus pyrethrum, Cynomorium songaricum and Morinda officinalis, the mechanism of actions of their active principles and crude extracts has been shown in both laboratory animals, in vitro, and human studies, and includes their antioxidant, anti-inflammatory, spermatogenesis-inducing, aphrodisiac, smooth muscle relaxing and androgenic properties. Several active chemical leads including glucosinolates, anthocyanins, protodioscin, ginsenosides, sesquiterpenes, phyto-oestrogens, quassinoids, diosgenin, thymoquinone, proanthocyanidins and bajijiasu isolated from these plants are known to have target effects on the testis, but efforts have been limited in their application at the clinical level. There still appear to be many more extracts of medicinal plants that have not been characterised to determine the phytochemicals unique to them that have target effects on the gonads. Further, collaborative efforts at isolating pro-drug candidates from medicinal plants for studies at the molecular, cellular and clinical level towards elucidating their mechanisms of action on the testes are therefore warranted in the light of the current male fertility crisis.

The Modern Use of an Ancient Plant: Exploring the Antioxidant and Nutraceutical Potential of the Maltese Mushroom (Cynomorium Coccineum L.)

In the continuous scientific search for new safe and effective drugs, there has recently been a rediscovery of natural substances as a potential reservoir of innovative therapeutic solutions for human health, with the prospect of integrating with and sometimes replacing conventional drugs. Cynomorium coccineum subsp. coccineum is a holoparasitic plant well known in ethnopharmacology, although its current use as a curative remedy is reported only in some ethnic groups of North Africa and the Arabian Peninsula. Often known as ‘Maltese mushroom’ due to its unique appearance and the absence of chlorophyll, C. coccineum is present in almost all of the Mediterranean Basin. It is only recently that a few research groups have begun to look for confirmation of some of its traditional uses to highlight previously unknown biological activities. Here, we review the recent scientific findings on the plant’s phytochemistry and the most significant descriptions of some of its antioxidant and biological activities (antimicrobial, anticancer, pro-erectile, and anti-tyrosinase enzyme) both in vivo and in vitro. Some of these may be promising from the perspective of food and cosmetic formulations. The purpose of this review is to provide an initial impetus to those who, in the foreseeable future, will want to increase the knowledge and possible applications of this plant full of history, charm, and mystery.

Mitochondrial genome evolution in parasitic plants

Background

Parasitic plants rely on their host to cover their nutritional requirements either for their entire life or a smaller part of it. Depending on the level of parasitism, a proportional reduction on the plastid genome has been found. However, knowledge on gene loss and evolution of the mitogenome of parasitic plants is only available for four hemiparasitic Viscum species (Viscaceae), which lack many of the mitochondrial genes, while the remaining genes exhibit very fast molecular evolution rates. In this study, we include another genus, Phoradendron, from the Viscaceae, as well as 10 other hemiparasitic or holoparasitic taxa from across the phylogeny of the angiosperms to investigate how fast molecular evolution works on their mitogenomes, and the extent of gene loss.

Results

Our observations from Viscum were replicated in Phoradendron liga, whereas the remaining parasitic plants in the study have a complete set of the core mitochondrial genes and exhibit moderate or only slightly raised substitution rates compared to most autotrophic taxa, without any statistically significant difference between the different groups (autotrophs, hemiparasites and holoparasites). Additionally, further evidence is provided for the placement of Balanophoraceae within the order Santalales, while the exact placement of Cynomoriaceae still remains elusive.

Conclusions

We examine the mitochondrial gene content of 11 hemiparasitic and holoparasitic plants and confirm previous observations in Viscaceae. We show that the remaining parasitic plants do not have significantly higher substitution rates than autotrophic plants in their mitochondrial genes. We provide further evidence for the placement of Balanophoraceae in the Santalales.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1401-8) contains supplementary material, which is available to authorized users.

Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant Balanophora

Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two Balanophora plastomes examined are remarkable, exhibiting features rarely if ever seen before in plastomes or in any other genomes. At 15.5 kb in size and with only 19 genes, they are among the most reduced plastomes known. They have no tRNA genes for protein synthesis, a trait found in only three other plastid lineages, and thus Balanophora plastids must import all tRNAs needed for translation. Balanophora plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all cis-spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the Balanophora genomes are the most AT-rich genomes known save for a single mitochondrial genome that is merely bloated with AT-rich spacer DNA. Most plastid protein genes in Balanophora consist of ≥90% AT, with several between 95% and 98% AT, resulting in the most biased codon usage in any genome described to date. A potential consequence of its radical compositional evolution is the novel genetic code used by Balanophora plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the Balanophora plastome must be functional because all examined genes are transcribed, its only intron is correctly trans-spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint.

Resolving the systematic positions of enigmatic taxa: Manipulating the chloroplast genome data of Saxifragales

Accurately resolving the phylogeny of enigmatic taxa is always a challenge in phylogenetic inference. Such uncertainties could be due to systematic errors or model violations. Here, we provide an example demonstrating how these factors affect the positioning of Paeoniaceae within Saxifragales based on chloroplast genome data. We newly assembled 14 chloroplast genomes from Saxifragales, and by combining these genomes with those of 63 other angiosperms, three datasets were assembled to test different hypotheses proposed by recent studies. These datasets were subjected to maximum parsimony, maximum likelihood and Bayesian analyses with site-homogeneous/heterogeneous models, different data partitioning strategies, and the inclusion/exclusion of weak phylogenetic signals. Three datasets exhibited remarkable heterogeneity among sites and among taxa of Saxifragales. Phylogenetic analyses under homogeneous models or maximum parsimony showed a closer relationship of Paeoniaceae with herbaceous families in the order. Data partitioning strategies did not change the general tree topology. However, PhyloBayes analysis under the CAT+GTR model resulted in a relationship closer to woody families. We conclude that although genomic data significantly increase the phylogenetic resolution of enigmatic taxa with high support, the phylogenetic results inferred from such data might be analysis or signal dependent. The analytical pipeline outlined here combines phylogenomic inference methods with evaluation of lineage-specific rates of substitution, model selection, and assessment of systematic error. These methods would be applicable to resolve similar difficult questions in the tree of life.

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

PREMISE OF THE STUDY

Phylogenetic support has been difficult to evaluate within the green plant tree of life partly due to a lack of specificity between conflicted versus poorly informed branches. As data sets continue to expand in both breadth and depth, new support measures are needed that are more efficient and informative.

METHODS

We describe the Quartet Sampling (QS) method, a quartet-based evaluation system that synthesizes several phylogenetic and genomic analytical approaches. QS characterizes discordance in large-sparse and genome-wide data sets, overcoming issues of alignment sparsity and distinguishing strong conflict from weak support. We tested QS with simulations and recent plant phylogenies inferred from variously sized data sets.

KEY RESULTS

QS scores demonstrated convergence with increasing replicates and were not strongly affected by branch depth. Patterns of QS support from different phylogenies led to a coherent understanding of ancestral branches defining key disagreements, including the relationships of Ginkgo to cycads, magnoliids to monocots and eudicots, and mosses to liverworts. The relationships of ANA-grade angiosperms (Amborella, Nymphaeales, Austrobaileyales), major monocot groups, bryophytes, and fern families are likely highly discordant in their evolutionary histories, rather than poorly informed. QS can also detect discordance due to introgression in phylogenomic data.

CONCLUSIONS

Quartet Sampling is an efficient synthesis of phylogenetic tests that offers more comprehensive and specific information on branch support than conventional measures. The QS method corroborates growing evidence that phylogenomic investigations that incorporate discordance testing are warranted when reconstructing complex evolutionary histories, in particular those surrounding ANA-grade, monocots, and nonvascular plants.

Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales

Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a Cynomorium specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites’ occurrence. Cynomorium has large genomes of 13.70–13.61 (Italy) to 13.95–13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.

Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes

Despite the enormous diversity among parasitic angiosperms in form and structure, life-history strategies, and plastid genomes, little is known about the diversity of their mitogenomes. We report the sequence of the wonderfully bizarre mitogenome of the hemiparasitic aerial mistletoe Viscum scurruloideum. This genome is only 66 kb in size, making it the smallest known angiosperm mitogenome by a factor of more than three and the smallest land plant mitogenome. Accompanying this size reduction is exceptional reduction of gene content. Much of this reduction arises from the unexpected loss of respiratory complex I (NADH dehydrogenase), universally present in all 300+ other angiosperms examined, where it is encoded by nine mitochondrial and many nuclear nad genes. Loss of complex I in a multicellular organism is unprecedented. We explore the potential relationship between this loss in Viscum and its parasitic lifestyle. Despite its small size, the Viscum mitogenome is unusually rich in recombinationally active repeats, possessing unparalleled levels of predicted sublimons resulting from recombination across short repeats. Many mitochondrial gene products exhibit extraordinary levels of divergence in Viscum, indicative of highly relaxed if not positive selection. In addition, all Viscum mitochondrial protein genes have experienced a dramatic acceleration in synonymous substitution rates, consistent with the hypothesis of genomic streamlining in response to a high mutation rate but completely opposite to the pattern seen for the high-rate but enormous mitogenomes of Silene. In sum, the Viscum mitogenome possesses a unique constellation of extremely unusual features, a subset of which may be related to its parasitic lifestyle.

The Effects of Cynomorium songaricum on the Reproductive Activity in Male Golden Hamsters

Cynomorium songaricum (CS) has been used in traditional Korean medicine in treating male impotence and sexual dysfunction. We investigated the effects of aqueous CS extract on the reproductive activity of golden hamsters whose spermatogenetic capacity is active in summer and inactive in winter. The animals were divided into 5 groups: long photoperiod (LP) control, short photoperiod (SP) control, and SP animals treated with low, middle, or high concentrations of CS. The animals were orally ingested with low (0.5 g/kg), middle (1.0 g/kg), or high (2.5 g/kg) concentrations of the aqueous extracts for 8 weeks on the daily basis. The control animals received the vehicle. As results, the LP control animals showed active testicular function but SP control animals displayed remarkably reduced testicular weights. The outcomes of the reproductive activity from low and middle concentrations of CS treatments were identical and marked as low dose. The consequences were a partial blocking of regressing activity by SP. On the other hand, the animals treated with high dose of CS extract showed remarkable significance in comparison to the SP control, indicative of a complete blocking effect of the CS on the regressing testes by SP. There were a dose-dependent effects of the CS on the sexual function. These results suggest that the CS extract promotes the male fertility by strengthening the spermatogenesis in the golden hamsters.

Chemical constituents and pharmacologic actions of Cynomorium plants

The stem of Cynomorium songaricum is a traditional Chinese medicine reputed to have tonic effects. C. coccineum growing in northern Africa and the Mediterranean region is regarded in Arabian medical practice as the "treasure of drugs". The major constituents of Cynomorium plants have been revealed to be phenolic compounds, steroids, triterpenes, etc. Pharmacologic studies showed that the Cynomorium plants had antioxidant, immunity-improving, anti-diabetic, neuroprotective, and other bioactivities. Some chemical constituents in Cynomorium plants are unstable, implying that the chemical components of the herbal medicines produced under different conditions may be variable. This review covers the literature published until December, 2011 and describes the pharmacologic effects and secondary metabolites of Cynomorium species.

Single-copy nuclear genes place haustorial Hydnoraceae within piperales and reveal a cretaceous origin of multiple parasitic angiosperm lineages

Extreme haustorial parasites have long captured the interest of naturalists and scientists with their greatly reduced and highly specialized morphology. Along with the reduction or loss of photosynthesis, the plastid genome often decays as photosynthetic genes are released from selective constraint. This makes it challenging to use traditional plastid genes for parasitic plant phylogenetics, and has driven the search for alternative phylogenetic and molecular evolutionary markers. Thus, evolutionary studies, such as molecular clock-based age estimates, are not yet available for all parasitic lineages. In the present study, we extracted 14 nuclear single copy genes (nSCG) from Illumina transcriptome data from one of the “strangest plants in the world”, Hydnora visseri (Hydnoraceae). A ∼15,000 character molecular dataset, based on all three genomic compartments, shows the utility of nSCG for reconstructing phylogenetic relationships in parasitic lineages. A relaxed molecular clock approach with the same multi-locus dataset, revealed an ancient age of ∼91 MYA for Hydnoraceae. We then estimated the stem ages of all independently originated parasitic angiosperm lineages using a published dataset, which also revealed a Cretaceous origin for Balanophoraceae, Cynomoriaceae and Apodanthaceae. With the exception of Santalales, older parasite lineages tend to be more specialized with respect to trophic level and have lower species diversity. We thus propose the “temporal specialization hypothesis” (TSH) implementing multiple independent specialization processes over time during parasitic angiosperm evolution.

Parasitic plants have increased rates of molecular evolution across all three genomes

Background

Theoretical models and experimental evidence suggest that rates of molecular evolution could be raised in parasitic organisms compared to non-parasitic taxa. Parasitic plants provide an ideal test for these predictions, as there are at least a dozen independent origins of the parasitic lifestyle in angiosperms. Studies of a number of parasitic plant lineages have suggested faster rates of molecular evolution, but the results of some studies have been mixed. Comparative analysis of all parasitic plant lineages, including sequences from all three genomes, is needed to examine the generality of the relationship between rates of molecular evolution and parasitism in plants.

Results

We analysed DNA sequence data from the mitochondrial, nuclear and chloroplast genomes for 12 independent evolutionary origins of parasitism in angiosperms. We demonstrated that parasitic lineages have a faster rate of molecular evolution than their non-parasitic relatives in sequences for all three genomes, for both synonymous and nonsynonymous substitutions.

Conclusions

Our results prove that raised rates of molecular evolution are a general feature of parasitic plants, not confined to a few taxa or specific genes. We discuss possible causes for this relationship, including increased positive selection associated with host-parasite arms races, relaxed selection, reduced population size or repeated bottlenecks, increased mutation rates, and indirect causal links with generation time and body size. We find no evidence that faster rates are due to smaller effective populations sizes or changes in selection pressure. Instead, our results suggest that parasitic plants have a higher mutation rate than their close non-parasitic relatives. This may be due to a direct connection, where some aspect of the parasitic lifestyle drives the evolution of raised mutation rates. Alternatively, this pattern may be driven by an indirect connection between rates and parasitism: for example, parasitic plants tend to be smaller than their non-parasitic relatives, which may result in more cell generations per year, thus a higher rate of mutations arising from DNA copy errors per unit time. Demonstration that adoption of a parasitic lifestyle influences the rate of genomic evolution is relevant to attempts to infer molecular phylogenies of parasitic plants and to estimate their evolutionary divergence times using sequence data.

Pollination and mating systems of Apodanthaceae and the distribution of reproductive traits in parasitic angiosperms

PREMISE OF THE STUDY

The most recent reviews of the reproductive biology and sexual systems of parasitic angiosperms were published 17 yr ago and reported that dioecy might be associated with parasitism. We use current knowledge on parasitic lineages and their sister groups, and data on the reproductive biology and sexual systems of Apodanthaceae, to readdress the question of possible trends in the reproductive biology of parasitic angiosperms. •

METHODS

Fieldwork in Zimbabwe and Iran produced data on the pollinators and sexual morph frequencies in two species of Apodanthaceae. Data on pollinators, dispersers, and sexual systems in parasites and their sister groups were compiled from the literature. •

KEY RESULTS

With the possible exception of some Viscaceae, most of the ca. 4500 parasitic angiosperms are animal-pollinated, and ca. 10% of parasites are dioecious, but the gain and loss of dioecy across angiosperms is too poorly known to infer a statistical correlation. The studied Apodanthaceae are dioecious and pollinated by nectar- or pollen-foraging Calliphoridae and other flies. •

CONCLUSIONS

Sister group comparisons so far do not reveal any reproductive traits that evolved (or were lost) concomitant with a parasitic life style, but the lack of wind pollination suggests that this pollen vector may be maladaptive in parasites, perhaps because of host foliage or flowers borne close to the ground.

The genus Cynomorium in China: an ethnopharmacological and phytochemical review

ETHNOPHARMACOLOGICAL RELEVANCE

Species of the genus Cynomorium (Cynomoriaceae), including C. songaricum Rupr. and C. coccineum L., have a long history of use in traditional medicine to treat various ailments such as impotence, premature ejaculation, kidney-yang deficiency, spermatorrhea, colic, and stomach ulcers. In addition, these species are used in health foods, tea, and cosmetics.

AIM OF THE REVIEW

The aim of this review is to provide comprehensive information on the botany, traditional uses, phytochemistry, pharmacological research, and toxicology of C. songaricum and C. coccineum and to explore the therapeutic potential and future research opportunities of these species.

MATERIALS AND METHODS

All available information on C. songaricum and C. coccineum was collected via electronic search (using PubMed, ACS, CNKI, Google Scholar, Baidu Scholar, and Web of Science).

RESULTS

The ethnomedical uses of C. songaricum and C. coccineum in Saudi Arabia, China, Afghanistan, Mongolia, and Iran for several types of ailments were recorded. A phytochemical investigation revealed the presence of flavonoids, terpenoids, phloroglucinol adducts, saccharides, phenylpropanoids, steroids, organic acids, and other compounds. The crude extracts and pure compounds from C. songaricum and C. coccineum exhibited a wide spectrum of in vitro and in vivo pharmacological activity, including anti-fatigue, anti-hypoxia, anti-oxidation, anti-diabetic, immune system modulating, and antiviral activity.

CONCLUSIONS

Cynomorium species have emerged as a source of traditional medicine. Many studies have provided evidence for the therapeutic efficacy of these species in treating various conditions and possible mechanisms. However, further research is required for the development of new drugs and therapies for the treatment of various diseases, especially cancer and diabetes. Therefore, this review on the ethnopharmacology, phytochemistry, and toxicity of Cynomorium species will provide helpful data for further studies and commercial exploitation of the species.

Phylogenetic niche conservatism: what are the underlying evolutionary and ecological causes?

Phylogenetic niche conservatism (PNC) is the tendency of lineages to retain their niche-related traits through speciation events. A recent surge in the availability of well-sampled molecular phylogenies has stimulated phylogenetic approaches to understanding ecological processes at large geographical scales and through macroevolutionary time. We stress that PNC is a pattern, not a process, and is found only in some traits and some lineages. At the simplest level, a pattern of PNC is an inevitable consequence of evolution - descent with modification and divergence of lineages - but several intrinsic causes, including physicochemical, developmental and genetic constraints, can lead directly to a marked pattern of PNC. A pattern of PNC can also be caused indirectly, as a by-product of other causes, such as extinction, dispersal limitation, competition and predation. Recognition of patterns of PNC can contribute to understanding macroevolutionary processes: for example, release from constraint in traits has been hypothesized to trigger adaptive radiations such as that of the angiosperms. Given the multiple causes of patterns of PNC, tests should address explicit questions about hypothesized processes. We conclude that PNC is a scientifically useful concept with applications to the practice of ecological research.

Rate heterogeneity in six protein-coding genes from the holoparasite Balanophora (Balanophoraceae) and other taxa of Santalales

BACKGROUND AND AIMS

The holoparasitic flowering plant Balanophora displays extreme floral reduction and was previously found to have enormous rate acceleration in the nuclear 18S rDNA region. So far, it remains unclear whether non-ribosomal, protein-coding genes of Balanophora also evolve in an accelerated fashion and whether the genes with high substitution rates retain their functionality. To tackle these issues, six different genes were sequenced from two Balanophora species and their rate variation and expression patterns were examined.

METHODS

Sequences including nuclear PI, euAP3, TM6, LFY and RPB2 and mitochondrial matR were determined from two Balanophora spp. and compared with selected hemiparasitic species of Santalales and autotrophic core eudicots. Gene expression was detected for the six protein-coding genes and the expression patterns of the three B-class genes (PI, AP3 and TM6) were further examined across different organs of B. laxiflora using RT-PCR.

KEY RESULTS

Balanophora mitochondrial matR is highly accelerated in both nonsynonymous (d(N)) and synonymous (d(S)) substitution rates, whereas the rate variation of nuclear genes LFY, PI, euAP3, TM6 and RPB2 are less dramatic. Significant d(S) increases were detected in Balanophora PI, TM6, RPB2 and d(N) accelerations in euAP3. All of the protein-coding genes are expressed in inflorescences, indicative of their functionality. PI is restrictively expressed in tepals, synandria and floral bracts, whereas AP3 and TM6 are widely expressed in both male and female inflorescences.

CONCLUSIONS

Despite the observation that rates of sequence evolution are generally higher in Balanophora than in hemiparasitic species of Santalales and autotrophic core eudicots, the five nuclear protein-coding genes are functional and are evolving at a much slower rate than 18S rDNA. The mechanism or mechanisms responsible for rapid sequence evolution and concomitant rate acceleration for 18S rDNA and matR are currently not well understood and require further study in Balanophora and other holoparasites.

Morphology and phylogenetics of two holoparasitic plants, Balanophora japonica and Balanophora yakushimensis (Balanophoraceae), and their hosts in Taiwan and Japan

Balanophora japonica and B. yakushimensis are two putatively agamospermic taxa previously reported from southern Japan. Their inflorescences superficially represent those of B. laxiflora and B. fungosa. In this study we confirmed their presence in Taiwan by morphological and phylogenetic analysis using nuclear 18S rDNA and nrITS sequences with related taxa. B. japonica, B. yakushimensis, and B. laxiflora formed a well-supported clade that is distinct from other Balanophora. All three taxa also show considerable differences on morphological and nucleotide sequence differences, therefore the name of B. yakushimensis is retained. The results provide new insights on the intrageneric classification of Balanophora and suggest the positioning of female flowers should be down-weighted. We also successfully identify the hosts of B. japonica and B. yakushimensis by amplifying chloroplast matK sequences from the connected root tissues. The results showed that B. japonica parasitizes on Symplocos species, and that B. yakushimensis parasitizes on Distylium racemosum in Japan and Schima superba in Taiwan's population.

Rate accelerations in nuclear 18S rDNA of mycoheterotrophic and parasitic angiosperms

Rate variation in genes from all three genomes has been observed frequently in plant lineages with a parasitic and mycoheterotrophic mode of life. While the loss of photosynthetic ability leads to a relaxation of evolutionary constraints in genes involved in the photosynthetic apparatus, it remains to be determined how prevalent increased substitution rates are in nuclear DNA of non-photosynthetic angiosperms. In this study we infer rates of molecular evolution of 18S rDNA of all parasitic and mycoheterotorphic plant families (except Lauraceae and Polygalaceae) using relative rate tests. In several holoparasitic and mycoheterotrophic plant lineages extremely high substitution rates are observed compared to other photosynthetic angiosperms. The position and frequency of these substitutions have been identified to understand the mutation dynamics of 18S rRNA in achlorophyllous plants. Despite the presence of significantly elevated substitution rates, very few mutations occur in major functional and structural regions of the small ribosomal molecule, providing evidence that the efficiency of the translational apparatus in non-photosynthetic plants has not been affected.

Multi-gene analysis provides a well-supported phylogeny of Rosales

Despite many attempts to resolve evolutionary relationships among the major clades of Rosales, some nodes have been extremely problematic and have remained unresolved. In this study, we use two nuclear and 10 plastid loci to infer phylogenetic relationships among all nine families of Rosales. Rosales were strongly supported as monophyletic; within Rosales all family relationships are well-supported with Rosaceae sister to all other members of the order. Remaining Rosales can be divided into two subclades: (1) Ulmaceae are sister to Cannabaceae plus (Urticaceae+Moraceae); (2) Rhamnaceae are sister to Elaeagnaceae plus (Barbeyaceae+Dirachmaceae). One noteworthy result is that we recover the first strong support for a sister relationship between the enigmatic Dirachmaceae and Barbeyaceae. These two small families have distinct morphologies and potential synapomorphies remain unclear. Future studies should try to identify nonDNA synapomorphies uniting Barbeyaceae with Dirachmaceae.

The worldwide holoparasitic Apodanthaceae confidently placed in the Cucurbitales by nuclear and mitochondrial gene trees

BACKGROUND

Of the c. 450 families of flowering plants, only two are left "unplaced" in the most recent APG classification of angiosperms. One of these is the Apodanthaceae, a clade of c. 19 holoparasitic species in two or three genera occurring in North and South America, Africa, the Near East, and Australia. Because of lateral gene transfer between Apodanthaceae and their hosts it has been difficult to infer the family's true closest relatives.

RESULTS

Here we report a phylogenetic analysis of 16 accessions representing six species of Apodanthaceae from the United States, Chile, Iran, and Australia, using the mitochondrial matR gene and the nuclear 18S gene. Data matrices include 190 matR sequences from up to 95 families in 39 orders of flowering plants and 197 18S sequences from 101 families representing the 16 orders of rosids. Analyses were performed at the nucleotide and at the amino acid level. Both gene trees agree with angiosperm phylogenies found in other studies using more genes. Apodanthaceae and the seven families of the order Cucurbitales form a clade with 100% bootstrap support from matR and 56% from 18 S. In addition, the Apodanthaceae and Cucurbitales matR gene sequences uniquely share two non-synonymous codon changes and one synonymous change, as well as a codon insertion, already found by Barkman et al. (2007).

CONCLUSIONS

Apodanthaceae belong in the Cucurbitales with which they share inferior ovaries, parietal placentation and a dioecious mating system, traits that are ancestral in Cucurbitales and which can now be interpreted as possible synapomorphies of an enlarged order Cucurbitales. The occurrence of Apodanthaceae in the Americas, Africa, the Near East, and Australia, and their adaptation to distantly related host species in the Fabaceae and Salicaceae suggest a long evolutionary history.

Cynomorium songaricum induces spermatogenesis with glial cell-derived neurotrophic factor (GDNF) enhancement in rat testes

AIM OF THE STUDY

Cynomorium songaricum Ruprecht has been used in traditional Korean medicine to treat male infertility, including sexual dysfunction, by improving kidney function. Glial cell-derived neurotrophic factor (GDNF) produced by Sertoli cells induces the proliferation of undifferentiated spermatogonia. We investigated the effects of Cynomorium songaricum on sperm parameters and GDNF expression in rat testes.

MATERIALS AND METHODS

Sperm analysis, RT-PCR, and Western blotting assays were performed after administration of CS to 8-week-old male Wistar rats for 56 consecutive days (1.0g/kg/day, p.o.), the period of sperm formation in the rat.

RESULTS AND CONCLUSIONS

The CS-treated animals showed significant increases in epididymal sperm count and absolute testes weights compared to the control group. CS also increased the expression of GDNF at both the mRNA and protein levels. These results suggest that CS may improve male fertility by enhancing spermatogenesis and GDNF expression.

On the brink of holoparasitism: plastome evolution in dwarf mistletoes (Arceuthobium, Viscaceae)

Chloroplast sequences spanning rps7 to 23S rDNA in Arceuthobium campylopodum and A. pendens were generated and compared to Arabidopsis and seven other parasitic plants. Pseudogenes for trnV, trnI (GAU), and trnA (UGC) were seen in both Arceuthobium species, paralleling the situation in the holoparasite Epifagus (Orobanchaceae). These tRNA genes were intact, however, in two other members of Santalales (Ximenia and Phoradendron). The 16S-23S rDNA intergenic spacer was sequenced for 13 additional species of Arceuthobium representing both Old and New World taxa. All species examined had pseudogenes for trnI and trnA, however, deletions in these tRNAs have occurred in different regions among various lineages of the genus. The aligned 16S-23S rDNA intergenic spacer was analyzed using maximum parsimony and compared with nuclear ITS rDNA using a similar suite of species. Overall species relationships were generally congruent, although two cases of potential lineage sorting or chloroplast capture were detected. Arceuthobium is a valuable genetic model to contrast with holoparasites because, despite significant alteration and truncation of its plastome, it still maintains photosynthetic function.

Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants

Background

Some of the most difficult phylogenetic questions in evolutionary biology involve identification of the free-living relatives of parasitic organisms, particularly those of parasitic flowering plants. Consequently, the number of origins of parasitism and the phylogenetic distribution of the heterotrophic lifestyle among angiosperm lineages is unclear.

Results

Here we report the results of a phylogenetic analysis of 102 species of seed plants designed to infer the position of all haustorial parasitic angiosperm lineages using three mitochondrial genes: atp1, coxI, and matR. Overall, the mtDNA phylogeny agrees with independent studies in terms of non-parasitic plant relationships and reveals at least 11 independent origins of parasitism in angiosperms, eight of which consist entirely of holoparasitic species that lack photosynthetic ability. From these results, it can be inferred that modern-day parasites have disproportionately evolved in certain lineages and that the endoparasitic habit has arisen by convergence in four clades. In addition, reduced taxon, single gene analyses revealed multiple horizontal transfers of atp1 from host to parasite lineage, suggesting that parasites may be important vectors of horizontal gene transfer in angiosperms. Furthermore, in Pilostyles we show evidence for a recent host-to-parasite atp1 transfer based on a chimeric gene sequence that indicates multiple historical xenologous gene acquisitions have occurred in this endoparasite. Finally, the phylogenetic relationships inferred for parasites indicate that the origins of parasitism in angiosperms are strongly correlated with horizontal acquisitions of the invasive coxI group I intron.

Conclusion

Collectively, these results indicate that the parasitic lifestyle has arisen repeatedly in angiosperm evolutionary history and results in increasing parasite genomic chimerism over time.

Mitochondrial matR sequences help to resolve deep phylogenetic relationships in rosids

Background

Rosids are a major clade in the angiosperms containing 13 orders and about one-third of angiosperm species. Recent molecular analyses recognized two major groups (i.e., fabids with seven orders and malvids with three orders). However, phylogenetic relationships within the two groups and among fabids, malvids, and potentially basal rosids including Geraniales, Myrtales, and Crossosomatales remain to be resolved with more data and a broader taxon sampling. In this study, we obtained DNA sequences of the mitochondrial matR gene from 174 species representing 72 families of putative rosids and examined phylogenetic relationships and phylogenetic utility of matR in rosids. We also inferred phylogenetic relationships within the "rosid clade" based on a combined data set of 91 taxa and four genes including matR, two plastid genes (rbcL, atpB), and one nuclear gene (18S rDNA).

Results

Comparison of mitochondrial matR and two plastid genes (rbcL and atpB) showed that the synonymous substitution rate in matR was approximately four times slower than those of rbcL and atpB; however, the nonsynonymous substitution rate in matR was relatively high, close to its synonymous substitution rate, indicating that the matR has experienced a relaxed evolutionary history. Analyses of our matR sequences supported the monophyly of malvids and most orders of the rosids. However, fabids did not form a clade; instead, the COM clade of fabids (Celastrales, Oxalidales, Malpighiales, and Huaceae) was sister to malvids. Analyses of the four-gene data set suggested that Geraniales and Myrtales were successively sister to other rosids, and that Crossosomatales were sister to malvids.

Conclusion

Compared to plastid genes such as rbcL and atpB, slowly evolving matR produced less homoplasious but not less informative substitutions. Thus, matR appears useful in higher-level angiosperm phylogenetics. Analysis of matR alone identified a novel deep relationship within rosids, the grouping of the COM clade of fabids and malvids, which was not resolved by any previous molecular analyses but recently suggested by floral structural features. Our four-gene analysis supported the placements of Geraniales, Myrtales at basal nodes of the rosid clade and placed Crossosomatales as sister to malvids. We also suggest that the core part of rosids should include fabids, malvids and Crossosomatales.

Phylogeny of the Oxycoryninae sensu lato (Coleoptera:Belidae) and evolution of host-plant associations

Phylogenetic relationships among the genera of the subfamily Oxycoryninae and other belids (Curculionoidea) were reconstructed by cladistic analysis using 21 terminals and 98 characters: 62 from imaginal morphology, 33 from larval morphology and three biological characters relating to host plants and larval feeding habits. Terminal taxa represent all extant genera of Oxycoryninae, two genera of each of the three tribes of Belinae plus two outgroup taxa used to root the tree. New information on the larvae and biology of the metrioxenines is used in phylogenetic reconstruction. In accord with the single optimal cladogram obtained, a revised classification of the Oxycoryninae is proposed. The subfamily is classified into three tribes (Oxycorynini, Metrioxenini and Aglycyderini), with the tribe Oxycorynini further classified into three subtribes (Oxycraspedina Marvaldi & Oberprieler, subtr. nov., Oxycorynina and Allocorynina) and the tribe Metrioxenini into two subtribes (Metrioxenina and Afrocorynina ( = Hispodini, syn. nov.)). Larval and adult unambiguous synapomorphies defining each clade are identified. Tracing the evolution of biological traits from the phylogenetic estimate indicates that drastic shifts to phylogenetically distant host plants occurred from the ancestral belid association with conifers. Structural, chemical and/or ecological similarities of the plant organs consumed apparently had a major influence in the colonisation of different plant taxa by this group of weevils.