A molecular phylogenetic study of southern African Apiaceae

It has been suggested that southern Africa is the origin of the predominantly herbaceous Apiaceae subfamily Apioideae and that the woody habit is plesiomorphic. We expand previous molecular phylogenetic analyses of the family by considering all but three of the approximately 38 genera native to southern Africa, including all genera whose members, save one, have a woody habit. Representatives of five other genera are included because they may be closely related to these southern African taxa. Chloroplast DNA rps16 intron and/or nuclear rDNA ITS sequences for 154 accessions are analyzed using maximum parsimony, Bayesian, and maximum likelihood methods. Within Apioideae, two major clades hitherto unrecognized in the subfamily are inferred. The monogeneric Lichtensteinia clade is sister group to all other members of the subfamily, whereas the Annesorhiza clade (Annesorhiza, Chamarea, and Itasina) plus Molopospermum (and Astydamia in the ITS trees) are the successive sister group to all Apioideae except Lichtensteinia. Tribe Heteromorpheae is expanded to include Pseudocarum, "Oreofraga" ined., and five genera endemic to Madagascar. The southern African origin of subfamily Apioideae is corroborated (with subsequent migration northward into Eurasia along two dispersal routes), and the positions of the herbaceous Lichtensteinia and Annesorhiza clades within the subfamily suggest, surprisingly, that its ancestor was herbaceous, not woody.     

Molecular evolution of flavonoid dioxygenases in the family Apiaceae

Plant species of the family Apiaceae are known to accumulate flavonoids mainly in the form of flavones and flavonols. Three 2-oxoglutarate-dependent dioxygenases, flavone synthase or flavanone 3 beta-hydroxylase and flavonol synthase are involved in the biosynthesis of these secondary metabolites. The corresponding genes were cloned recently from parsley (Petroselinum crispum) leaves. Flavone synthase I appears to be confined to the Apiaceae, and the unique occurrence as well as its high sequence similarity to flavanone 3beta-hydroxylase laid the basis for evolutionary studies. In order to examine the relationship of these two enzymes throughout the Apiaceae, RT-PCR based cloning and functional identification of flavone synthases I or flavanone 3beta-hydroxylases were accomplished from Ammi majus, Anethum graveolens, Apium graveolens, Pimpinella anisum, Conium maculatum and Daucus carota, yielding three additional synthase and three additional hydroxylase cDNAs. Molecular and phylogenetic analyses of these sequences were compatible with the phylogeny based on morphological characteristics and suggested that flavone synthase I most likely resulted from gene duplication of flavanone 3beta-hydroxylase, and functional diversification at some point during the development of the apiaceae subfamilies. Furthermore, the genomic sequences from Petroselinum crispum and Daucus carota revealed two introns in each of the synthases and a lack of introns in the hydroxylases. These results might be explained by intron losses from the hydroxylases occurring at a later stage of evolution.     

Bias and conflict in phylogenetic inference of myco-heterotrophic plants: a case study in Thismiaceae

Due to morphological reduction and absence of amplifiable plastid genes, the identification of photosynthetic relatives of heterotrophic plants is problematic. Although nuclear and mitochondrial gene sequences may offer a welcome alternative source of phylogenetic markers, the presence of rate heterogeneity in these genes may introduce bias/systematic error in phylogenetic analyses. We examine the phylogenetic position of Thismiaceae based on nuclear 18S rDNA and mitochondrial atpA DNA sequence data, as well as using parsimony, likelihood and Bayesian inference methods. Significant differences in evolutionary rates of these genes between closely related taxa lead to conflicting results: while parsimony analyses of 18S rDNA and combined data strongly support the monophyly of Thismiaceae, Bayesian inference, with and without a relaxed molecular clock, as well as the Swofford–Olsen–Waddell–Hillis (SOWH) test confidently reject this hypothesis. We show that rate heterogeneity in our data leads to long-branch attraction artifacts in parsimony analysis. However, using model-based inference methods the question of whether Thismiaceae are monophyletic remains elusive. On the one hand maximum likelihood nonparametric bootstrapping and parametric hypothesis tests fail to support a paraphyletic Thismiaceae, on the other hand Bayesian inference methods (both without and with a relaxed clock) significantly reject a monophyletic Thismiaceae. These results show that an adequate sampling, the use of rate homogeneous data, and the application of different inference methods are important factors for developing phylogenetic hypotheses of myco-heterotrophic plants. © The Willi Hennig Society 2009.     

药用植物中UGT家族研究进展

尿苷二磷酸葡萄糖醛酸转移酶(UDP-glucuronosyltransferase,UGT)家族是植物体内最大的糖基转移酶家族。编码合成UGT的基因属于UGT基因家族。UGT催化的糖基化反应广泛地存在于药用植物次生代谢物质的合成过程中。作为代谢通路中的下游修饰,供体分子在UGT的催化下,将糖基连接到受体分子上。这一过程往往会改变终产物的理化及生物学性质,最终影响其实际的利用价值及利用方式。本文综述分析了药用植物UGT家族基因挖掘分析、功能验证和生产应用等方面近年来的研究进展。     

Root cryopreservation to biobank medicinal plants: a case study for Hypericum perforatum L.

In this study, an effective root-based cryopreservation method was developed for Hypericum perforatum L., an important medicinal species, using in vitro plants. A systematic approach was applied to determine effective combinations of protocol steps such as preculture, osmoprotection, vitrification solution treatment, and unloading, followed by protocol optimization using a single-factor approach. The effects of root section type (root tips, middle sections, or basal sections), duration of root section culture after excision, and donor plant age were also investigated. In a wild genotype, middle and basal root sections excised from 8-wk-old plants and cryopreserved at the age of 10 d after excision showed the highest plant regrowth after cryopreservation. In the optimized protocol, root sections were precultured in 10% (w/v) sucrose for 17 h, osmoprotected with a solution composed of 17.5% (w/v) glycerol and 17.5% (w/v) sucrose for 20 min, followed by a vitrification solution of 40% (w/v) glycerol and 40% (w/v) sucrose for 30 min, and cryopreserved using aluminum foil strips (droplet-vitrification). After rewarming in preheated 25% (w/v) sucrose solution and 30-min unloading, root segments were recovered on medium supplemented with 1.0 mg L⁻¹ gibberellic acid and showed 78% plant regrowth. This cryopreservation method was successfully adapted for five elite lines of H. perforatum with a 45 to 87% regrowth rate after cryopreservation. These results suggest that root cryopreservation may be an effective method for medicinal plant conservation and should be tested with a broader range of species.

     

Molecular mechanisms and hormonal regulation underpinning morphological dormancy: a case study using Apium graveolens (Apiaceae)

Underdeveloped (small) embryos embedded in abundant endosperm tissue, and thus having morphological dormancy (MD) or morphophysiological dormancy (MPD), are considered to be the ancestral state in seed dormancy evolution. This trait is retained in the Apiaceae family, which provides excellent model systems for investigating the underpinning mechanisms. We investigated Apium graveolens (celery) MD by combined innovative imaging and embryo growth assays with the quantification of hormone metabolism, as well as the analysis of hormone and cell-wall related gene expression. The integrated experimental results demonstrated that embryo growth occurred inside imbibed celery fruits in association with endosperm degradation, and that a critical embryo size was required for radicle emergence. The regulation of these processes depends on gene expression leading to gibberellin and indole-3-acetic acid (IAA) production by the embryo and on crosstalk between the fruit compartments. ABA degradation associated with distinct spatiotemporal patterns in ABA sensitivity control embryo growth, endosperm breakdown and radicle emergence. This complex interaction between gibberellins, IAA and ABA metabolism, and changes in the tissue-specific sensitivities to these hormones is distinct from non-MD seeds. We conclude that the embryo growth to reach the critical size and the associated endosperm breakdown inside MD fruits constitute a unique germination programme.     

Genetic diversity study of some medicinal plant accessions belong to Apiaceae family based on seed storage proteins patterns

Cumin (Cuminum cyminum L.), Fennel (Foeniculum vulgare L.) and Longleaf (Falcaria vulgaris Bernh) that all belong to Apiaceae family as medicinal plants are very important in many countries. Study of genetic diversity for medicinal plant is important for researches in future. One of the methods to evaluate plant genetic diversity and classification of them is the electrophoresis of seed storage proteins. This research was conducted in order to evaluate seed protein variability in different Iranian Cumin, Fennel and Longleaf accessions and grouping them based on these proteins as a biochemical marker. For this purpose, the samples were first powdered in liquid nitrogen and seed protein was extracted with extraction buffer. Then total soluble proteins were resolved on 12.5?% sodium dodecyl sulphate polyacrylamide gel electrophoresis gels. The electrophoretic protein pattern showed 38 bands that were low polymorphism among the accessions. The result of cluster analysis showed that the accessions were classified in three groups (all 29 Cumin accessions in the first group, three Fennel ecotypes in second group and three Longleaf accessions in the last one).     

The phylogenetic significance of the carpophore in Apiaceae

Background and aims

Fruit structural characters have traditionally been important in the taxonomy of the family Apiaceae. Previous investigations using a limited number of taxa have shown that the carpophore may be especially useful in helping to circumscribe subfamily Azorelloideae. The present study examines, for the first time, carpophore structure in 92 species from 43 genera, representing all subfamilies of Apiaceae, and including all genera assigned to subfamily Azorelloideae. Phylogenetic interpretations are made for the first time, using all available information, and a standard terminology is proposed to describe the various character states found in carpophores.

Methods

Carpophore structure was studied in detail using light microscopy.

Key Results

Carpophores, when present, may be categorized into two main groups (B and C) based mainly on the arrangement of the vascular bundles in transverse section, and further divided into six sub-types according to the length of the carpophore (short in B1 and C1) and whether they are entire (B1–B3 and C1) or bifurcate (B4 and C2). Free carpophores are absent in subfamily Mackinlayoideae, and in tribes Lichtensteinieae and Phlyctidocarpeae, which have two opposite vascular bundles (Group A). Entire carpophores with one or two vascular bundles, or bifurcate carpophores with lateral vascular bundles (arranged side by side within the commissural plane), are the main types characterizing Azorelloideae. The short, hygroscopic carpophores found in Choritaenia are unique in Apiaceae and provide additional evidence for the exclusion of this genus from Azorelloideae. Carpophore type C2 is typical for most Apioideae sensu lato (exceptions are, for example, Arctopus and Alepidea, which have type B2).

Conclusions

A single carpophore and ventral vascular bundles not forming free carpophores are proposed to be the ancestral conditions in Apiaceae, while bifurcate carpophores with opposite vascular bundles are the derived state, present in most Apioideae. Secondary reductions seem to have occurred in several unrelated lineages in all major groups, e.g. many Azorelloideae, several protoapioids (including nearly all members of the tribe Saniculeae) and 29 euapioid genera (e.g. some Oenantheae).     

Molecular perspective and anticancer activity of medicinal plants

To evaluate phytochemical constituents from the methanolic extracts of medicinal plants Aloe castellorum and Aloe pseudorubroviolacea. The cytotoxic activity of Aloe castellorum and Aloe pseudorubroviolacea leaf extracts against Human colon cancer cell line (HCT-116) was also assessed. The two medicinal plant extracts having significant cytotoxic activity, meanwhile the methanolic extract of Aloe castellorum shows higher cytotoxic activity than Aloe pseudorubroviolacea extract. The Aloe castellorum shows remarkable activity against respective cell line than control. The characteristic chemical constituents of Aloe castellorum and Aloe pseudorubroviolacea leaf extracts were recognized from Gas chromatography and Mass spectrometry (GC–MS) technique. The molecular docking studies also support the cytotoxic activity.     

Molecular evolution and phylogenetic utility of the petD group II intron: a case study in basal angiosperms

Sequences of spacers and group I introns in plant chloroplast genomes have recently been shown to be very effective in phylogenetic reconstruction at higher taxonomic levels and not only for inferring relationships among species. Group II introns, being more frequent in those genomes than group I introns, may be further promising markers. Because group II introns are structurally constrained, we assumed that sequences of a group II intron should be alignable across seed plants. We designed universal amplification primers for the petD intron and sequenced this intron in a representative selection of 47 angiosperms and three gymnosperms. Our sampling of taxa is the most representative of major seed plant lineages to date for group II introns. Through differential analysis of structural partitions, we studied patterns of molecular evolution and their contribution to phylogenetic signal. Nonpairing stretches (loops, bulges, and interhelical nucleotides) were considerably more variable in both substitutions and indels than in helical elements. Differences among the domains are basically a function of their structural composition. After the exclusion of four mutational hotspots accounting for less than 18% of sequence length, which are located in loops of domains I and IV, all sequences could be aligned unambiguously across seed plants. Microstructural changes predominantly occurred in loop regions and are mostly simple sequence repeats. An indel matrix comprising 241 characters revealed microstructural changes to be of lower homoplasy than are substitutions. In showing Amborella first branching and providing support for a magnoliid clade through a synapomorphic indel, the petD data set proved effective in testing between alternative hypotheses on the basal nodes of the angiosperm tree. Within angiosperms, group II introns offer phylogenetic signal that is intermediate in information content between that of spacers and group I introns on the one hand and coding sequences on the other.     

Molecular systematics of the trans-Pacific alpine genus Oreomyrrhis (Apiaceae): phylogenetic affinities and biogeographic implications

The alpine ecosystem is the only terrestrial biogeographic unit that is distributed globally. Studying phylogenetics of the plant species in this widespread ecosystem can provide insights into the historical biogeographic processes that have shaped the global biodiversity. The trans-Pacific disjunct alpine genus Oreomyrrhis (Apiaceae) was investigated using nrDNA ITS sequences to test the taxonomic and biogeographic hypotheses. Phylogenetic analyses using maximum parsimony, maximum likelihood, and Bayesian inference revealed that species of Oreomyrrhis form a weakly supported monophyletic clade that is nested within Chaerophyllum sect. Chaerophyllum (subtribe Scandicinae, tribe Scandiceae). The optimal solutions of dispersal-vicariance analysis indicate that the ancestor of Chaerophyllum sect. Chaerophyllum (including Oreomyrrhis) was distributed in Eurasia and subsequently dispersed to North America and southern Pacific Rim. Based on dating using ITS sequence variation, these dispersal events were most likely recent, probably during late Tertiary to Quaternary. The structure of the ITS haplotype network suggests that a rapid range expansion via long-distance dispersal had been crucial in generating the trans-Pacific disjunction of Oreomyrrhis. Furthermore, evolution toward smaller mericarp size and a transition from outcrossing to selfing during Oreomyrrhis's evolution might have increased the chances for long-distance dispersal, facilitating its range expansion and occupation on alpine environments.     

Assessing conservation priorities of threatened medicinal plants in China: A new comprehensive phylogenetic scoring system

Over-harvesting, habitat loss and fragmentation, and biological invasions have led to a sharp decline in wild medicinal plants population in China, where they are an essential component of traditional medicine and used widely. The current national list of protected medicinal materials, the State Key-protected Wild Medicinal Species List (SKPWMSL), which has not been revised for 30 years, is in urgent need of an update. This study proposes a new scoring system with seven indicators that set the conservation priorities of threatened medicinal plants. The advantages of our approach include: (i) quantitative methods with high repeatability and comparability; and (ii) consideration of the evolutionary history of medicinal species. After assessing 911 threatened medicinal angiosperms in China, we identified 112 species as key medicinal plants for conservation priority (KMPCP). We suggest promoting the SKPWMSL with KMPCP as a supplement and update. Meanwhile, our scoring system will improve the future setting of conservation priority and can be extended to other countries or regions.     

Molecular approaches for improvement of medicinal and aromatic plants

Medicinal and aromatic plants (MAPs) are important sources for plant secondary metabolites, which are important for human healthcare. Improvement of the yield and quality of these natural plant products through conventional breeding is still a challenge. However, recent advances in plant genomics research has generated knowledge leading to a better understanding of the complex genetics and biochemistry involved in biosynthesis of these plant secondary metabolites. This genomics research also concerned identification and isolation of genes involved in different steps of a number of metabolic pathways. Progress has also been made in the development of functional genomics resources (EST databases and micro-arrays) in several medicinal plant species, which offer new opportunities for improvement of genotypes using perfect markers or genetic transformation. This review article presents an overview of the recent developments and future possibilities in genetics and genomics of MAP species including use of transgenic approach for their improvement.     

Molecular phylogenetic analysis of methylenetetrahydrofolate reductase family of proteins

Methylenetetrahydrofolate reductase (MTHFR) family of proteins catalyze the conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate. They contain a flavin adenine dinucleotide (FAD) as the cofactor and the enzyme in eukaryotes, except in yeast, is known to be allosterically regulated by S-adenosylmethionine. Some cardiovascular diseases, neural tube defects, neuropsychiatric diseases and certain type of cancers in humans are associated with certain polymorphisms of MTHFR. Here, we analyzed 57 of MTHFR polypeptide sequences by multiple sequence alignment and determined previously unrecognized conserved residues that may have a functional or structural importance. A previously unrecognized ATP synthase motif was found in all of the examined plant MTHFRs, suggesting a different functional capability to the plant MTHFRs in addition to the known function. On a phylogenetic tree built, eukaryotic MTHFR proteins formed a clear cluster separated from prokaryotic and archeal relatives. The sequence identities among the eukaryotic MTHFRs were less divergent than the bacterial MTHFRs.     

Directional biases in phylogenetic structure quantification: a Mediterranean case study

Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure, and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well‐resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that sensitivity of phylogenetic structure measures to low phylogenetic resolution can strongly vary depending on phylogenetic tree shape.     

Molecular phylogenetic position of podostemaceae, a marvelous aquatic flowering plant family

Podostemaceae are aquatic herbs and are famous for their anomalous vegetative morphology, occurring only in rapids. Because of its peculiar morphology, there were no established theory nor accepted opinion on the phylogenetic position. Especially, Cusset and Cusset (1988) proposed the new class, Podostemopsida beside the Magnollopsida and Liliopsida. We, therefore, consequences extensive and detailled analyses using nucleotide sequences ofrbcL genes for two genera and three species of the family together with many representatives of the families of flowering plants to determine the closest ally. The conclusion was that the Crassulaceae is a sister group to the Podostemaceae.