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PubMed2025

Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae).

Whereas genome sequencing and assembly technologies are improving, cost can still be prohibitive for plant species with large, complex genomes. As a consequence, genomics work on some taxa in evolutionarily pivotal positions in the vascular plant tree of life has been hampered. The species-rich genus Ranunculus (Ranunculaceae) is an important angiosperm group for the study of polyploidy, apomixis, and reticulate evolution. However, neither mitochondrial nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) and PacBio (HiFi) long-read, and hybrid-read assembly strategies. We sequenced the diploid progenitor species R. cassubicifolius (R. auricomus species complex) and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., infA, ycf15, or rps) with evolutionary implications. For the nuclear genome sequence, we favored a PacBio-based assembly polished three times with filtered short reads and subsequently scaffolded into eight pseudochromosomes by chromatin conformation data (Hi-C). We obtained a haploid genome sequence of 2.69 Gbp, with 94.1% complete BUSCO genes found and 35 482 annotated genes, and inferred ancient gene duplications compared to existing Ranunculales genomes. The genomic information presented here will enable advanced evolutionary-functional analyses for the species complex, but also for the genus and beyond Ranunculaceae.

Ranunculus↗

PubMed2006

[Preliminary pharmaphylogenetic study on Ranunculaceae].

OBJECTIVE: To deal with the correlation between phylogeny, chemical constituents and pharmaceutical aspects of Ranunculaceae, namely a pharmaphylogenic study of this taxon. METHOD: Based on chemical, pharmaceutical (both ethnopharmacologic and pharmacological) information, linking with different plant systems of Ranunculaceae. RESULT: Chemical constituents of this taxon included several natural groups: benzylisoquinoline alkaloid, ranunculin, triterpenoid glycoside and diterpene alkaloid etc. Ranunculin and magoflorine were found to present simultaneously in some plants of this taxon. CONCLUSION: Combining with therapeutic information, pharmaphylogenic research were in accordance with the phylogenetic system presented by Tamura that Ranunculaceae was proposed to be divided into six sub-families: Helleboroideae, Ranunculoideae, Cimicfugoideae, Isopyroideae, Thalictroideae and Coptidoideae. Results also supported the establishment of Cimicifugoideae.

Benzylisoquinolines↗

PubMed2006

[Pharmaphylogenetic study on isopyroideae (Ranunculaceae)].

OBJECTIVE: To study the pharmaphylogenetic of medicinal plants of Isopyroideae (Ranunculaceae). METHOD: Comprehensively analyze the correlation between phylogeny, chemical constituents and pharmaceutical aspects of Isopyroideae plants, based on chemical, pharmaceutical (both ethnopharmacologic and pharmacological) information, linking with different plant systems of Ranunculaceae. RESULT: Plants from Aquilegia mainly contain flavonoids constituents while the major chemical constituents of Isopyrum are bisbenzylisoquinoline alkaloids. Chemical characteristics also support that this taxon should be separated from Thalictrodeae, and constituted an independent subfamily, namely, Isopyroideae.

Anti-Infective Agents↗

PubMed1997

Molecular phylogenetic study of the Ranunculaceae: utility of the nuclear 26S ribosomal DNA in inferring intrafamilial relationships.

There are only a small number of molecular markers currently proven to be useful for phylogenetic inference within the flowering plants. We demonstrate that the 5' end of the 26S ribosomal DNA (ca. 1100 bp) is of great value for investigating generic to subfamilial relationships. We analyzed DNA sequences from 31 species of the Ranunculaceae and four species of the Berberidaceae to test phylogenetic relationships within the Ranunculaceae. The inferred phylogeny strongly supports the concept that the Thalictrum chromosome group is not monophyletic, but consists of three independent lineages: (1) Hydrastis, (2) Xanthorhiza and Coptis, and (3) Thalictrum, Aquilegia, and Enemion. Based on comparison with conventional taxonomic characters, we propose a hypothesis that the third group also includes the rest of the Thalictrum chromosome taxa that have a base chromosome number of seven. For the Ranunculus chromosome group, our study suggests several relationships that have not been recognized by conventional systematics. The inferred 26S rDNA topology is compared with results from two previously published molecular data sets: DNA sequences from rbcL, atpB, and 18S rDNA genes and restriction fragment length polymorphism data from chloroplast DNA. The three topologies are highly congruent and agree with karyological characters, but not with fruit type, both of which have often been used for the higher classification of the Ra- nunculaceae.

Base Sequence↗

PubMed2005

Inhibition of COXs and 5-LOX and activation of PPARs by Australian Clematis species (Ranunculaceae).

The species of Clematis (Ranunculaceae) have been traditionally used for inflammatory conditions by indigenous Australians. We have previously reported that the ethanol extract of Clematis pickeringii inhibited COX-1. In this study, we examined the ethanol extracts and fractions of three Clematis species, Clematis pickeringii, Clematis glycinoides and Clematis microphylla, on cyclooxygenase-1 (COX-1), cyclooxygenase-2 (COX-2) and 5-lipoxygenase (5-LOX). We further examined the activating effects on the protein expression of peroxisome proliferator-activated receptor alpha (PPARalpha) and gamma (PPARgamma) in HepG2 cells. The ethanol extracts of three Clematis species inhibited the activities of COX-1, COX-2 and 5-LOX in the different extents. The stem extract of Clematis pickeringii showed the highest inhibitory activities among the three species on COX-1, COX-2 and 5-LOX with the IC(50) values of 73.5, 101.2 and 29.3 microg/mL. One of its fractions also significantly elevated PPARalpha expression by 173, 280 and 435% and PPARgamma expression by 140, 228 and 296% at 4, 8 and 16 microg/mL, respectively.

Animals↗

PubMed2007

Endosperm formation in aposporous Crataegus (Rosaceae, Spiraeoideae, tribe Pyreae): parallels to Ranunculaceae and Poaceae.

Apomixis in Crataegus is primarily aposporous and requires pollination. The embryo sac is of the Polygonum type. A combination of meiotically unreduced embryo sacs with apparently reduced pollen would violate the usual requirement for a 2 : 1 ratio of maternal to paternal contributions to the endosperm. We therefore investigated the origin of endosperm in seeds of sexual diploids and apomictic polyploids of the sister genera Crataegus and Mespilus. Flow-cytometric DNA measurements from embryo and endosperm in mature seeds were converted to ploidy levels using leaf-tissue information. The diploids had triploid endosperm. In c. 60% of seed from polyploids, one sperm apparently contributes to the endosperm, while 25% or more may involve two sperm. Additional results suggest that trinucleate central cells also occur. Fertilization of meiotically unreduced eggs is indicated. The ratio of maternal to paternal contributions to the endosperm in these apomictic Crataegus is not constrained to 2 : 1. They thus resemble some Sorbus (Pyreae) and very distantly related Ranunculus (Ranunculaceae). It is suggested that Paspalum (Poaceae) may have similarly flexible endosperm ploidy levels.

Crataegus↗

PubMedDate not supplied

Phytodermatitis caused by Ceratocephalus falcatus (Ranunculacea).

Ceratocephalus falcatus is a member of Ranunculacea family that forms part of the flora of the Sinanpasa and Dinar regions of Afyon city in Turkey. Ceratocephalus falcatus has laxative properties and has been used for treating hemorrhoids, rheumatismal diseases and wounds. Here, a case of phytodermatitis caused by this remedy used for relieving knee pain is presented. This plant should be kept in mind when a case of phytodermatitis with vesicles or bullae presents at clinics.

Dermatitis, Irritant↗

PubMed2003

Evaluation of diuretic activity of the constituents of Clematis montevidensis Spreng. (Ranunculaceae) in rats.

The effects of Clematis montevidensis Spreng. (Ranunculaceae) on urinary excretion of water, sodium and potassium were investigated in rats loaded with isotonic saline solution. The data reported in the present work indicate that the infusions of the root and aerial part of Clematis montevidensis showed a moderate diuretic activity. This effect could be due, at least in part, to the presence of oleanolic acid isolated from this plant.

Animals↗

PubMed1984

Counter-irritant and other medicinal uses of plants in Ranunculaceae by native peoples in British Columbia and neighbouring areas.

At least 20 species in Ranunculaceae, the buttercup family, are reported as having been used medicinally by 19 different groups of native peoples in British Columbia and adjacent areas. These species are known to contain the skin-irritating, blister-causing compound, protoanemonin, in their fresh state. Protoanemonin is almost certainly the active principle involved in many of these medicinal applications. A majority involved the use of the plants as external poultices for boils, cuts, abrasions and other skin sores. Other disorders having a high frequency of treatment with ranunculaceous species include: muscular aches, colds and other respiratory ailments, and general, unspecified illness. Native groups in other parts of North America also used many ranunculaceous species as poultices, and for colds, headaches and many other ailments. A number were used for stimulation and "revival" of unconscious persons. It is suggested that the protoanemonin contained in these plants may have, through several different mechanisms, positively influenced the healing process physiologically and not just psychologically. If future research confirms this, these protoanemonin containing plants may have potential in certain treatments in modern medicine.

British Columbia↗

PubMed2005

Plant traits, environmental factors, and pollinator visitation in winter-flowering Helleborus foetidus (Ranunculaceae).

BACKGROUND AND AIMS: This study examined the effect of plant traits and environmental factors on pollinator visitation in the winter-flowering Helleborus foetidus (Ranunculaceae) in three distant regions in the Iberian Peninsula. METHODS: Geographical variation in floral visitor assemblage, plant traits and environmental factors were analysed during the flowering season. KEY RESULTS: Differences were found in all plant traits measured (number of open flowers, flower size, number of stamens per flower, and number of nectaries) both within and among regions, and differences among regions in all the environmental factors considered (air temperature, exposure to sunlight, canopy cover, and distance to the nearest neighbour). Differences were also found among regions in the probability that plants would be visited by pollinators. CONCLUSIONS: The results show that, although floral display (i.e. number of open flowers on a plant on a given day) consistently explained among-plant differences in visitation rate in all regions, visitation rate was not significantly affected by any other biological or environmental variable. In Helleborus foetidus, then, 'how' the plant is would seem to be more important than 'where' is it.

Animals↗

PubMed2004

Experimental dissection of inbreeding and its adaptive significance in a flowering plant, Aquilegia canadensis (Ranunculaceae).

Inbreeding is a major component of the mating system in populations of many plants and animals, particularly hermaphroditic species. In flowering plants, inbreeding can occur through self-pollination within flowers (autogamy), self-pollination between flowers on the same plant (geitonogamy), or cross-pollination between closely related individuals (biparental inbreeding). We performed a floral emasculation experiment in 10 populations of Aquilegia canadensis (Ranunculaceae) and used allozyme markers to estimate the relative contribution of each mode of inbreeding to the mating system. We also examined how these modes of inbreeding were influenced by aspects of population structure and floral morphology and display predicted to affect the mating system. All populations engaged in substantial inbreeding. On average, only 25% of seed was produced by outcrossing (range among populations = 9-37%), which correlated positively with both population size (r = +0.61) and density (r = +0.64). Inbreeding occurred through autogamy and biparental inbreeding, and the relative contribution of each was highly variable among populations. Estimates of geitonogamy were not significantly greater than zero in any population. We detected substantial biparental inbreeding (mean = 14% of seeds, range = 4-24%) by estimating apparent selfing in emasculated plants with no opportunity for true selfing. This mode of inbreeding correlated negatively with population size (r = -0.87) and positively with canopy cover (r = +0.90), suggesting that population characteristics that increase outcross pollen transfer reduce biparental inbreeding. Autogamy was the largest component of the mating system in all populations (mean = 58%, range = 37-84%) and, as expected, was lowest in populations with the most herkogamous flowers (r = -0.59). Although autogamy provides reproductive assurance in natural populations of A. canadensis, it discounts ovules from making superior outcrossed seed. Hence, high autogamy in these populations seems disadvantageous, and therefore it is difficult to explain the extensive variation in herkogamy observed both among and especially within populations.

Adaptation, Biological↗

PubMed2026

The genome sequence of Aquilegia vulgaris L., 1753 (Ranunculales: Ranunculaceae).

We present a genome assembly of Aquilegia vulgaris (Columbine; Streptophyta; Magnoliopsida; Ranunculales; Ranunculaceae). The assembly consists of two haplotypes with total lengths of 296.10 megabases and 289.22 megabases. Most of haplotype 1 (98.81%) is scaffolded into 7 chromosomal pseudomolecules. Most of haplotype 2 (94.35%) is scaffolded into 7 chromosomal pseudomolecules. The mitochondrial sequences have lengths of 388.22 and 83.91 kilobases and the plastid genome assembly has a length of 161.5 kilobases. Gene annotation of this assembly on Ensembl identified 23 898 protein-coding genes. This assembly was generated as part of the Darwin Tree of Life project, which produces reference genomes for eukaryotic species found in Britain and Ireland.

Aquilegia vulgaris↗

PubMed1989

[Medicinal plant resources of Ranunculaceae in Zhejiang Province].

This paper reports the general situation on medicinal plant resources of Ranunculaceae in Zhejiang. There are 13 genera and 51 species (including varieties). Suggestions have been made with regard to the preservation, development and utilization of the natural resources.

China↗

PubMed2005

Nuclear DNA content in the genus Hepatica (Ranunculaceae).

Using flow cytometry, we measured the nuclear DNA contents of all known taxa in Hepatica. Nuclear DNA content of Hepatica falconeri (diploid, crenate leaf lobes) was significantly lower than that of diploid entire species. Among the tetraploid species, crenate species had lower DNA contents than the entire taxon H. nobilis var. pubescens. The DNA content of the tetraploid species was more than double that of the diploid species among the same leaf-type groups.

Cell Nucleus↗

PubMed2002

Geographic pattern of genetic variation in the European globeflower Trollius europaeus L. (Ranunculaceae) inferred from amplified fragment length polymorphism markers.

The distribution of genetic variation and the phylogenetic relationships between 18 populations of the arctic-alpine plant Trollius europaeus were analysed in three main regions (Alps, Pyrenees and Fennoscandia) by using dominant AFLP markers. Analysis of molecular variance revealed that most of the genetic variability was found within populations (64%), although variation among regions (17%) and among populations within regions (19%) was highly significant (P < 0.001). Accordingly, the global fixation index FST averaged over loci was high (0.39). The among-population differentiation indicates restricted gene flow, congruent with limited dispersal of specific globeflower's pollinating flies (Chiastocheta spp.). Within-population diversity levels were significantly higher in the Alps (mean Nei's expected heterozygosity HE = 0.229) than in the Pyrenees (HE= 0.197) or in Fennoscandia (HE = 0.158). This finding is congruent with the species-richness of the associated flies, which is maximum in the Alps. We discuss the processes involved in shaping observed patterns of genetic diversity within and among T. europaeus populations. Genetic drift is the major factor acting on the small Pyrenean populations at the southern edge of T. europaeus distribution, while large Fennoscandian populations result probably from a founder effect followed by demographic expansion. The Alpine populations represent moderately fragmented relics of large southern ancestral populations. The patterns of genetic variability observed in the host plant support the hypothesis of sympatric speciation in associated flies, rather than recurrent allopatric speciations.

France↗

PubMed2003

Out of the Alps: colonization of Northern Europe by East Alpine populations of the Glacier Buttercup Ranunculus glacialis L. (Ranunculaceae).

Ranunculus glacialis ssp. glacialis is an arctic-alpine plant growing in central and southern European and Scandinavian mountain ranges and the European Arctic. In order to elucidate the taxon's migration history, we applied amplified fragment length polymorphism (AFLP) to populations from the Pyrenees, Tatra mountains and Northern Europe and included data from a previous study on Alpine accessions. Populations from the Alps and the Tatra mountains were genetically highly divergent and harboured many private AFLP fragments, indicating old vicariance. Whereas nearly all Alpine populations of R. glacialis were genetically highly variable, the Tatrean population showed only little variation. Our data suggest that the Pyrenees were colonized more recently than the separation of the Tatra from the Alps. Populations in Northern Europe, by contrast, were similar to those of the Eastern Alps but showed only little genetic variation. They harboured no private AFLP fragments and only a subset of East Alpine ones, and they exhibited no phylogeographical structure. It is very likely therefore that R. glacialis colonized Northern Europe in postglacial times from source populations in the Eastern Alps.

DNA Primers↗

PubMed2002

Allocation to floral structures in Thalictrum pubescens (Ranunculaceae), a cryptically dioecious species.

Females of Thalictrum pubescens produce stamens that contain sterile pollen, whereas males are both functionally and morphologically unisexual. This study examines the investment in stamen production by females of T. pubescens by comparing the female structures with those of their fully functional male counterparts. Stamens from females had the same biomass and contained the same amount of nitrogen and phosphorus as stamens from males. Anther size was the same in males and females, but filaments were longer in stamens from males. Females produced more pollen per anther than males, and pollen size was the same in both sexes. Within flowers, there was a positive correlation between the amount of pollen per anther and the length of anthers in males, but not in females. This would be expected if males growing in better environmental conditions or with greater vigour invested more resources in pollen production, thereby increasing fitness. Females, who receive no fitness benefits from increased pollen production, did not show this pattern. There was also evidence of a trade-off within female flowers between the number of stamens and the number of pistils. This trade-off was noted in conditions when variance among plants was reduced, namely in the field during a year when flower size was particularly small and in a previous glasshouse study. Therefore, it appears that when environmental variance is low, stamens are produced at the expense of producing more pistils, and hence seeds. In conclusion, stamen production does not appear to be inconsequential to females of Thalictrum pubescens.

Pollen↗

PubMed2005

Floral MADS box genes and homeotic gender dimorphism in Thalictrum dioicum (Ranunculaceae) - a new model for the study of dioecy.

In most dioecious angiosperm species, flowers are initially perfect but abort either stamens or carpels during their development, indicating that sex determination occurs after floral organ identity has been established. Dioecious members of the genus Thalictrum (meadow-rue), however, produce flowers that lack aborted organs. Examination of early flower development of T. dioicum confirms that flowers are male or female from inception, raising the possibility that genetic mechanisms working at or above the level of organ identity promote sex determination through a homeotic-like mechanism. In order to investigate this possibility, we identified homologs of the organ identity genes PISTILLATA (PI), APETALA3 (AP3) and AGAMOUS (AG) from T. dioicum and the hermaphroditic species T. thalictroides. A combination of early and late duplication events was uncovered in these gene lineages and expression analyses indicate that these events are generally associated with divergence in gene regulation. In light of these findings, we discuss the potential of T. dioicum as a new model for the study of sex determination in the basal eudicots.

Amino Acid Sequence↗