Genome size variation and evolution in the grape family Vitaceae

Genome size variation is of fundamental biological importance and has been a longstanding puzzle in evolutionary biology. In the present study, the genome size of 61 accessions corresponding to 11 genera and 50 species of Vitaceae and Leeaceae is determined using flow cytometry. Phylogenetically based statistical analyses were used to infer ancestral character reconstructions of nuclear DNA contents. The DNA 1C‐values of 38 species are reported for the first time, with the largest genome (Cyphostemma humile (N. E. Br.) Desc. ex Wild & R. B. Drumm, 1C = 3.25 pg) roughly 10.48‐fold larger than the smallest (Vitis vulpina L., 1C = 0.31 pg). The large genomes are restricted to the tribe Cayratieae, and most other extant species in the family possess relatively small genomes. Ancestral genome size reconstruction revealed that the most recent common ancestor for the family had a relatively small genome (1C = 0.85 pg). Genome evolution in Vitaceae has been characterized by a trend towards genome size reduction, with just one episode of apparent DNA accumulation in the Cayratieae lineage. Such contrasting patterns of genome size evolution probably resulted from transposable elements and chromosome rearrangements, while neopolyploidization seems to contribute to recent genome increase in some species at the tips in the family tree.     

Occurrence of Crassulacean acid metabolism in Cissus trifoliata L. (Vitaceae)

Summary Evidence for the operation of CAM in the deciduous climber, Cissus trifoliata L., was obtained in field and laboratory studies. Under natural conditions, diurnal oscillations of titratable acidity and colorimetric measurements of night CO₂ fixation, determined for a period of two and a half years, suggested that acid accumulation was related to plant water status, assessed through the daily courses of stomatal resistance and xylem water potential during dry and rainy seasons. These findings were confirmed by gas exchange studies under controlled conditions which showed that the plant fixed all its CO₂ during the day when it was well irrigated; as water stress increased, dark CO₂ uptake gradually replaced fixation during the day until the plant only performed dark fixation. In severe water stress, even the rate of the latter process decreased until leaves fell.Abbreviations CAM Crassulacean acid metabolism - FW leaf fresh weight - SWC relative soil water content - PAR photosynthetically active radiation - TR total radiation; r, leaf diffusive resistance - WSD water saturation deficit (leaf-air vapour concentration difference) - RWC relative water content of leaves     

白粉藤的木脂素和三萜成分

从白粉藤（Cissus repens Lank）地上部分分离得到5个木脂素和8个三萜,其中一个木脂素是新化合物,它的结构通过波谱分析和碱水解的方法鉴定为：（＋）-异落叶松树脂醇-9′-（2-对-香豆酰）-O-β-D-吡喃木糖苷（1）。其余化合物分别是：（＋）-异落叶松树脂醇-9′-O-β-D-吡喃木糖苷（2）,（＋）-Lyoniside（3）,（—）-开环异落叶松树脂醇-9-O-β-D-吡喃木糖苷（4）,（7′R,8′S）-4′-hydroxy-3′,5-dimethoxy-7,8′-dihydrobenzofuran-1-propanolneolignan-9′-O-β-D-xylopyranoside（5）,木栓酮（6）,表木栓醇（7）,蒲公英赛醇乙酸酯（8）,熊果酸（9）,2α-羟基乌索酸（10）,积雪草酸（11）,Niga-ichigoside F1（12）,羽扇豆醇（13）。这些化合物都是首次从该植物中分离得到。     

A new phylogenetic tribal classification of the grape family (Vitaceae)

Vitaceae (the grape family) consist of 16 genera and ca. 950 species primarily distributed in tropical regions. The family is well‐known for the economic importance of grapes, and is also ecologically significant with many species as dominant climbers in tropical and temperate forests. Recent phylogenetic and phylogenomic analyses of sequence data from all three genomes have supported five major clades within Vitaceae: (i) the clade of Ampelopsis, Nekemias, Rhoicissus, and Clematicissus; (ii) the Cissus clade; (iii) the clade of Cayratia, Causonis, Cyphostemma, Pseudocayratia, Tetrastigma, and an undescribed genus “Afrocayratia”; (iv) the clade of Parthenocissus and Yua; and (v) the grape genus Vitis and its close tropical relatives Ampelocissus, Pterisanthes and Nothocissus, with Nothocissus and Pterisanthes nested within Ampelocissus. Based on the phylogenetic and morphological (mostly inflorescence, floral and seed characters) evidence, the new classification places the 950 species and 16 genera into five tribes: (i) tribe Ampelopsideae J.Wen & Z.L.Nie, trib. nov. (47 species in four genera; Ampelopsis, Nekemias, Rhoicissus and Clematicissus); (ii) tribe Cisseae Rchb. (300 species in one genus; Cissus); (iii) tribe Cayratieae J.Wen & L.M.Lu, trib. nov. (370 species in seven genera; Cayratia, Causonis, “Afrocayratia”, Pseudocayratia, Acareosperma, Cyphostemma and Tetrastigma); (iv) tribe Parthenocisseae J.Wen & Z.D.Chen, trib. nov. (ca. 16 spp. in two genera; Parthenocissus and Yua); and (v) tribe Viteae Dumort. (ca. 190 species in two genera; Ampelocissus and Vitis).     

Phylogenetic analysis of Toxicodendron （Anacardiaceae） and its biogeographic implications on the evolution of north temperate and tropical intercontinental disjunctions

Toxicodendron is a genus in the Rhus complex of Anacardiaceae with a disjunct distribution between eastern Asia and North America, extending to southeastern Asia and the neotropics. Nuclear （internal transcribed spacer, external transcribed spacer, and NIA-i3） and chloroplast （ndhF and trnL-F） sequences were used to construct phylogenetic relationships of Toxicodendron. Phylogenetic analysis of these data strongly support Toxieodendron as a monophyletic group distinct from other genera of the Rhus complex, and the phylogeny does not fully corroborate classification at the sectional level. Two temperate disjunct lineages were detected, one from section Toxicodendron and the other between the eastern North American Toxicodendron vernix and the eastern Asian Toxicodendron vernieifluum. Their divergence times were estimated to be 13.46 （7.95-19.42） and 7.53 （2.76-12.86） mya, respectively. The disjunction between section Griffithii （taxa from warm temperate to tropical Asia） and Toxieodendron striatum （from the neotropics） was supported and their divergence time was estimated to be 20.84 （11.1 6-30.52） mya in the early Miocene. Our biogeographic results and the paleontological data support the Bering land bridge as the most likely route to explain the temperate disjunctions, yet the tropical disjunction in Toxicodendron seems to be best explained by the North Atlantic land bridge hypothesis.     

A New Ceramide from Cissus Aralioides Baker (Vitaceae) and its Antimicrobial Activity

Purification through repeated column chromatography over silica gel and Sephadex LH-20 of the ethanol extract of the stems of Cissus aralioides (Baker) Planch. resulted in the isolation of a new ceramide, aralioidamide A ( 1 ), along with five known compounds ( 2–6 ). Their structures were determined by the extensive analyses of their spectroscopic (1D and 2D NMR) and spectrometric data, and comparison with those reported in the literature. Aralioidamide A ( 1 ) displayed weak antibacterial activity (MIC=256 μg/mL) against Bacillus subtilis, Staphylococcus aureus and Shigella flexneri and was inactive (MIC>256 μg/mL) against the tested fungi.     

Molecular phylogeny of the genus Vitis (Vitaceae) based on plastid markers

? Premise of the study: This work represents the first molecular phylogeny of the economically important genus Vitis, an important genetic resource for breeding in grapevine, Vitis vinifera. ? Methods: A molecular phylogeny of Vitis using a combined data set of three noncoding regions of the plastid DNA genome was constructed from 47 accessions covering 30 species of Vitis. The data for the trnL-F marker were combined with previously published data across the Vitaceae. ? Key results: The molecular phylogeny demonstrated monophyly of the genus Vitis. Based on the combined analysis of three genes, Vitis is split into three clades that mirror the continental distribution of these accessions. The diversity is highest in the Asian clade, but the general genetic distances across taxa from different continents are relatively small. ? Conclusions: The findings support a relatively recent and intense gene flow between East Asia and North America and the possible impact of hybridization on the evolution of the genus Vitis. Taxon identity in important stock collections should be screened carefully because roughly 10% of the accessions analyzed in the present study had been misidentified.     

Phylogenetic analysis of the grape family (Vitaceae) based on three chloroplast markers

Seventy-nine species representing 12 genera of Vitaceae were sequenced for the trnL-F spacer, 37 of which were subsequently sequenced for the atpB-rbcL spacer and the rps16 intron. Phylogenetic analysis of the combined data provided a fairly robust phylogeny for Vitaceae. Cayratia, Tetrastigma, and Cyphostemma form a clade. Cyphostemma and Tetrastigma are each monophyletic, and Cayratia may be paraphyletic. Ampelopsis is paraphyletic with the African Rhoicissus and the South American Cissus striata nested within it. The pinnately leaved Ampelopsis form a subclade, and the simple and palmately leaved Ameplopsis constitutes another with both subclades containing Asian and American species. Species of Cissus from Asia and Central America are monophyletic, but the South American C. striata does not group with other Cissus species. The Asian endemic Nothocissus and Pterisanthes form a clade with Asian Ampelocissus, and A. javalensis from Central America is sister to this clade. Vitis is monophyletic and forms a larger clade with Ampelocissus, Pterisanthes, and Nothocissus. The eastern Asian and North American disjunct Parthenocissus forms a clade with Yua austro-orientalis, a species of a small newly recognized genus from China to eastern Himalaya. Vitaceae show complex multiple intercontinental relationships within the northern hemisphere and between northern and southern hemispheres.     

Molecular phylogeny and intra- and intercontinental biogeography of Calycanthaceae

Based on nuclear and chloroplast sequences we resolve species relationships in Calycanthaceae and develop a biogeographic hypothesis that explains their intercontinental disjunctions and intra-continental diversification in eastern Asia. Fossil-calibrated penalized likelihood and Bayesian divergence time estimates indicate that the Northern Hemisphere Calycanthus and Chimonanthus diverged from each other in the mid-Miocene, while the Australian Idiospermum had already diverged by the Upper Cretaceous and likely represents a remnant of a former Gondwanan distribution of Calycanthaceae that included South America, as indicated by the occurrence of Cretaceous Calycanthaceae fossils in Brazil. Relationships within Calycanthus were difficult to resolve, but a shared 155-bp deletion in the trnL-F intergenic spacer unites the two North American species, which were also sisters in a cpDNA restriction site study. Their ancestor apparently crossed the Bering land bridge in the Miocene. The six species of Chimonanthus, by contrast, diverged from each other as recently as 1-2my ago, and a DIVA analysis with four areas of endemism recognized within China suggests three vicariance and two dispersal events within Chimonanthus, with initial vicariance having occurred between eastern and southwestern or central China. Further divergence then appears to have involved eastern and south-central China, and southwestern and central China.     

Two notable new species of Cissus (Vitaceae) from South America

Two new species ofCissus are described and illustrated:Cissus boliviana, a simple-leaved species from Bolivian forests, andC. bracteosa, a species with an unusual indumentum from rain forests of Colombia, Ecuador, and Peru.     

Molecular phylogeny and evolution of the plant-specific seven-transmembrane MLO family

Homologues of barley Mlo encode the only family of seven-transmembrane (TM) proteins in plants. Their topology, subcellular localization, and sequence diversification are reminiscent of those of G-protein coupled receptors (GPCRs) from animals and fungi. We present a computational analysis of MLO family members based on 31 full-size and 3 partial sequences, which originate from several monocot species, the dicot Arabidopsis thaliana, and the moss Ceratodon purpureus. This enabled us to date the origin of the Mlo gene family back at least to the early stages of land plant evolution. The genomic organization of the corresponding genes supports a monophyletic origin of the Mlo gene family. Phylogenetic analysis revealed five clades, of which three contain both monocot and dicot members, while two indicate class-specific diversification. Analysis of the ratio of nonsynonymous-to-synonymous changes in coding sequences provided evidence for functional constraint on the evolution of the DNA sequences and purifying selection, which appears to be reduced in the first extracellular loop of 12 closely related orthologues. The 31 full-size sequences were examined for potential domain-specific intramolecular coevolution. This revealed evidence for concerted evolution of all three cytoplasmic domains with each other and the C-terminal cytoplasmic tail, suggesting interplay of all intracellular domains for MLO function.     

Molecular phylogeny and biogeographic diversification of Parthenocissus (Vitaceae) disjunct between Asia and North America

? Premise of the study: Parthenocissus is a genus of the grape family Vitaceae and has a disjunct distribution in Asia and North America with members in both tropical and temperate regions. The monophyly of Parthenocissus has not yet been tested, and the species relationships and the evolution of its intercontinental disjunction have not been investigated with extensive sampling and molecular phylogenetic methods. ? Methods: Plastid (trnL-F, rps16, and atpB-rbcL) and nuclear GAI1 sequences of 56 accessions representing all 12 Parthenocissus species were analyzed with parsimony, likelihood, and Bayesian inference. Divergence times of disjunct lineages were estimated with relaxed Bayesian dating. Evolution of the leaflet number was assessed by tracing this character onto Bayesian trees using the Trace Character Over Trees option in the program Mesquite. ? Key results: Parthenocissus is monophyletic and sister to the newly described segregate genus Yua. Two major clades within Parthenocissus are recognizable corresponding to their distribution in Asia and North America. The disjunction between the two continents is estimated to be at 21.64 (95% higher posterior densities 10.23-34.89) million years ago. ? Conclusions: Parthenocissus is likely to have derived from the Eocene boreotropical element. Its current Asian-North American disjunction is dated to the early Miocene, congruent with fossil and paleoclimatic evidence. The tropical species is nested within the temperate clade and is inferred to have dispersed from the adjacent temperate regions. Parthenocissus and Yua are best treated as distinct genera. Leaflet number in this genus has a complex history and cannot be used as a character for infrageneric classification.     

Molecular phylogeny and morphological evolution of the Acantharia (Radiolaria)

Acantharia are ubiquitous and abundant rhizarian protists in the world ocean. The skeleton made of strontium sulphate and the fact that certain harbour microalgal endosymbionts make them key planktonic players for the ecology of marine ecosystems. Based on morphological criteria, the current taxonomy of Acantharia was established by W.T. Schewiakoff in 1926, since when no major revision has been undertaken. Here, we established the first comprehensive molecular phylogeny from single morphologically-identified acantharian cells, isolated from various oceans. Our phylogenetic analyses based on 78 18S rDNA and 107 partial 28S rDNA revealed the existence of 6 main clades, sub-divided into 13 sub-clades. The polyphyletic nature of acantharian families and genera demonstrates the need for revision of the current taxonomy. This molecular phylogeny, which highlights the taxonomic relevance of specific morphological criteria, such as the presence of a shell and the organisation of the central junction, provides a robust phylogenetic framework for future taxonomic emendation. Finally, mapping all the existing environmental sequences available to date from different marine ecosystems onto our reference phylogeny unveiled another 3 clades and improved the understanding of the biogeography and ecology of Acantharia.     

Molecular phylogeny and evolution of the AsianAconitum subgenusAconitum (Ranunculaceae)

Classification of the genusAconitum (Ranunculaceae) has long been considered quite difficult because its species show high levels of morphological and ecological variability. The molecular phylogeny of Asian aconites,Aconitum subgenusAconitum was, therefore, studied based on RFLP and sequences of the intergenic spacer between thetrnL (UAA) 3′ exon andtrnF (GAA), and of thetrnL intron, of the chloroplast DNA. UsingAconitum subgenusLycoctonum as an outgroup, we obtained a statistically reliable molecular tree composed of six clades branched radiatively at the very base. There are three clades of Japanese aconites, a single clade of the species of Yunnan and Himalayas, and two clades of Siberian plants. All the tetraploid taxa of Japan we studied did not show any difference based on the molecular characters analyzed, though they have been classified into many taxa. Evolution and phytogeography of the Asian aconites as well as the phylogeny are discussed.     

Evaluation of traditional medicinal plant,Cissus setosa Roxb. (Vitaceae) for antiulcer property

Cissus setosa is an indigenous medicinal herb commonly used for the treatment of gastro ulcers. In the current investigation the aerial methanolic extract of C. setosa was investigated for their antiulcer activity using pylorus ligation and ethanol in experimental rats. The extract was administered at the doses of 200 and 400 mg/kg b.w. orally for 3 days. However, higher dose of the extract subsequently reduced gastric ulcer induced aberrations by pylorus ligation (70.05%) and ethanol (78.16%) as judged by their altered biochemical parameters such as free acidity, total acidity, total carbohydrate, total protein and pepsin activity. Furthermore, macroscopic examination of rat’s stomach also showed that the pretreatment with methanolic extract notably lowered the pylorus ligation and ethanol induced ulcers. As perceived in the present study, evidently, our findings basically supports the potency of the methanol extracts of C. setosa to treat gastrointestinal related disorders, thus lends pharmacological credence to the suggested folklore use.     

Molecular phylogeny of the Magnoliaceae: the biogeography of tropical and temperate disjunctions

The boreotropical flora concept suggests that relictual tropical disjunctions between Asia and the Americas are a result of the expansion of the circumboreal tropical flora from the middle to the close of the Eocene. Subsequently, temperate species diverged at high latitudes and migrated to other continents. To test this concept, we conducted a molecular phylogenetic analysis (using cpDNA) of the Magnoliaceae, a former boreotropical element that currently contains both tropical and temperate disjuncts. Divergence times of the clades were estimated using sequences of matK and two intergenic regions consisting of psbA-trnH and atpB-rbcL. Results indicate the tropical American section Talauma branched first, followed by the tropical Asian clade and the West Indies clade. Within the remaining taxa, two temperate disjunctions were formed. Assuming the temperate disjunction of Magnolia acuminata and Asian relatives occurred 25 mya (late Oligocene; based on seed fossil records), section Talauma diverged 42 mya (mid-Eocene), and tropical Asian and the West Indies clades 36 mya (late Eocene). These events correlate with cooling temperatures during the middle to late Eocene and probably caused the tropical disjunctions.     

Molecular phylogeny and plumage evolution in gulls (Larini)

We used DNA sequence data of the mitochondrial control region and cytochrome b gene to assess phylogenetic relationships among 32 gull species and two outgroup representatives. We tentatively estimated divergence times from transversional substitutions calibrated against DNA–DNA hybridization data. Several strongly supported species groups are identified, but the relationships between these species groups and the rooting of the gull tree remain unresolved. Geographical range extension appears as a factor of speciation, but several related, well‐differentiated species seem to have evolved within comparatively restricted areas. Some plumage characters used in the past for delimiting species groups appear inappropriate. The dark hooded species, for instance, do not constitute a natural assemblage. Molecular data also allowed the identification of several striking plumage convergences that had obscured the true relationships between gull species until now. For example, the dark tropical gulls analysed here each belong to totally different clades and are independent examples of convergent plumage evolution under common environmental constraints. The reverse situation also happened, with two arctic‐distributed species, the ivory gull (Pagophila eburnea) and the Sabine’s gull (Xema sabini), appearing as sister taxa despite completely different plumage features. Molecular data have thus significantly improved our understanding of gull evolution.     

Food bodies in Cissus verticillata (Vitaceae): ontogenesis, structure and functional aspects

Background and Aims

The distinction between pearl bodies (or pearl glands) and food bodies (FBs) is not clear; neither is our understanding of what these structures really represent. The present work examined the ontogenesis, structure, ultrastructure and histochemical aspects of the protuberances in Cissus verticillata, which have been described since the beginning of the 19th century as pearl glands or pearl bodies, in order to establish a relationship between their structure and function.

Methods

Segments of stems and leaves in different stages of development were collected and fixed for study under light microscopy as well as electron transmission and scanning microscopy. Samples of FBs were subjected to chemical analysis using thin-layer chromatography.

Key Results

The FBs in C. verticillata are globose and attached to the plant by a short peduncle. These structures are present along the entire stem during primary growth, and on the inflorescence axis and the abaxial face of the leaves. The FBs were observed to be of mixed origin, with the participation of both the epidermis and the underlying parenchymatic cells. The epidermis is uniseriate with a thin cuticle, and the cells have dense cytoplasm and a large nucleus. The internal parenchymatic cells have thin walls; in the young structures these cells have dense cytoplasm with a predominance of mitochondria and plastids. In the mature FBs, the parenchymatic cells accumulate oils and soluble sugars; dictyosomes and rough endoplasmic reticulum predominate in the cytoplasm; the vacuoles are ample. Removal of the FBs appears to stimulate the formation of new ones, at the same place.

Conclusions

The vegetative vigour of the plant seems to influence the number of FBs produced, with more vigorous branches having greater densities of FBs. The results allow the conclusion that the structures traditionally designated pearl glands or pearl bodies in C. verticillata constitute FBs that can recruit large numbers of ants.Key words: Ant–plant interactions, Cissus verticillata, food bodies, myrmecophily, pearl glands, pearl bodies, cell ultrastructure, Vitaceae