Phylogenomic analyses based on genome-skimming data reveal cyto-nuclear discordance in the evolutionary history of Cotoneaster (Rosaceae).

As a consequence of hybridization, polyploidization, and apomixis, the genus Cotoneaster (Rosaceae) represents one of the most complicated and controversial lineages in Rosaceae, with ca. 370 species which have been classified into two subgenera and several sections, and is notorious for its taxonomic difficulty. The infrageneric relationships and taxonomy of Cotoneaster have remained poorly understood. Previous studies have focused mainly on natural hybridization involving only several species, and phylogeny based on very limited markers. In the present study, the sequences of complete chloroplast genomes and 204 low-copy nuclear genes of 72 accessions, representing 69 species as ingroups, were used to conduct the most comprehensive phylogenetic analysis so far for Cotoneaster. Based on the sequences of complete chloroplast genomes and many nuclear genes, our analyses yield two robust phylogenetic trees respectively. Chloroplast genome and nuclear data confidently resolved relationships of this genus into two major clades which largely supported current classification based on morphological evidence. However, conflicts between the chloroplast genome and low-copy nuclear phylogenies were observed in both the species level and clade level. Cyto-nuclear discordance in the phylogeny could be caused by frequent hybridization events and incomplete sorting lineage (ILS). In addition, our divergence-time analysis revealed an evolutionary radiation of the genus from late Miocene to date.

Diversity of plant defense elicitor peptides within the Rosaceae.

BACKGROUND: Plant elicitor peptides (Peps) are endogenous molecules that induce and amplify the first line of inducible plant defense, known as pattern-triggered immunity, contributing to protect plants against attack by bacteria, fungi and herbivores. Pep topic application and transgenic expression have been found to enhance disease resistance in a small number of model plant-pathogen systems. The action of Peps relies on perception by specific receptors, so displaying a family-specific activity. Recently, the presence and activity of Peps within the Rosaceae has been demonstrated. Here we characterized the population of Pep sequences within the economically important plant family of Rosaceae, with special emphasis on the Amygdaleae and Pyreae tribes, which include the most relevant edible species such as apple, pear and peach, and numerous ornamental and wild species (e.g. photinia, firethorn and hawthorn). RESULTS: The systematic experimental search for Pep and the corresponding precursor PROPEP sequences within 36 Amygdaleae and Pyreae species, and 100 cultivars had a highly homogeneous pattern, with two tribe-specific Pep types per plant, i.e. Pep1 and Pep2 (Amygdaleae) or Pep3 and Pep4 (Pyreae). Pep2 and Pep3 are highly conserved, reaching identity percentages similar to those of genes used in plant phylogenetic analyses, while Pep1 and Pep4 are somewhat more variable, with similar values to the corresponding PROPEPs. In contrast to Pep3 and Pep4, Pep1 and Pep2 sequences of different species paralleled their phylogenetic relationships, and putative ancestor sequences were identified. The large amount of sequences allowed refining of a C-terminal consensus sequence that would support the protective activity of Pep1-4 in a Prunus spp. and Xanthomonas arboricola pv. pruni system. Moreover, tribe-specific consensus sequences were deduced at the center and C-terminal regions of Peps, which might explain the higher protection efficiencies described upon topic treatments with Peps from the same tribe. CONCLUSIONS: The present study substantially enhances the knowledge on Peps within the Amygdaleae and Pyreae species. It can be the basis to design and fine-tune new control tools against important plant pathogens affecting Prunus, Pyrus and Malus species.

Ribosome Inactivating Proteins from Rosaceae.

Ribosome-inactivating proteins (RIPs) are widespread among higher plants of different taxonomic orders. In this study, we report on the RIP sequences found in the genome/transcriptome of several important Rosaceae species, including many economically important edible fruits such as apple, pear, peach, apricot, and strawberry. All RIP domains from Rosaceae share high sequence similarity with conserved residues in the catalytic site and the carbohydrate binding sites. The genomes of Malus domestica and Pyrus communis contain both type 1 and type 2 RIP sequences, whereas for Prunus mume, Prunus persica, Pyrus bretschneideri, and Pyrus communis a complex set of type 1 RIP sequences was retrieved. Heterologous expression and purification of the type 1 as well as the type 2 RIP from apple allowed to characterize the biological activity of the proteins. Both RIPs from Malus domestica can inhibit protein synthesis. Furthermore, molecular modelling suggests that RIPs from Rosaceae possess three-dimensional structures that are highly similar to the model proteins and can bind to RIP substrates. Screening of the recombinant type 2 RIP from apple on a glycan array revealed that this type 2 RIP interacts with terminal sialic acid residues. Our data suggest that the RIPs from Rosaceae are biologically active proteins.

Anthocyanin Profile and Antioxidant Activity of Various Berries Cultivated in Korea.

This study examined the anthocyanin composition and antioxidant activity of various berries cultivated in Korea: blueberry, crowberry, Korean black raspberry, mulberry, and strawberry. The anthocyanins in berries were identified by high-performance liquid chromatography (HPLC) analysis, and each component was quantitatively analyzed. Furthermore, the antioxidant activity of berries was evaluated using 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical-scavenging, 2,2'-azinobis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) radical cation decolorization, oxygen radical absorbance capacity (ORAC), and ferric ion reducing antioxidant (FRAP) assays. The results revealed that the total content of anthocyanins in crowberry was 35.1 mg/g of extract, which was higher than that in the other four major berry species (1.9-27.7 mg/g of extract). Nineteen anthocyanins were identified in the various berries. The major anthocyanins of crowberry were cyanidin-3-galactoside and delphinidin-3-galactoside, and those from Korean black raspberry were cyanidin-3-rutinoside and cyanidin-3-sambubioside-5-rhamnoside. These two berries also had relatively strong antioxidant activity accompanied by high total polyphenol contents. Thus, consumption of crowberry and Korean black raspberry may be beneficial in reducing the risk of developing lifestyle-related chronic diseases because of their strong antioxidant activity.

Potencial inseticida de óleos de origem vegetal sobre Grapholita molesta (Busck) (Lepidoptera: Tortricidae) / Insecticidal potential of vegetable oil extracts on Grapholita molesta (Busck) (Lepidoptera: Tortricidae)

Em decorrência do estudo das interações químicas entre insetos e herbívoros, e do avanço da pesquisa fitoquímica, é conhecida ampla variedade de produtos naturais com potencial inseticida. Grapholita molesta (Busck) (Lepidoptera: Tortricidae), mariposa-oriental, é uma das principais pragas do pessegueiro, danificando brotações e frutos. O objetivo do presente estudo foi verificar a mortalidade, atratividade e deterrência de óleos vegetais em G. molesta. Ovos e pupas de insetos provindos de criação artificial foram imersos nos óleos essenciais de Elionurus muticus (Spreng.) Kuntze e Cymbopogon winterianus Jowitt ex Bor nas concentrações de 0,25%, 0,5%, 1% e 0,5%, 1%, 5%. Os testes de atratividade foram realizados em olfatômetro do tipo "Y". A deterrência à oviposição foi testada em gaiolas sem escolha e de dupla escolha. O óleo de E. muticus aplicado em ovos de G. molesta nas três concentrações causou mortalidades maiores que 30%, diferindo significativamente dos controles (p<0,05). A mortalidade causada pelo óleo de citronela foi em torno de 70%, significativamente superior ao controle (p<0,01). O óleo de citronela aplicado a 1% em pupas causou mortalidade de 99,8%. No teste com o olfatômetro, não houve atratividade dos adultos para nenhum dos óleos. A média de ovos no substrato com o tratamento (0,33±0,33), foi significativamente menor que no controle (7,3±0,88) (p<0,01), indicando deterrência à oviposição.

As a result of the study on the chemical interactions between insects and herbivores and the advancement of phytochemical research studies, a variety of natural products with great insecticidal potential are described in the literature. The Grapholita molesta (Busck) (Lepidoptera: Tortricidae), commonly known as Oriental Fruit Moth, is a major peach pest damaging shoots and fruits. The purpose of this study was to assess the mortality, attractiveness and deterrence of vegetable oils in G. molesta. Insect eggs and pupae artificially created were immersed in the essential oils of Elionurus muticus (Spreng.) Kuntze and/or Cymbopogon winterianus Jowitt ex Bor at the concentrations of 0.25%, 0.5%, 1% and 0.5%, 1%, 5%, respectively. The attractiveness tests were performed in a Y-Tube olfactometer. Oviposition deterrence was tested in no-choice and dual-choice cages. Oil of E. muticus applied in eggs of G. molesta at three concentrations caused mortality above 30%, which differs significantly from controls (p<0.05). Mortality caused by citronella oil was approximately 70%, significantly higher than control (p<0.01). The application of citronella oil at 1% in pupae caused mortality of 99.8%. There was no attractiveness of adults in the olfactometer test for any of the oils. Citronella oil presented oviposition deterrence, as the mean number of eggs in the substrate with the treatment (0.33 ± 0.33) is significantly lower than in the control (7.3 ± 0.88) (p<0.01).

Polyphenolic composition, antioxidant activity, and polyphenol oxidase (PPO) activity of quince (Cydonia oblonga Miller) varieties.

Phytochemical profiles (phenolic compounds, L-ascorbic acid, antioxidant and PPO activities) of 13 different quince varieties and 5 genotypes were studied. Polyphenols were identified by LC-PDA-QTof/MS and quantified by UPLC-PDA and UPLC-FL. A total of 26 polyphenolic compounds found in quince tissues were identified and presented: 9 flavan-3-ols ((-)-epicatechin, procyanidin B2, 3 procyanidin dimers and trimers, and 1 tetramer); 8 hydroxycinnamates, derivatives of caffeoylquinic and coumaroylquinic acid; and 9 kaempferol and quercetin derivatives. The content of total polyphenols was between 1709.43 (genotype 'S1') and 3436.56 mg/100 g dry weight ('Leskovac'). Flavan-3-ols, which are the major class of quince polyphenols, represented between 78 and 94% of the total polyphenolic compounds. The activity of PPO enzyme ranged from 709.85 to 1284.59 ΔU/min, and that of L-ascorbic acid ranged from 5.86 to 26.42 mg/100 g. Some quince varieties and their products characterized by a higher content of phenolic compounds may be selected to promote their positive effect on health.

Neuroprotective effects of digested polyphenols from wild blackberry species.

PURPOSE: Blackberry ingestion has been demonstrated to attenuate brain degenerative processes with the benefits ascribed to the (poly)phenolic components. The aim of this work was to evaluate the neuroprotective potential of two wild blackberry species in a neurodegeneration cell model and compare them with a commercial variety. METHODS: This work encompasses chemical characterization before and after an in vitro digestion and the assessment of neuroprotection by digested metabolites. Some studies targeting redox/cell death systems were also performed to assess possible neuroprotective molecular mechanisms. RESULTS: The three blackberry extracts presented some quantitative differences in polyphenol composition that could be responsible for the different responses in the neurodegeneration cell model. Commercial blackberry extracts were ineffective but both wild blackberries, Rubus brigantinus and Rubus vagabundus, presented neuroprotective effects. It was verified that a diminishment of intracellular ROS levels, modulation of glutathione levels and activation of caspases occurred during treatment. The last effect suggests a preconditioning effect since caspase activation was not accompanied by diminution in cell death and loss of functionality. CONCLUSIONS: This is the first time that metabolites obtained from an in vitro digested food matrix, and tested at levels approaching the concentrations found in human plasma, have been described as inducing an adaptative response.

Taxon analysis of seed plants used in studies of blood platelet function.

The characterization of isolated polyphenolic compounds present in the diet--especially in the context of their therapeutic effect (for instance their antiplatelet activity)--is often based on the generally accepted flavonoid classification. In the case of plant extracts it usually refers to common names of plants rather than scientific botanical nomenclature. Hence, it is often difficult to even roughly estimate how many and which plant taxa exhibit biological activity towards the modulation of blood platelet activity. In this paper, based on a review of literature from the last 50 years (1962-2011), we developed a list of seed plants (Spermatophyta) taxa investigated in studies on blood platelets. We used the PubMed database, as well as the database of species' names--Taxonomy, in order to gather information about the investigated taxa. The review of the literature was made with the use of advanced options, on the basis of keywords (or combinations of keywords) and selected journals. Record search strategies were evaluated on the basis of the sensitivity of search (number of papers meeting the criteria of search strategy) and the specificity of search (number of papers containing in their title and/or abstract information on taxa used in blood platelet research). The publications were considered specific if they reported either Latin or common names of plants (or both). The main search strategy was characterised by high sensitivity, but low specificity. The basis for plant taxonomic specification was the list of 1080 articles, published in 434 journals. The list of taxa used in blood platelet studies covered 98 genera belonging to 47 families of seed plants. The richest in genera, and also in species, appeared to be the families Asteraceae, Fabaceae, and Rosaceae, the most abundant in species all over the world. This study may be a starting point for the selection of plant species to be used for biomedical research and--at the same time--may help in the search for an effective strategy of literature tracking concerning flavonoids and blood platelets.

Using genomics to improve fruit quality

New fruit varieties are needed to satisfy consumers, and the industry is facing new challenges in order to respond to these demands. The emergence of genomic tools is releasing information on polymorphisms that can be utilized to expedite breeding processes in species that are difficult to breed, given the long periods of time required to get new varieties. The present review describes the current stages of the ongoing efforts that are being taken to apply these technologies to obtain varieties with improved fruit quality in species of the family Rosaceae.

Allopolyploidy in Fragariinae (Rosaceae): comparing four DNA sequence regions, with comments on classification.

Potential events of allopolyploidy may be indicated by incongruences between separate phylogenies based on plastid and nuclear gene sequences. We sequenced two plastid regions and two nuclear ribosomal regions for 34 ingroup taxa in Fragariinae (Rosaceae), and six outgroup taxa. We found five well supported incongruences that might indicate allopolyploidy events. The incongruences involved Aphanes arvensis, Potentilla miyabei, Potentilla cuneata, Fragaria vesca/moschata, and the Drymocallis clade. We evaluated the strength of conflict and conclude that allopolyploidy may be hypothesised in the four first cases. Phylogenies were estimated using Bayesian inference and analyses were evaluated using convergence diagnostics. Taxonomic implications are discussed for genera such as Alchemilla, Sibbaldianthe, Chamaerhodos, Drymocallis and Fragaria, and for the monospecific Sibbaldiopsis and Potaninia that are nested inside other genera. Two orphan Potentilla species, P. miyabei and P. cuneata are placed in Fragariinae. However, due to unresolved topological incongruences they are not reclassified in any genus.

Molecular phylogenetics of Alchemilla, Aphanes and Lachemilla (Rosaceae) inferred from plastid and nuclear intron and spacer DNA sequences, with comments on generic classification.

Alchemilla (the lady's mantles) is a well known but inconspicuous group in the Rosaceae, notable for its ornamental leaves and pharmaceutical properties. The systematics of Alchemilla has remained poorly understood, most likely due to confusion resulting from apomixis, polyploidisation and hybridisation, which are frequently observed in the group, and which have led to the description of a large number of (micro-) species. A molecular phylogeny of the genus, including all sections of Alchemilla and Lachemilla as well as five representatives of Aphanes, based on the analysis of the chloroplast trnL-trnF and the nuclear ITS regions is presented here. Gene phylogenies reconstructed from the nuclear and chloroplast sequence data were largely congruent. Limited conflict between the data partitions was observed with respect to a small number of taxa. This is likely to be the result of hybridisation/introgression or incomplete lineage sorting. Four distinct clades were resolved, corresponding to major geographical division and life forms: Eurasian Alchemilla, annual Aphanes, South American Lachemilla and African Alchemilla. We argue for a wider circumscription of the genus Alchemilla, including Lachemilla and Aphanes, based on the morphology and the phylogenetic relationships between the different clades.