Analysis of flavonoid metabolism of compounds in succulent fruits and leaves of three different colors of Rosaceae.

Red flesh apple (Malus pumila var. medzwetzkyana Dieck), purple leaf plum (Prunus cerasifera Ehrhar f), and purple leaf peach (Prunus persica 'Atropurpurea') are significant ornamental plants within the Rosaceae family. The coloration of their fruits and leaves is crucial in their appearance and nutritional quality. However, qualitative and quantitative studies on flavonoids in the succulent fruits and leaves of multicolored Rosaceae plants are lacking. To unveil the diversity and variety-specificity of flavonoids in these three varieties, we conducted a comparative analysis of flavonoid metabolic components using ultra-high-performance liquid phase mass spectrometry (UPLC-MS/MS). The results revealed the detection of 311 metabolites, including 47 flavonoids, 105 flavonols, 16 chalcones, 37 dihydroflavonoids, 8 dihydroflavonols, 30 anthocyanins, 14 flavonoid carbon glycosides, 23 flavanols, 8 isoflavones, 11 tannins, and 12 proanthocyanidins. Notably, although the purple plum and peach leaves exhibited distinct anthocyanin compounds, paeoniflorin and corythrin glycosides were common but displayed varying glycosylation levels. While the green purple leaf peach fruit (PEF) and red flesh apple leaf (AL) possessed the lowest anthocyanin content, they exhibited the highest total flavonoid content. Conversely, the red flesh apple fruit (AF) displayed the highest anthocyanin content and a diverse range of anthocyanin glycosylation modifications, indicating that anthocyanins predominantly influenced the fruit's color. Purple PLF, PLL, and PEL showcased varying concentrations of anthocyanins, suggesting that their colors result from the co-color interaction between specific types of anthocyanins and secondary metabolites, such as flavonols, flavonoids, and dihydroflavonoids. This study provides novel insights into the variations in tissue metabolites among Rosaceae plants with distinct fruit and leaf colors.

Comparative genomics analysis provide insights into evolution and stress responses of Lhcb genes in Rosaceae fruit crops.

BACKGROUND: Light-harvesting chlorophyll a/b b evelopment of higher plants and in response to abiotic stress. Previous works has demonstrated that that Lhcb genes were involved in the phytochrome regulation and responded to the different light and temperature conditions in Poaceae (such as maize). However, the evolution and functions of Lhcb genes remains poorly characterized in important Rosaceae species. RESULTS: In this investigation, we conducted a genome-wide analysis and identified a total of 212 Lhcb genes across nine Rosaceae species. Specifically, we found 23 Lhcb genes in Fragaria vesca, 20 in Prunus armeniaca, 33 in Malus domestica 'Gala', 21 in Prunus persica, 33 in Rosa chinensis, 29 in Pyrus bretschneideri, 18 in Rubus occidentalis, 20 in Prunus mume, and 15 in Prunus salicina. Phylogenetic analysis revealed that the Lhcb gene family could be classified into seven major subfamilies, with members of each subfamily sharing similar conserved motifs. And, the functions of each subfamily was predicted based on the previous reports from other species. The Lhcb proteins were highly conserved within their respective subfamilies, suggesting similar functions. Interestingly, we observed similar peaks in Ks values (0.1-0.2) for Lhcb genes in apple and pear, indicating a recent whole genome duplication event (about 30 to 45 million years ago). Additionally, a few Lhcb genes underwent tandem duplication and were located across all chromosomes of nine species of Rosaceae. Furthermore, the analysis of the cis-acting elements in the 2000 bp promoter region upstream of the pear Lhcb gene revealed four main categories: light response correlation, stress response correlation, hormone response correlation, and plant growth. Quantitative expression analysis demonstrated that Lhcb genes exhibited tissue-specific expression patterns and responded differently to low-temperature stress in Rosaceae species. CONCLUSIONS: These findings shed light on the evolution and phylogeny of Lhcb genes in Rosaceae and highlight the critical role of Lhcb in pear's response to low temperatures. The results obtained provide valuable insights for further investigations into the functions of Lhcb genes in Rosaceae, and these functional genes will be used for further fruit tree breeding and improvement to cope with the current climate changes.

The Aqueous Lyophilisate of Alchemilla Kiwuensis Engl. (Rosaceae) Displays Antiepileptogenic and Antiepileptic Effects on PTZ-induced Kindling in rats: Evidence of Modulation of Glutamatergic and GABAergic Pathways Coupled to Antioxidant Properties.

Alchemilla kiwuensis Engl. (Rosaceae) (A. kiwuensis) is an herbaceous plant traditionally used by Cameroonians to treat epilepsy and other central nervous system disorders. The present study evaluated the antiepileptogenic and antiepileptic effects of A. kiwuensis (40 mg/kg, 80 mg/kg) following Pentylenetetrazole (PTZ)-induced kindling as well as its sub-chronic toxicity. Following an initial i.p administration of a challenge dose (70 mg/kg), Wistar rats of both sexes received sub convulsive doses (35 mg/kg) of PTZ every other day, one hour after the oral gavage of animals with treatments, until two consecutive stage 4, in all animals of negative control. Seizure progression, latency, duration, and repetition were noted. Twenty-four hours later, animals were dissected to extract their hippocampi. The resulting homogenates were used to evaluate Malondialdehyde, reduced glutathione, catalase activity, GABA, GABA-Transaminase, glutamate, glutamate transporter 2, IL-1ß and TGF-1 ß. Sub-chronic toxicity was conducted according to OECD 407 guidelines. The lyophilisate of A. kiwuensis significantly increased the latency of seizure appearance, delayed seizure progression and decreased seizure repetition and duration. Biochemical analysis revealed that the lyophilisate significantly increased the catalase activity, reduced glutathione, GABA, glutamate transporter 2 and TGF-1B levels. The lyophilisate equally caused a significant decreased in the GABA-Transaminase activity, malondialdehyde, and IL-1 ß levels. There was no noticeable sign of toxicity. A. kiwuensis possesses antiepileptic and antiepiletogenic effects by enhancing GABAergic neurotransmission and antioxidant properties, coupled to modulation of glutamatergic and neuroinflammatory pathways and is innocuous in a sub-chronic model. These justifies its local use for the treatment of epilepsy.

Comparative genomics analysis of WAK/WAKL family in Rosaceae identify candidate WAKs involved in the resistance to Botrytis cinerea.

BACKGROUND: Wall associated kinase (WAK) and WAK-like (WAKL) are typical pattern recognition receptors act as the first sentry of plant defense. But little of WAK/WAKL family is known in Rosaceae. RESULTS: In this study, 131 WAK/WAKL genes from apple, peach and strawberry were identified using a bioinformatics approach. Together with 68 RcWAK/RcWAKL in rose, we performed a comparative analysis of 199 WAK/WAKL in four Rosaceae crops. The phylogenetic analysis divided all the WAK/WAKL into five clades. Among them, the cis-elements of Clade II and Clade V promoters were enriched in jasmonic acid (JA) signaling and abiotic stress, respectively. And this can also be verified by the rose transcriptome responding to different hormone treatments. WAK/WAKL families have experienced a considerable proportion of purifying selection during evolution, but still 26 amino acid sites evolved under positive selection, which focused on extracellular conserved domains. WAK/WAKL genes presented collinearity relationship within and between crops, throughout four crops we mined four orthologous groups (OGs). The WAK/WAKL genes in OG1 and OG4 were speculated to involve in plant-Botrytis cinerea interaction, which were validated in rose via VIGS as well as strawberry by qRT-PCR. CONCLUSIONS: These results not only provide genetic resources and valuable information for the evolutionary relationship of WAK/WAKL gene family, but also offer a reference for future in-depth studies of Rosaceae WAK/WAKL genes.

Drought-induced CsMYB6 interacts with CsbHLH111 to regulate anthocyanin biosynthesis in Chaenomeles speciosa.

Chaenomeles speciosa is a plant with high ornamental value, and the color of its petals deepens obviously under drought stress. To understand the mechanism of drought-induced reddening of C. speciosa petal color, the metabolites and transcriptomics of petals from 4% PEG-8000-treated and control cuttings were analyzed. In this study, the analysis of metabolites revealed the accumulation of anthocyanins in petals of PEG-treated cuttings, indicating anthocyanins might be the reason for the deepening of petal color. By using transcriptomics, we identified CsMYB6 as an overexpressed transcription factor in PEG-treated samples. Transient overexpression and suppression of CsMYB6 revealed that it is a key transcription factor for anthocyanin synthesis. We identified genes related to anthocyanin biosynthesis and constructed a network of drought- and anthocyanin-related genes (such as CsMYB6, CsbHLH111, CsANS, CsDFR, and CsUFGT). Further experiments indicated that CsMYB6 directly interacted with CsbHLH111, and this interaction increased the binding ability of CsMYB6 to the promoter regions of three structural genes of anthocyanin biosynthesis: CsANS, CsDFR, and CsUFGT. Our findings provide a molecular basis and new insight into drought-induced anthocyanin biosynthesis in C. speciosa.

Evolutionary and functional analysis reveals the crucial roles of receptor-like proteins in resistance to Valsa canker in Rosaceae.

Rosaceae is an economically important plant family that can be affected by a multitude of pathogenic microbes, some of which can cause dramatic losses in production. As a type of pattern-recognition receptor, receptor-like proteins (RLPs) are considered vital regulators of plant immunity. Based on genome-wide identification, bioinformatic analysis, and functional determination, we investigated the evolutionary characteristics of RLPs, and specifically those that regulate Valsa canker, a devastating fungal disease affecting apple and pear production. A total of 3028 RLPs from the genomes of 19 species, including nine Rosaceae, were divided into 24 subfamilies. Five subfamilies and seven co-expression modules were found to be involved in the responses to Valsa canker signals of the resistant pear rootstock Pyrus betulifolia 'Duli-G03'. Fourteen RLPs were subsequently screened as candidate genes for regulation of resistance. Among these, PbeRP23 (Chr13.g24394) and PbeRP27 (Chr16.g31400) were identified as key resistance genes that rapidly enhance the resistance of 'Duli-G03' and strongly initiate immune responses, and hence they have potential for further functional exploration and breeding applications for resistance to Valsa canker. In addition, as a consequence of this work we have established optimal methods for the classification and screening of disease-resistant RLPs.

Evolution and functional analysis of the GRAS family genes in six Rosaceae species.

BACKGROUND: GRAS genes formed one of the important transcription factor gene families in plants, had been identified in several plant species. The family genes were involved in plant growth, development, and stress resistance. However, the comparative analysis of GRAS genes in Rosaceae species was insufficient. RESULTS: In this study, a total of 333 GRAS genes were identified in six Rosaceae species, including 51 in strawberry (Fragaria vesca), 78 in apple (Malus domestica), 41 in black raspberry (Rubus occidentalis), 59 in European pear (Pyrus communis), 56 in Chinese rose (Rosa chinensis), and 48 in peach (Prunus persica). Motif analysis showed the VHIID domain, SAW motif, LR I region, and PFYRE motif were considerably conserved in the six Rosaceae species. All GRAS genes were divided into 10 subgroups according to phylogenetic analysis. A total of 15 species-specific duplicated clades and 3 lineage-specific duplicated clades were identified in six Rosaceae species. Chromosomal localization presented the uneven distribution of GRAS genes in six Rosaceae species. Duplication events contributed to the expression of the GRAS genes, and Ka/Ks analysis suggested the purification selection as a major force during the evolution process in six Rosaceae species. Cis-acting elements and GO analysis revealed that most of the GRAS genes were associated with various environmental stress in six Rosaceae species. Coexpression network analysis showed the mutual regulatory relationship between GRAS and bZIP genes, suggesting the ability of the GRAS gene to regulate abiotic stress in woodland strawberry. The expression pattern elucidated the transcriptional levels of FvGRAS genes in various tissues and the drought and salt stress in woodland strawberry, which were verified by RT-qPCR analysis. CONCLUSIONS: The evolution and functional analysis of GRAS genes provided insights into the further understanding of GRAS genes on the abiotic stress of Rosaceae species.

The Inhibition of α-Glucosidase, α-Amylase and Protein Glycation by Phenolic Extracts of Cotoneaster bullatus, Cotoneaster zabelii, and Cotoneaster integerrimus Leaves and Fruits: Focus on Anti-Hyperglycemic Activity and Kinetic Parameters.

Cotoneaster species have gained significant importance in traditional Asian medicine for their ability to prevent and treat hyperglycemia and diabetes. Therefore, in this study, some aspects of the beneficial health effects of hydromethanolic extracts of C. bullatus, C. zabelii, and C. integerrimus leaves and fruits were evaluated, including their influence on α-glucosidase, α-amylase, and nonenzymatic protein glycation. The activity was investigated in relation to the polyphenolic profile of the extracts determined by UV-spectrophotometric and HPLC-PDA-fingerprint methods. It was revealed that all leaf and fruit extracts are a promising source of biological components (caffeic acid pseudodepsides, proanthocyanidins, and flavonols), and the leaf extracts of C. bullatus and C. zabelii contain the highest levels of polyphenols (316.3 and 337.6 mg/g in total, respectively). The leaf extracts were also the most effective inhibitors of digestive enzymes and nonenzymatic protein glycation. IC50 values of 8.6, 41.8, and 32.6 µg/mL were obtained for the most active leaf extract of C. bullatus (MBL) in the α-glucosidase, α-amylase, and glycation inhibition tests, respectively. In the kinetic study, MBL was displayed as a mixed-type inhibitor of both enzymes. The correlations between the polyphenol profiles and activity parameters (|r| > 0.72, p < 0.05) indicate a significant contribution of proanthocyanidins to the tested activity. These results support the traditional use of Cotoneaster leaves and fruits in diabetes and suggest their hydrophilic extracts be promising in functional applications.

Computational analysis of potential candidate genes involved in the cold stress response of ten Rosaceae members.

BACKGROUND: Plant species from Rosaceae family are economically important. One of the major environmental factors impacting those species is cold stress. Although several Rosaceae plant genomes have recently been sequenced, there have been very few research conducted on cold upregulated genes and their promoter binding sites. In this study, we used computational approaches to identify and analyse potential cold stress response genes across ten Rosaceae family members. RESULTS: Cold stress upregulated gene data from apple and strawberry were used to identify syntelogs in other Rosaceae species. Gene duplication analysis was carried out to better understand the distribution of these syntelog genes in different Rosaceae members. A total of 11,145 popular abiotic stress transcription factor-binding sites were identified in the upstream region of these potential cold-responsive genes, which were subsequently categorised into distinct transcription factor (TF) classes. MYB classes of transcription factor binding site (TFBS) were abundant, followed by bHLH, WRKY, and AP2/ERF. TFBS patterns in the promoter regions were compared among these species and gene families, found to be quite different even amongst functionally related syntelogs. A case study on important cold stress responsive transcription factor family, AP2/ERF showed less conservation in TFBS patterns in the promoter regions. This indicates that syntelogs from the same group may be comparable at the gene level but not at the level of cis-regulatory elements. Therefore, for such genes from the same family, different repertoire of TFs could be recruited for regulation and expression. Duplication events must have played a significant role in the similarity of TFBS patterns amongst few syntelogs of closely related species. CONCLUSIONS: Our study overall suggests that, despite being from the same gene family, different combinations of TFs may play a role in their regulation and expression. The findings of this study will provide information about potential genes involved in the cold stress response, which will aid future functional research of these gene families involved in many important biological processes.

Computational identification of bioactive compounds from Cydonia oblonga Mill. against hepatocellular carcinoma by targeting pTEN and HBx-interacting protein.

Phytochemicals derived from Cydonia oblonga have been investigated for their anti-oxidant and anti-cancer activities in various cancer cell lines. The reported bioactive compounds are evaluated in silico to develop a novel antagonist against pTEN (phosphatase and tensin homolog) and HBx (hepatitis B X-interacting protein) to target hepatocellular carcinoma. Lower expression of pTEN or higher expression of HBx represents the progression of hepatocellular carcinoma. This research is intended to identify the best candidate who interacts with our target proteins (pTEN and HBx) from the quince seeds by using computational methodologies. The ternary structures of the proteins and phytochemicals are retrieved from the online databases (RCSB and PubChem). The drug likeness analysis of the reported seventeen compounds was done, but only five follow the selection criteria. ADMET profiling of these five compounds was done, followed by docking analysis and molecular dynamics study of the best complexes to determine the stability of the complexes. A docking study revealed that caffeoylquinic acids (CQA) derivatives have the significant inhibitory potential of 3-O-caffeoylquinic acid (3CQA) and 5-O-caffeoylquinic acid (5CQA) with binding affinity of - 7.53 and - 7.49 against pTEN and - 5.94 and - 6.01 against HBx in comparison to the doxorubicin. The average root mean square deviation and root mean square fluctuation values for protein-ligand complexes were found quite stable compared to the standard, while parameters like gyration and SASA (solvent-accessible surface area) supported the complexes significant binding and stability. The results obtained from the evaluation show that 3CQA and 5CQA have the best stability, especially with the pTEN protein target. Hence, these compounds have to be considered for detailed experimental studies to understand their biological function against hepato-carcinoma.

HDACs Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in Prunus mume.

Histone deacetylases (HDACs) play important roles in plant growth, development, and stress response. However, the pattern of how they are expressed in response to cold stress in the ornamental woody plant Prunus mume is poorly understood. Here, we identify 121 RoHDACs from eight Rosaceae plants of which 13 PmHDACs genes are from P. mume. A phylogenetic analysis suggests that the RoHDACs family is classified into three subfamilies, HDA1/RPD3, HD2, and SIR2. We identify 11 segmental duplication gene pairs of RoHDACs and find, via a sequence alignment, that the HDACs gene family, especially the plant-specific HD2 family, has experienced gene expansion and contraction at a recent genome evolution history. Each of the three HDACs subfamilies has its own conserved domains. The expression of PmHDACs in mei is found to be tissue-specific or tissue-wide. RNA-seq data and qRT-PCR experiments in cold treatments suggest that almost all PmHDACs genes-especially PmHDA1/6/14, PmHDT1, and PmSRT1/2-significantly respond to cold stress. Our analysis provides a fundamental insight into the phylogenetic relationship of the HDACs family in Rosaceae plants. Expression profiles of PmHDACs in response to cold stress could provide an important clue to improve the cold hardiness of mei.

PbrCalS5, a callose synthase protein, is involved in pollen tube growth in Pyrus bretschneideri.

MAIN CONCLUSION: Identification of CalS genes in seven Rosaceae species and functional characterization of PbrCalS5 in pear pollen tube growth by regulating callose deposition. Callose exists widely in angiosperms and has significant functions in a range of developmental processes. Callose is synthesized by callose synthase (CalS). However, the members of the callose synthase gene family and their evolutionary profiles, along with their biological functions, in species of the Rosaceae remain unknown. In this study, a total of 69 members of the CalS gene family in seven Rosaceae species (Fragaria vesca, Malus × domestica, Prunus avium, Pyrus bretschneideri, Prunus mume, Prunus persica and Rubus occidentalis) were identified and divided into six clades. Different types of gene duplication events contributed to the expansions of the CalS gene family in the seven species, with purifying selection playing a key role in the evolution of the CalS genes. Tissue-specific expression patterns analysis revealed that PbrCalS5 was highly expressed in the pear pollen tube and was selected for further functional analysis. Subcellular localization indicated that PbrCalS5 was localized in the plasma membrane and cell wall. Antisense oligodeoxynucleotide (AS-ODN) assays resulted in the inhibition of PbrCalS5 expression, leading to the decreased callose deposition in the pollen tube wall and subsequent inhibition of pear pollen tube growth. These results provide the theoretical basis for exploring the functional roles of CalS genes in pear pollen tube growth.

Chaenomeles Fructus (CF), the Fruit of Chaenomeles sinensis Alleviates IL-1ß Induced Cartilage Degradation in Rat Articular Chondrocytes.

Osteoarthritis (OA) causes persistent pain, joint dysfunction, and physical disability. It is the most prevalent type of degenerative arthritis, affecting millions of people worldwide. OA is currently treated with a focus on pain relief, inflammation control, and artificial joint surgery. Hence, a therapeutic agent capable of preventing or delaying the progression of OA is needed. OA is strongly associated with the degeneration of the articular cartilage and changes in the ECM, which are primarily associated with a decrease in proteoglycan and collagen. In the progress of articular cartilage degradation, catabolic enzymes, such as matrix metalloproteinases (MMPs), are activated by IL-1ß stimulation. Given the tight relationship between IL-1ß and ECM (extra-cellular matrix) degradation, this study examined the effects of Chaenomeles Fructus (CF) on IL-1ß-induced OA in rat chondrocytes. The CF treatment reduced IL-1ß-induced MMP3/13 and ADAMTS-5 production at the mRNA and protein levels. Similarly, CF enhanced col2a and aggrecan accumulation and chondrocyte proliferation. CF inhibited NF-κB (nuclear factor kappa B) activation, nuclear translocation induced by IL-1ß, reactive oxygen species (ROS) production, and ERK phosphorylation. CF demonstrated anti-OA and articular regeneration effects on rat chondrocytes, thus, suggesting that CF is a viable and fundamental therapeutic option for OA.

Extended seed rain period of Adenostoma fasciculatum impacts diverse seed predators.

AIMS: The principal chaparral species in California, Adenostoma fasciculatum, an evergreen, sclerophyllous shrub, is broadly distributed and provides habitat and food resources for a large and diverse animal community. The effects of climate change, including elevated temperatures, fire frequency and severity, along with increased urban encroachment, have placed pressure on chaparral habitats in California. Our goal is to investigate aspects of reproductive ecology as a measure of the potential resiliency of A. fasciculatum. We focus on seed rain (all seed falling into the seed traps regardless of origin) and seed banks in the context of plant-animal interactions and regeneration. METHODS: Stand recovery following disturbance is achieved through both resprouting and germination from established persistent soil seed banks. In this study we focus on seed ecology using a series of experiments to document the length and quantity of seed rain, seed predation, parsing the importance of the community of granivores, and evaluating the connection between stand age and germination rate from soil seed banks. IMPORTANT FINDINGS: Our research documented an 8-month seed rain duration with over 1 million seeds per m2, multiple seed predators including passerines (songbirds) and rodents, and points to the possibility of native ants playing a role in the seed dispersal process. This is important given the recent advancement of the invasive Argentine ant (Linepthema humile) into Californian chaparral. This research demonstrates a clear relationship between A. fasciculatum and both resident and migratory granivores in the chaparral. We documented that a 39-year-old stand had higher germination rates than those which were 16, 20, 41 and 71 years old and how seed banks play a major role in assuring resiliency following fire. These findings are important for wildland managers to assure the continued resiliency of A. fasciculatum.

Pancreatic lipase and α-amylase inhibitory activity of extracts from selected plant materials after gastrointestinal digestion in vitro.

A screening of inhibitory activity of α-amylase, as well as pancreatic lipase (PL), under the influence of aqueous and ethanolic preparations from 12 plant materials was performed. The most active aqueous extracts from the fruits of Chaenomeles japonica (CJ) and Hippophaë rhamnoides (HR) were selected for artificial gastrointestinal digestion (GID). The aim of this study was to evaluate the inhibitory effect of the fractions obtained after GID on PL and α-amylase activities using a fluorescence assay. The changes in the composition of crude extracts in GID aliquots were followed by analysis with HPLC-DAD-MSn method in order to indicate active constituents. The main constituents of CJ and HR extracts were procyanidins and isorhamnetin derivatives, respectively. The most abundant compounds of extracts were found in all compartments of the digestion model correlated with relevant lipase/α-amylase inhibitory activity. What is more, the gastric and intestinal fractions inhibited enzymatic activity by at least 40%.

Genome-wide characterization of PEBP family genes in nine Rosaceae tree species and their expression analysis in P. mume.

BACKGROUND: Phosphatidylethanolamine-binding proteins (PEBPs) constitute a common gene family found among animals, plants and microbes. Plant PEBP proteins play an important role in regulating flowering time, plant architecture as well as seed dormancy. Though PEBP family genes have been well studied in Arabidopsis and other model species, less is known about these genes in perennial trees. RESULTS: To understand the evolution of PEBP genes and their functional roles in flowering control, we identified 56 PEBP members belonging to three gene clades (MFT-like, FT-like, and TFL1-like) and five lineages (FT, BFT, CEN, TFL1, and MFT) across nine Rosaceae perennial species. Structural analysis revealed highly conserved gene structure and protein motifs among Rosaceae PEBP proteins. Codon usage analysis showed slightly biased codon usage across five gene lineages. With selection pressure analysis, we detected strong purifying selection constraining divergence within most lineages, while positive selection driving the divergence of FT-like and TFL1-like genes from the MFT-like gene clade. Spatial and temporal expression analyses revealed the essential role of FT in regulating floral bud breaking and blooming in P. mume. By employing a weighted gene co-expression network approach, we inferred a putative FT regulatory module required for dormancy release and blooming in P. mume. CONCLUSIONS: We have characterized the PEBP family genes in nine Rosaceae species and examined their phylogeny, genomic syntenic relationship, duplication pattern, and expression profiles during flowering process. These results revealed the evolutionary history of PEBP genes and their functions in regulating floral bud development and blooming among Rosaceae tree species.

Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework.

DNA N6-methyladenine (6mA) represents important epigenetic modifications, which are responsible for various cellular processes. The accurate identification of 6mA sites is one of the challenging tasks in genome analysis, which leads to an understanding of their biological functions. To date, several species-specific machine learning (ML)-based models have been proposed, but majority of them did not test their model to other species. Hence, their practical application to other plant species is quite limited. In this study, we explored 10 different feature encoding schemes, with the goal of capturing key characteristics around 6mA sites. We selected five feature encoding schemes based on physicochemical and position-specific information that possesses high discriminative capability. The resultant feature sets were inputted to six commonly used ML methods (random forest, support vector machine, extremely randomized tree, logistic regression, naïve Bayes and AdaBoost). The Rosaceae genome was employed to train the above classifiers, which generated 30 baseline models. To integrate their individual strength, Meta-i6mA was proposed that combined the baseline models using the meta-predictor approach. In extensive independent test, Meta-i6mA showed high Matthews correlation coefficient values of 0.918, 0.827 and 0.635 on Rosaceae, rice and Arabidopsis thaliana, respectively and outperformed the existing predictors. We anticipate that the Meta-i6mA can be applied across different plant species. Furthermore, we developed an online user-friendly web server, which is available at http://kurata14.bio.kyutech.ac.jp/Meta-i6mA/.

Gut microbiota influence on oral bioaccessibility and intestinal transport of pesticides in Chaenomeles speciosa.

There is limited research focusing on the effects of human gut microbiota on the oral bioaccessibility and intestinal absorption of pesticide residues in food. In the present study, we use a modified setup of the Simulator of the Human Intestinal Microbial Ecosystem for the determination of pesticide residue bioaccessibility in Chaenomeles speciosa, and a Caco-2 cell model of human intestinal absorption. Results showed that gut microbiota played a dual role based their effects on contaminant release and metabolism in the bioaccessibility assay, and Lactobacillus plantarum was one of key bacterial species in the gut microbiota that influenced pesticide stability significantly. The addition of L. plantarum to the system reduced the relative amounts (by 11.40-86.51%) of six pesticides. The interaction between the food matrix and human gut microbiota led to different absorption rates, and the barrier effects increased with an increase in incubation time.

Biological activity, phytochemical parameters, and potential bioaccessibility of wheat bread enriched with powder and microcapsules made from Saskatoon berry.

The aim of the present study was to determine the impact of Saskatoon powder addition on phytochemical parameters, biological activity, and nutritional value of wheat bread. Supplementation increased phenolics content up to 72% in the bread with 6% powder content. This increase was reflected in the improved antioxidative properties of breads, especially after their supplementation with the microencapsulated additives (an increase by 93% in the bread enriched with 6% of powder covered with maltodextrin). The in vitro digestion released the antioxidative compounds, leading to higher bioaccessibility of the breads enriched with the microencapsulated powders. The highest inhibition of activities of cyclooxygenase 1 and -2, as well as amylase and glucosidase was recorded for the breads enriched with the additive microencapsulated with maltodextrin and inulin. Thus, Saskatoon berry powders, especially the microencapsulated ones, may be used as functional components in designing innovative bakery products.

Variations in Triterpenoid Deposition in Cuticular Waxes during Development and Maturation of Selected Fruits of Rosaceae Family.

The process of fruit ripening involves many chemical changes occurring not only in the mesocarp but also in the epicarp, including changes in the triterpenoid content of fruit cuticular waxes that can modify the susceptibility to pathogens and mechanical properties of the fruit surface. The aim of the study was the determination of the ripening-related changes in the triterpenoid content of fruit cuticular waxes of three plant species from the Rosaceae family, including rugosa rose (Rosa rugosa), black chokeberry (Aronia melanocarpa var. "Galicjanka") and apple (Malus domestica var. "Antonovka"). The triterpenoid and steroid content in chloroform-soluble cuticular waxes was determined by a GC-MS/FID method at four different phenological stages. The profile of identified compounds was rather similar in selected fruit samples with triterpenoids with ursane-, oleanane- and lupane-type carbon skeletons, prevalence of ursolic acid and the composition of steroids. Increasing accumulation of triterpenoids and steroids, as well as the progressive enrichment of the composition of these compounds in cuticular wax during fruit development, was observed. The changes in triterpenoid content resulted from modifications of metabolic pathways, particularly hydroxylation and esterification, that can alter interactions with complementary functional groups of aliphatic constituents and lead to important changes in fruit surface quality.