Browse
Submit Data
Databases
API
Help

Dataset Information

30 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Insights of Phenolic Pathway in Fruits: Transcriptional and Metabolic Profiling in Apricot (Prunus armeniaca).

ABSTRACT: There is an increasing interest in polyphenols, plant secondary metabolites, in terms of fruit quality and diet, mainly due to their antioxidant effect. However, the identification of key gene enzymes and their roles in the phenylpropanoid pathway in temperate fruits species remains uncertain. Apricot (Prunus armeniaca) is a Mediterranean fruit with high diversity and fruit quality properties, being an excellent source of polyphenol compounds. For a better understanding of the phenolic pathway in these fruits, we selected a set of accessions with genetic-based differences in phenolic compounds accumulation. HPLC analysis of the main phenolic compounds and transcriptional analysis of the genes involved in key steps of the polyphenol network were carried out. Phenylalanine ammonia-lyase (PAL), dihydroflavonol-4-reductase (DFR) and flavonol synthase (FLS) were the key enzymes selected. Orthologous of the genes involved in transcription of these enzymes were identified in apricot: ParPAL1, ParPAL2, ParDFR, ParFLS1 and ParFLS2. Transcriptional data of the genes involved in those critical points and their relationships with the polyphenol compounds were analyzed. Higher expression of ParDFR and ParPAL2 has been associated with red-blushed accessions. Differences in expression between paralogues could be related to the presence of a BOXCOREDCPAL cis-acting element related to the genes involved in anthocyanin synthesis ParFLS2, ParDFR and ParPAL2.

SUBMITTER: Gomez-Martinez H

PROVIDER: S-EPMC8037730 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Comparative transcriptome profiling and morphology provide insights into endocarp cleaving of apricot cultivar (Prunus armeniaca L.).

Project description:BackgroundA complete and hardened endocarp is a typical trait of drupe fruits. However, the 'Liehe' (LE) apricot cultivar has a thin, soft, cleavable endocarp that represents 60.39% and 63.76% of the thickness and lignin content, respectively, of the 'Jinxihong' (JG) apricot (with normal hardened-endocarp). To understand the molecular mechanisms behind the LE apricot phenotype, comparative transcriptomes of Prunus armeniaca L. were sequenced using Illumina HiSeq™ 2500.ResultsIn this study, we identified 63,170 unigenes including 15,469 genes >1000 bp and 25,356 genes with Gene Function annotation. Pathway enrichment and expression patterns were used to characterize differentially expression genes. The DEGs encoding key enzymes involved in phenylpropanoid biosynthesis were significantly down-regulated in LE apricot. For example, CAD gene expression levels, encoding cinnamyl alcohol dehydrogenase, were only 1.3%, 0.7%, 0.2% and 2.7% in LE apricot compared with JG cultivar at 15, 21, 30, 49 days after full bloom (DAFB). Furthermore, transcription factors regulating secondary wall and lignin biosynthesis were identified. Especially for SECONDARY WALL THICKENING PROMOTING FACTOR 1 (NST 1), its expression levels in LE apricot were merely 2.8% and 9.3% compared with JG cultivar at 15 and 21 DAFB, respectively.ConclusionsOur comparative transcriptome analysis was used to understand the molecular mechanisms underlie the endocarp-cleaving phenotype in LE apricot. This new apricot genomic resource and the candidate genes provide a useful reference for further investigating the lignification during development of apricot endocarp. Transcription factors such as NST1 may regulate genes involved in phenylpropanoid pathway and affect development and lignification of the endocarp.

| S-EPMC5387262 | biostudies-literature

Transcriptional regulatory networks controlling taste and aroma quality of apricot (Prunus armeniaca L.) fruit during ripening.

Project description:BackgroundTaste and aroma, which are important organoleptic qualities of apricot (Prunus armeniaca L.) fruit, undergo rapid and substantial changes during ripening. However, the associated molecular mechanisms remain unclear. The goal of this study was to identify candidate genes for flavor compound metabolism and to construct a regulatory transcriptional network.ResultsWe characterized the transcriptome of the 'Jianali' apricot cultivar, which exhibits substantial changes in flavor during ripening, at 50 (turning), 73 (commercial maturation) and 91 (full ripe) days post anthesis (DPA) using RNA sequencing (RNA-Seq). A weighted gene co-expression network analysis (WGCNA) revealed that four of 19 modules correlated highly with flavor compound metabolism (P < 0.001). From them, we identified 1237 differentially expressed genes, with 16 intramodular hubs. A proposed pathway model for flavor compound biosynthesis is presented based on these genes. Two SUS1 genes, as well as SPS2 and INV1 were correlated with sugar biosynthesis, while NADP-ME4, two PK-like and mitochondrial energy metabolism exerted a noticeable effect on organic acid metabolism. CCD1 and FAD2 were identified as being involved in apocarotenoid aroma volatiles and lactone biosynthesis, respectively. Five sugar transporters (Sweet10, STP13, EDR6, STP5.1, STP5.2), one aluminum-activated malate transporter (ALMT9) and one ABCG transporter (ABCG11) were associated with the transport of sugars, organic acids and volatiles, respectively. Sixteen transcription factors were also highlighted that may also play regulatory roles in flavor quality development.ConclusionsApricot RNA-Seq data were obtained and used to generate an annotated set of predicted expressed genes, providing a platform for functional genomic research. Using network analysis and pathway mapping, putative molecular mechanisms for changes in apricot fruit taste and aroma during ripening were elucidated.

| S-EPMC6332858 | biostudies-literature

Purification and Characterization of Latent Polyphenol Oxidase from Apricot (Prunus armeniaca L.).

Project description:Polyphenol oxidase from apricot (Prunus armeniaca) (PaPPO) was purified in its latent form (L-PaPPO), and the molecular weight was determined to be 63 kDa by SDS-PAGE. L-PaPPO was activated in the presence of substrate at low pH. The activity was enhanced by CuSO4 and low concentrations (≤ 2 mM) of SDS. PaPPO has its pH and temperature optimum at pH 4.5 and 45 °C for catechol as substrate. It showed diphenolase activity and highest affinity toward 4-methylcatechol (KM = 2.0 mM) and chlorogenic acid (KM = 2.7 mM). L-PaPPO was found to be spontaneously activated during storage at 4 °C, creating a new band at 38 kDa representing the activated form (A-PaPPO). The mass of A-PaPPO was determined by mass spectrometry as 37 455.6 Da (Asp102 → Leu429). Both L-PaPPO and A-PaPPO were identified as polyphenol oxidase corresponding to the known PaPPO sequence (UniProt O81103 ) by means of peptide mass fingerprinting.

| S-EPMC5609118 | biostudies-literature

Polyphenol oxidase and enzymatic browning in apricot (Prunus armeniaca L.): Effect on phenolic composition and deduction of main substrates.

Project description:In this study, we investigate the effect of enzymatic browning on the phenolic composition of apricot in vivo and in vitro. The in vitro browning was caused by the recombinant latent apricot polyphenol oxidase (L-PaPPO). Successful heterologous expression of PaPPO in Escherichia coli yielded substantial amounts of enzyme containing both copper ions in the catalytic active site. The expressed L-PaPPO was characterized with regard to its molecular mass (56531.3 Da), pH optimum (7.0), activation by SDS, and enzyme kinetics. LC-MS/MS was used to compare the phenolic profiles of brown and non-brown apricots. The browning reactions did significantly decrease total phenolics and antioxidant capacity (measured with DPPH and CUPRAC assays). Catechin, epicatechin, and B-type procyanidins were the individual phenolics most affected by browning, followed by chlorogenic and neochlorogenic acid. These phenolics are most likely the main endogenous substrates of L-PaPPO, as they were oxidized much faster than the other identified phenolics.

| S-EPMC8789516 | biostudies-literature

Potential Toxic Levels of Cyanide in Almonds (Prunus amygdalus), Apricot Kernels (Prunus armeniaca), and Almond Syrup.

Project description:Under normal environmental conditions, many plants synthesize cyanogenic glycosides, which are able to release hydrogen cyanide upon hydrolysis. Each year, there are frequent livestock and occasional human victims of cyanogenic plants consumption. The present work aims to determine the hydrocyanic acid content in different samples of cyanogenic plants, selected from the Tunisian flora, and in the almond syrup. In order to evaluate their toxicity and their impact on the consumer health in the short term as well as in the long term, using the ISO 2164-1975 NT standard, relating to the determination of cyanogenic heterosides in leguminous plants.

| S-EPMC3793392 | biostudies-literature

Monitoring Apricot (Prunus armeniaca L.) Ripening Progression through Candidate Gene Expression Analysis.

Project description:This study aimed at the monitoring of the apricot (Prunus armeniaca L.) ripening progression through the expression analysis of 25 genes related to fruit quality traits in nine cultivars with great differences in fruit color and ripening date. The level of pigment compounds, such as anthocyanins and carotenoids, is a key factor in food taste, and is responsible for the reddish blush color or orange skin and flesh color in apricot fruit, which are desirable quality traits in apricot breeding programs. The construction of multiple linear regression models to predict anthocyanins and carotenoids content from gene expression allows us to evaluate which genes have the strongest influence over fruit color, as these candidate genes are key during biosynthetic pathways or gene expression regulation, and are responsible for the final fruit phenotype. We propose the gene CHS as the main predictor for anthocyanins content, CCD4 and ZDS for carotenoids content, and LOX2 and MADS-box for the beginning and end of the ripening process in apricot fruit. All these genes could be applied as RNA markers to monitoring the ripening stage and estimate the anthocyanins and carotenoids content in apricot fruit during the ripening process.

| S-EPMC9105867 | biostudies-literature

Gene Expression Analysis of Plum pox virus (Sharka) Susceptibility/Resistance in Apricot (Prunus armeniaca L.).

Project description:RNA-Seq has proven to be a very powerful tool in the analysis of the Plum pox virus (PPV, sharka disease)/Prunus interaction. This technique is an important complementary tool to other means of studying genomics. In this work an analysis of gene expression of resistance/susceptibility to PPV in apricot is performed. RNA-Seq has been applied to analyse the gene expression changes induced by PPV infection in leaves from two full-sib apricot genotypes, "Rojo Pasión" and "Z506-7", resistant and susceptible to PPV, respectively. Transcriptomic analyses revealed the existence of more than 2,000 genes related to the pathogen response and resistance to PPV in apricot. These results showed that the response to infection by the virus in the susceptible genotype is associated with an induction of genes involved in pathogen resistance such as the allene oxide synthase, S-adenosylmethionine synthetase 2 and the major MLP-like protein 423. Over-expression of the Dicer protein 2a may indicate the suppression of a gene silencing mechanism of the plant by PPV HCPro and P1 PPV proteins. On the other hand, there were 164 genes involved in resistance mechanisms that have been identified in apricot, 49 of which are located in the PPVres region (scaffold 1 positions from 8,050,804 to 8,244,925), which is responsible for PPV resistance in apricot. Among these genes in apricot there are several MATH domain-containing genes, although other genes inside (Pleiotropic drug resistance 9 gene) or outside (CAP, Cysteine-rich secretory proteins, Antigen 5 and Pathogenesis-related 1 protein; and LEA, Late embryogenesis abundant protein) PPVres region could also be involved in the resistance.

| S-EPMC4684361 | biostudies-literature

The apricot (Prunus armeniaca L.) genome elucidates Rosaceae evolution and beta-carotenoid synthesis.

Project description:Apricots, scientifically known as Prunus armeniaca L, are drupes that resemble and are closely related to peaches or plums. As one of the top consumed fruits, apricots are widely grown worldwide except in Antarctica. A high-quality reference genome for apricot is still unavailable, which has become a handicap that has dramatically limited the elucidation of the associations of phenotypes with the genetic background, evolutionary diversity, and population diversity in apricot. DNA from P. armeniaca was used to generate a standard, size-selected library with an average DNA fragment size of ~20 kb. The library was run on Sequel SMRT Cells, generating a total of 16.54 Gb of PacBio subreads (N50 = 13.55 kb). The high-quality P. armeniaca reference genome presented here was assembled using long-read single-molecule sequencing at approximately 70× coverage and 171× Illumina reads (40.46 Gb), combined with a genetic map for chromosome scaffolding. The assembled genome size was 221.9 Mb, with a contig NG50 size of 1.02 Mb. Scaffolds covering 92.88% of the assembled genome were anchored on eight chromosomes. Benchmarking Universal Single-Copy Orthologs analysis showed 98.0% complete genes. We predicted 30,436 protein-coding genes, and 38.28% of the genome was predicted to be repetitive. We found 981 contracted gene families, 1324 expanded gene families and 2300 apricot-specific genes. The differentially expressed gene (DEG) analysis indicated that a change in the expression of the 9-cis-epoxycarotenoid dioxygenase (NCED) gene but not lycopene beta-cyclase (LcyB) gene results in a low β-carotenoid content in the white cultivar "Dabaixing". This complete and highly contiguous P. armeniaca reference genome will be of help for future studies of resistance to plum pox virus (PPV) and the identification and characterization of important agronomic genes and breeding strategies in apricot.

| S-EPMC6861294 | biostudies-literature

Profiling of Primary Metabolites and Volatiles in Apricot (Prunus armeniaca L.) Seed Kernels and Fruits in the Context of Its Different Cultivars and Soil Type as Analyzed Using Chemometric Tools.

Project description:The goal of this study was to assess nutrient primary metabolites and aroma determinants in Prunus armeniaca L. fruits and seed kernels grown in Egypt represented by its different cultivars and agricultural conditions i.e., two different soil types (muddy versus sandy). Two techniques were employed to assess non-volatile and volatile metabolites using gas chromatography mass-spectrometry (GC-MS) post silylation, and headspace solid-phase micro-extraction (HS-SPME) coupled GC-MS, respectively. A total of 36 peaks belonging to sugars, fatty acids/esters and organic acids were identified by GC-MS in various apricot fruits and seed kernels cultivars. Glucose and sucrose were enriched in apricot fruits compared to the seed kernels. A total of 70 volatiles were identified, with lactones, alcohols and esters representing the main classes of apricot volatiles accounting for its discrete aroma. (E)-Anethole, β-ionone, γ-decanolactone and methyl palmitate were the major peaks contributing to the discrimination between various fruit cultivars and providing novel insight on apricot metabolome.

| S-EPMC9104916 | biostudies-literature

Monitoring Fruit Growth and Development in Apricot (Prunus armeniaca L.) through Gene Expression Analysis.

Project description:The main objective of this study was to monitor apricot development and ripening through gene expression analysis of key candidate genes using the RT-qPCR technique. Eight apricot cultivars were selected to analyze phenological and genetic patterns from pre-ripening stages through to postharvest. In addition, 19 selected genes were analyzed in the contrasting cultivars 'Cebas Red' and 'Rojo Pasión' in different stages (two preharvest stages S1 and S2, one harvest stage S3, and two postharvest stages S4 and S5). This pool of genes included genes related to fruit growth and ripening, genes associated with fruit color, and genes linked to the fruit's nutraceutical aspects. Among the studied genes, Polygalacturonase (PG), Pectin methylesterase (PME), Aminocyclopropane-1-carboxylate synthase (ACS), and Myo-inositol-1-phosphate synthase (INO1) were directly related to fruit maturation and quality. Significant differential expression was observed between the cultivars, which correlated with variations in firmness, shelf life, and sensory characteristics of the apricots. 'Rojo Pasión' displayed high levels of PG, associated with rapid maturation and shorter postharvest shelf life, whereas 'Cebas Red' exhibited lower levels of this gene, resulting in greater firmness and extended shelf life. Genes CCD4, CRTZ, and ZDS, related to carotenoids, showed varied expression patterns during growth and postharvest stages, with higher levels in 'Rojo Pasión'. On the other hand, Sucrose synthase (SUSY) and Lipoxygenase (LOX2) were prominent during the postharvest and growth stages, respectively. Additionally, GDP-L-galactose phosphorylase (VTC2_5) was linked to better postharvest performance. This research provides valuable insights for future breeding initiatives aimed at enhancing the quality and sustainability of apricot cultivation.

| S-EPMC11354700 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data