Cucurbita pepo Metabolomics Analysis

Cucurbita pepo Metabolomics Analysis

Service Details Case Study

What is Cucurbita pepo?

Cucurbita pepo, commonly known as the summer squash or pumpkin, is a species of squash belonging to the Cucurbitaceae family. This versatile plant exhibits a diverse array of cultivars, including zucchini, acorn squash, and various types of pumpkins. Cultivated globally for its culinary and ornamental purposes, Cucurbita pepo holds nutritional significance and is a staple in many cuisines.

Cucurbita pepo Metabolomics Analysis Projects in Creative Proteomics

Nutritional Profiling: Uncover the nutritional richness of Cucurbita pepo cultivars. Our analysis precisely quantifies essential nutrients, vitamins, and bioactive compounds, offering a detailed nutritional profile for informed dietary choices.

Metabolic Pathway Mapping: Navigate through the biochemical pathways of Cucurbita pepo. We provide a detailed map of the metabolic routes, shedding light on the plant's responses to environmental factors, developmental stages, and stress conditions.

Bioactive Compound Identification: Dive into the realm of bioactive compounds. Our analysis identifies and quantifies compounds with potential health benefits, contributing to research in nutraceuticals, pharmacology, and functional food development.

Varietal-Specific Metabolite Analysis: Explore the diversity within Cucurbita pepo cultivars. Our services include varietal-specific metabolite analysis, allowing you to understand the unique metabolic fingerprints of different squash varieties.

Quality Control Markers: Ensure product excellence in the food industry. We monitor key metabolites that define flavor, aroma, and nutritional value, providing quality control markers for Cucurbita pepo-derived products.

Environmental Stress Response Profiling: Gain insights into how Cucurbita pepo responds to environmental stressors. Our analysis includes stress response profiling, contributing valuable information for sustainable cultivation practices.

Customized Data Analysis: Tailor the analysis to meet your specific research objectives. Creative Proteomics provides customized data analysis, ensuring that the results align with your unique goals and research questions.

Methodology and Analytical Techniques for Cucurbita pepo Metabolomics

Metabolomics analytical techniques for Cucurbita pepo typically involve mass spectrometry (MS) coupled with various separation techniques. Several instrumental platforms are commonly used in metabolomics studies, and the choice of a specific instrument depends on the research objectives and the type of metabolites being targeted.

Gas Chromatography-Mass Spectrometry (GC-MS): GC-MS is suitable for volatile and semi-volatile metabolites. Gas chromatography separates compounds based on their volatility, and mass spectrometry is used for compound identification.

  • Instrument Model: Agilent 7890A GC coupled with Agilent 5975C MSD

Liquid Chromatography-Mass Spectrometry (LC-MS): LC-MS is versatile and can analyze a wide range of metabolites, including polar and non-polar compounds. High-performance liquid chromatography (HPLC) or ultra-high-performance liquid chromatography (UHPLC) is commonly coupled with MS.

  • Instrument Model: Thermo Fisher Scientific Q Exactive series

Nuclear Magnetic Resonance (NMR) Spectroscopy: NMR spectroscopy provides information on the molecular structure of metabolites. It is non-destructive and does not require extensive sample preparation. However, it is generally less sensitive than mass spectrometry.

  • Instrument Model: Bruker Avance series

Capillary Electrophoresis-Mass Spectrometry (CE-MS): CE-MS is suitable for analyzing charged and polar metabolites. Capillary electrophoresis separates compounds based on their charge and size, and MS is used for detection.

  • Instrument Model: Agilent 7100 series CE coupled with Agilent 6210 TOF MS

Direct Infusion Mass Spectrometry: Direct infusion MS allows for the rapid analysis of samples without the need for chromatographic separation. It is particularly useful for high-throughput screening of metabolites.

  • Instrument Model: Waters Xevo G2-XS QTof MS

Workflow for Metabolomics ServiceWorkflow for Metabolomics Service

Sample Requirements for Cucurbita pepo Metabolomics

Sample Type Sample Matrix Sample Weight Extraction Solvent Extraction Time Storage Conditions
Zucchini Leaves Fresh plant material 100 mg 80% Methanol:Water 24 hours -80°C (short-term storage)
Pumpkin Seeds Dried seeds 50 mg 2:1 Chloroform:Methanol 2 hours -20°C (long-term storage)
Zucchini Fruit Pulp Fresh fruit tissue 200 mg 50% Acetonitrile:Water 30 minutes -80°C (short-term storage)
Pumpkin Flower Petals Freeze-dried petals 30 mg 100% Ethanol 1 hours -20°C (long-term storage)
Zucchini Root Extract Frozen root samples 150 mg 70% Acetone 12 hours -80°C (short-term storage)
Pumpkin Stem Sections Homogenized stem tissue 120 mg 1:1 Methanol:Water 15 minutes -20°C (long-term storage)

Case. Transcriptomic Profiling and Metabolite Analysis of Squash Nectaries


This study marks the inaugural exploration of the global gene expression profile of cucurbit nectaries, focusing specifically on squash. While existing research has extensively examined Arabidopsis and Nicotiana spp. as genetic models for nectar production, this investigation extends molecular biology approaches to systems with larger nectaries. The primary aim is to enhance understanding of nectary biology, particularly in terms of quantitative biochemical, physiological, and comparative studies. The research builds upon prior studies in Arabidopsis and pennycress, providing a comprehensive analysis of gene expression and metabolic processes involved in squash nectary maturation and secretion.


The study utilizes squash nectaries for transcriptomic and metabolite analyses. The RNAseq analysis maps reads to 8,863 unique genes in C. pepo and C. melo, demonstrating consistency with gene expression in Arabidopsis nectaries. The research also includes validation through qRT-PCR analysis of eight targeted genes. Metabolite analysis identifies over 40 compounds in both male and female nectar, showcasing the complexity of nectar composition.

Technological Methods

Metabolite Profiling:

  • Systematically collected male and female squash nectar samples.
  • Utilized extraction methods to capture a diverse range of metabolites.

Analytical Tools:

  • Leveraged mass spectrometry (MS) and nuclear magnetic resonance (NMR) for accurate metabolite identification.
  • Identified and characterized over 40 metabolites in both male and female nectars.

Quantitative Analysis:

  • Applied quantitative measures, including calibration curves and standards.
  • Provided precise quantification of metabolite abundance.

Integration with Gene Expression:

  • Correlated metabolite data with RNAseq gene expression analysis.
  • Established connections between genetic regulation and nectar biochemical composition.

Statistical Approaches:

  • Employed advanced statistical methods such as PCA and clustering.
  • Uncovered variations in metabolite profiles between male and female nectar.

Validation and Replication:

  • Ensured result reliability through replication of experiments.
  • Validated metabolite findings against existing literature for robust conclusions.

Integration of Transcriptomic Data:

  • Merged metabolomic insights with RNAseq data.
  • Formed a comprehensive understanding of molecular processes governing nectar production.


The study presents the inaugural global gene expression profile of cucurbit nectaries, filling a gap in research on nectar production. Unlike previous models focusing on Arabidopsis and Nicotiana spp., this research extends molecular biology approaches to larger nectary systems, specifically in squash.

Utilizing RNAseq, the study mapped reads to 8,863 unique genes in C. pepo and C. melo, comparable to Arabidopsis nectaries. Numerous genes exhibited stage-specific expression during nectary maturation, validated through qRT-PCR, emphasizing the dataset's quality.

The analysis identified candidate genes involved in crucial steps of nectar synthesis, such as starch and sucrose dynamics. Notably, the expression pattern of CpCWINV4 in squash differed from Arabidopsis, suggesting a distinct role in influencing final nectar quality through sucrose hydrolysis.

Metabolite analysis revealed over 40 compounds in male and female nectars, with notable differences. Female nectar contained approximately five times more GABA, correlated with the expression of a putative GABA transporter. Additionally, a previously unreported neurotransmitter, gamma-hydroxybutyric acid, was identified in both male and female nectars.

Exploring transcription factors, MYB305 exhibited little difference in expression between male and female nectaries, while others like SHI-related sequence 1 showed preferential expression in female nectaries. This suggests potential links between transcription factors and variations in nectar composition.

Volcano plot of the Cucurbita pepo nectar metabolomeVolcano plot of the Cucurbita pepo nectar metabolome


  1. Solhaug, Erik M., et al. "An integrated transcriptomics and metabolomics analysis of the Cucurbita pepo nectary implicates key modules of primary metabolism involved in nectar synthesis and secretion." Plant Direct 3.2 (2019): e00120.