Citrus sinensis (Sweet Orange) Metabolomics Analysis

Citrus sinensis (Sweet Orange) Metabolomics Analysis

Service Details Case Study

What is Citrus sinensis?

Citrus sinensis, commonly known as sweet orange, is a widely cultivated citrus fruit with significant economic and nutritional importance. It belongs to the Rutaceae family and is renowned for its juicy, sweet-tasting flesh. Sweet oranges are not only consumed fresh but are also processed into various products such as orange juice, marmalade, and flavorings. They are rich in essential nutrients like vitamin C, dietary fiber, and antioxidants.

Metabolism and Metabolic Analysis of Citrus sinensis (Sweet Orange)

Metabolism in Citrus sinensis, as in all living organisms, constitutes a complex sequence of biochemical reactions responsible for converting nutrients into energy and synthesizing essential molecules required for growth, maintenance, and reproduction. Primary metabolic processes within Citrus sinensis include glycolysis, the citric acid cycle (Krebs cycle), and oxidative phosphorylation, all of which serve to produce energy. Additionally, secondary metabolism in Citrus sinensis involves the production of various compounds such as flavonoids, terpenoids, and alkaloids, contributing to the fruit's fragrance, flavor, and resistance to pathogens.

The study of Citrus sinensis metabolism is a crucial research domain, aiming to unravel the intricate biochemical pathways inherent to the plant. Researchers employ techniques like metabolomics, enabling them to identify and quantify the diverse metabolites present in the fruit and its tissues. Metabolomics provides insights into the dynamic fluctuations in metabolite levels under varying environmental conditions, during fruit development, and in response to stress factors.

Scientists also explore the metabolic routes involved in the synthesis of significant compounds present in Citrus sinensis, including vitamin C (ascorbic acid) and limonoids, known for their potential health benefits. These investigations seek to optimize citrus cultivation practices and develop novel citrus varieties with improved nutritional attributes and heightened resistance to diseases.

What We Can Provide

Metabolite Profiling: We excel in profiling the diverse array of metabolites found in Citrus sinensis tissues. Our state-of-the-art mass spectrometry techniques enable us to identify and quantify a wide range of primary and secondary metabolites. Whether you're interested in characterizing the nutritional content of sweet oranges or investigating dynamic changes in metabolite profiles under varying environmental conditions, our metabolomics analysis services provide comprehensive insights.

Metabolic Pathway Mapping: Creative Proteomics can help you map the intricate metabolic pathways within Citrus sinensis. By elucidating these pathways, we enable you to pinpoint critical metabolic hubs, identify potential regulatory nodes, and gain a deeper understanding of the metabolic adaptations that Citrus sinensis undergoes in response to different stimuli or developmental stages.

Metabolomics Data Interpretation: Our team of experts not only generates high-quality metabolomics data but also provides in-depth data interpretation and analysis. We offer valuable insights into the significance of identified metabolites, helping you draw meaningful conclusions from your research.

Comparative Metabolomics: Explore the variations in Citrus sinensis metabolomes by comparing different tissues, developmental stages, or genotypes. Comparative metabolomics analysis can shed light on the factors influencing metabolite composition and abundance, leading to a better understanding of Citrus sinensis biology.

Customized Research Projects: At Creative Proteomics, we recognize that each research project is unique. We offer customizable metabolomics solutions tailored to your specific research objectives and questions. Our experienced scientists will collaborate closely with you to design experiments and analyze data to meet your research needs.

Sweet Orange Metabolomics Analysis Techniques

Liquid Chromatography-Mass Spectrometry (LC-MS): Creative Proteomics utilizes state-of-the-art LC-MS systems, such as the Agilent 1290 Infinity II LC System coupled with the Agilent 6550 iFunnel Q-TOF LC/MS, for accurate and high-throughput analysis. This technique excels in identifying and quantifying diverse metabolites, including sugars, organic acids, and secondary metabolites.

Gas Chromatography-Mass Spectrometry (GC-MS): For volatile and semi-volatile metabolites, GC-MS is an indispensable tool. Creative Proteomics employs the Agilent 7890B GC System coupled with the Agilent 5977B MSD, allowing for precise profiling of compounds like terpenoids and fatty acids.

Workflow for Metabolomics ServiceWorkflow for Metabolomics Service

Applications of Metabolomics Analysis in Citrus sinensis Research:

Nutritional Value Understanding: Citrus sinensis is rich in vitamin C and other essential nutrients. Metabolomics analysis allows you to precisely quantify the content of various nutrients in sweet oranges, revealing their potential as healthy foods and optimizing their nutritional value.

Improving Fruit Quality: Metabolomics analysis can aid in understanding the formation of flavors and aromas in Citrus sinensis fruits. By delving into secondary metabolites in fruits, you can identify key compounds influencing flavor, thus enhancing the overall quality of sweet oranges.

Environmental Response Studies: Citrus sinensis may exhibit metabolic adaptations under varying environmental conditions. Metabolomics analysis helps uncover how sweet oranges respond to changes in temperature, humidity, light, and soil conditions, aiding in the optimization of cultivation practices.

Disease and Pest Resistance: Through the analysis of Citrus sinensis metabolism, you can identify metabolites potentially associated with disease and pest resistance. This contributes to the development of more resilient orange varieties, reducing the impact of diseases and pests on crops.

Biotechnological Advancements: Metabolomics analysis plays a crucial role in evaluating new Citrus sinensis varieties introduced through gene editing and genetic modification. It helps validate and optimize the effects of newly introduced metabolic pathways, leading to improved traits.

Food Industry Applications: Metabolomics analysis is also vital in the production of Citrus sinensis-based products. It can be used to monitor components in orange juice and other Citrus sinensis products, ensuring quality and consistency.

Sample Requirements for Sweet Orange Metabolomics

Requirement Description
Sample Type - Fresh, healthy, and disease-free sweet orange tissues, including but not limited to: - Fruit peel - Fruit pulp - Leaves - Roots - Flowers - Phloem and xylem tissues - Any other relevant plant parts
Sample Size Minimum of 100 grams of tissue
Sample Selection Criteria - Select tissues that represent different developmental stages (e.g., mature vs. immature)
- Choose tissues from various locations on the tree (e.g., canopy vs. base)
- Consider using tissues from different sweet orange varieties or cultivars, if applicable
Sample Collection - Harvest samples during the appropriate season and time of day to minimize metabolic fluctuations
- Collect samples using sterile tools to avoid contamination
- Store samples in liquid nitrogen immediately after collection to preserve metabolite integrity
Sample Storage - Maintain frozen storage at -80°C or colder to prevent metabolite degradation
- Use a secure sample tracking system to ensure sample traceability throughout the study
Sample Homogenization Prior to analysis, grind frozen tissues to a fine powder using liquid nitrogen to ensure uniformity and consistency in metabolite extraction
Sample Replicates At least three biological replicates per sample type

Case. Metabolic and Transcriptomic Profiling Reveals the Response of Sweet Orange (Citrus sinensis) Leaves to Low pH Stress


Acidic soil is a prevalent environmental stress factor in agriculture that can severely impact plant growth and overall crop productivity. Understanding how plants respond to low pH stress is crucial for improving agricultural practices and ensuring sustainable food production. In this study, sweet orange seedlings (Citrus sinensis) were chosen as the model plant to investigate the metabolic responses to low pH stress. Sweet orange is an economically important citrus fruit crop, and understanding its response to acidic conditions can have practical implications for citrus cultivation.


Seedlings of sweet orange (Citrus sinensis) were grown in a greenhouse under controlled conditions. They were subjected to two different pH treatments: low pH (pH 2.5) and control pH (pH 6.0). Leaves were harvested nine months after the pH treatments.

Technological Methods

Seedling Culture: Sweet orange seeds were germinated and grown in sand-filled pots within a greenhouse. The nutrient solution was adjusted to the respective pH conditions.

RNA Extraction, Library Construction, RNA-Seq, and Analysis: RNA was extracted from leaf samples using the Biomarker Plant Total RNA Isolation Kit. Libraries for RNA sequencing (RNA-Seq) were constructed, followed by sequencing using an Illumina HiSeq™ X-TEN platform. Data processing involved the removal of low-quality reads and reads with adapters or poly-N content. High-quality clean reads were mapped to the Citrus sinensis reference sequences. Differentially expressed genes (DEGs) were identified based on specific criteria. Additionally, a subset of 26 DEGs was selected for validation using quantitative reverse transcription-polymerase chain reaction (qRT-PCR).

Metabolite Analysis: Detailed metabolite analysis was performed to understand the metabolic changes in leaves. Organic acids (OAs) and free amino acids (FAAs) in the leaves were analyzed using ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS). This highly sensitive technique enabled the accurate qualitative and quantitative analysis of OAs and FAAs in the leaf samples.

Statistical Analysis: Statistical analysis was conducted to compare means between treatments.


  • Impact on Photosynthesis: Low pH impaired photosynthetic pigment biosynthesis, light reactions, and carbon fixation, resulting in reduced pigment levels and photosynthesis.
  • Metabolic Changes: Low pH led to a decrease in carbon and carbohydrate metabolism, OA biosynthesis, and ATP production in leaves.
  • Amino Acid Biosynthesis: The biosynthesis of nitrogen compounds, proteins, and FAAs was downregulated in low pH-treated leaves.
  • Oxidative Damage: Low pH disrupted the balance between ROS and aldehyde production and detoxification, leading to oxidative damage in leaves.
  • Adaptive Responses to Pi Starvation: Low pH-treated leaves exhibited adaptive responses to phosphorus (Pi) starvation, including Pi recycling, lipid remodeling, and Pi transport, enhancing their tolerance to acidic conditions.

Concentrations of FAAs and OAs in Leaves.Concentrations of FAAs and OAs in Leaves.


  1. Lai, Ning-Wei, et al. "Molecular and physiological responses of Citrus sinensis leaves to long-term low pH revealed by RNA-Seq integrated with targeted metabolomics." International Journal of Molecular Sciences 23.10 (2022): 5844.