Chemical Structure

Metabolite Name

Flower Color

Explore the fascinating world of flower colors, from their genetic basis to the pigments that create nature's beautiful palette.

Anthocyanins: The Most Common Flower Pigments

Anthocyanins are water-soluble pigments belonging to the flavonoid class, responsible for many of the red, purple, and blue colors observed in flowers, fruits, and leaves. Their specific color depends on their chemical structure and the cellular environment (like pH).

Definition and Classification

The core structure of an anthocyanin is called an anthocyanidin (or aglycone). There are six primary anthocyanidins commonly found in nature:

  • Cyanidin (Basis for red/purple colors)
  • Delphinidin (Basis for blue/purple colors)
  • Pelargonidin (Basis for orange/red colors)
  • Peonidin (Methylated Cyanidin, magenta/red)
  • Petunidin (Methylated Delphinidin, purple)
  • Malvidin (Dimethylated Delphinidin, purple)

These anthocyanidins are typically stabilized by the attachment of sugar molecules (glycosylation), most commonly at the 3-position, forming the actual anthocyanins (e.g., Cyanidin-3-O-glucoside).

Anthocyanin Biosynthesis Pathway

This simplified pathway illustrates the synthesis of common anthocyanidin glucosides starting from Phenylalanine. Hover over the metabolite rectangles to view their chemical structures.

Phenylalanine trans-cinnamic acid p-Coumaric acid Coumaroyl-CoA Naringenin chalcone Naringenin Dihydrokaempferol (DHK) Dihydroquercetin (DHQ) Dihydromyricetin (DHM) Leucopelargonidin Leucocyanidin Leucodelphinidin Pelargonidin Cyanidin Delphinidin Pelargonidin-3-O-glucoside Cyanidin-3-O-glucoside Delphinidin-3-O-glucoside PAL C4H 4CL CHS CHI F3H F3'H F3'5'H DFR DFR DFR ANS ANS ANS UFGT UFGT UFGT

Interactive Anthocyanidin Cards

Click on a card below for more details about the specific anthocyanidin, or adjust the pH slider to see how the cellular environment influences their color. The images shown are representative structures of the core anthocyanidins.

pH: 7.0
Pelargonidin Structure

Pelargonidin

(Typically Red/Orange)

Cyanidin Structure

Cyanidin

(Red/Magenta/Blue)

Delphinidin Structure

Delphinidin

(Blue/Purple/Red)

Peonidin Structure

Peonidin

(Red/Pink/Purple/Blue)

Petunidin Structure

Petunidin

(Dark Red/Purple)

Malvidin Structure

Malvidin

(Red/Purple/Blue)

Factors Affecting Color Diversity

The vast array of flower colors arises not only from the type of anthocyanidin but also from various modifications and interactions:

  • Glycosylation: Adding different sugars at various positions affects solubility and stability.
  • Acylation: Attaching organic acids (acyl groups) to the sugars often shifts the color towards blue and increases stability.
  • Methylation: Adding methyl groups changes the anthocyanidin structure (e.g., cyanidin to peonidin).
  • pH: The acidity of the cell vacuole drastically alters the structure and thus the color of the anthocyanin (as simulated above).
  • Co-pigmentation: Anthocyanins can interact with other (often colorless) molecules like flavonols or tannins, intensifying and shifting their color (often towards blue).
  • Metal Ion Complexation: Formation of complexes with metal ions (e.g., Mg²⁺, Al³⁺, Fe³⁺) can produce stable blue colors.

Key References (Anthocyanins)

[1] Sunil, L., & Shetty, N. P. (2022). Biosynthesis and regulation of anthocyanin pathway genes. Applied Microbiology and Biotechnology, 106(5-6), 1783-1798.
[2] Yin, X., Wang, T., Zhang, M., Zhang, Y., Irfan, M., Chen, L., & Zhang, L. (2021). Role of core structural genes for flavonoid biosynthesis and transcriptional factors in flower color of plants. Biotechnology & Biotechnological Equipment, 35(1), 1214-1229.

Carotenoids: The Yellows, Oranges, and Reds

Carotenoids are lipid-soluble pigments found in the plastids of plant cells. They are responsible for many of the bright yellow, orange, and red colors in flowers, as well as in fruits and autumn leaves. Besides coloration, they play crucial roles in photosynthesis (accessory light harvesting) and photoprotection.

Definition and Classification

Carotenoids are tetraterpenoids, meaning they are built from eight isoprene units. They are broadly classified into two groups:

  • Carotenes: Hydrocarbons, such as β-carotene (orange) and lycopene (red).
  • Xanthophylls: Oxygenated derivatives of carotenes, containing hydroxyl, epoxy, or keto groups, such as lutein (yellow) and zeaxanthin (yellow).

The specific carotenoids present and their concentrations determine the final hue. For example, daffodils are rich in various xanthophylls, while tomatoes get their red from lycopene.

Carotenoid Biosynthesis Pathway (Simplified)

This simplified pathway illustrates the synthesis of common carotenoids starting from Geranylgeranyl Pyrophosphate (GGPP), which itself is derived from the MEP pathway in plastids. Hover over the metabolite rectangles to view their chemical structures.

Geranylgeranyl-PP (GGPP) Phytoene Lycopene (Red) β-Carotene (Orange) α-Carotene (Yellow-Orange) Zeaxanthin (Yellow) Lutein (Yellow) PSY PDS, ZDS, CRTISO LCYB LCYE/LCYB CHYB (BCH) CHYE (CYP97C), CHYB (BCH)

Factors Affecting Carotenoid Colors

  • Type and Concentration: The specific carotenoids present and their relative amounts are the primary determinants of color.
  • Physical State: Aggregation state and association with proteins can influence color.
  • Environmental Factors: Light intensity and temperature can affect carotenoid biosynthesis and degradation.
  • Genetic Regulation: The expression of genes in the carotenoid biosynthesis pathway dictates which carotenoids are produced.

Reference (Carotenoids - General)

Tang W, Wang Y, Zhang J, Cai Y, He Z. Biosynthetic Pathway of Carotenoids in Rhodotorula and Strategies for Enhanced Their Production. J Microbiol Biotechnol. 2019;29(4):507-517.

Betalains: Vibrant and Unique Pigments

Betalains are water-soluble, nitrogen-containing pigments found primarily in plants of the order Caryophyllales (e.g., cacti, beets, bougainvillea, amaranth). They produce a range of colors from yellow/orange (betaxanthins) to red/violet (betacyanins). An important characteristic is that betalains and anthocyanins are mutually exclusive in plants; a plant species will produce one type or the other, but not both.

Definition and Classification

Betalains are derived from tyrosine. They are classified into two main groups based on their structure and color:

  • Betacyanins: Red-violet pigments. They are glycosides of betanidin (e.g., betanin from beetroot, which is betanidin 5-O-β-glucoside).
  • Betaxanthins: Yellow-orange pigments. They are formed by the condensation of betalamic acid with various amino acids or amines (e.g., indicaxanthin from prickly pear).

The vivid colors of flowers like bougainvillea (actually colored bracts) and portulaca are due to betalains.

Betalain Biosynthesis Pathway (Simplified)

This simplified pathway shows the synthesis of betalains from Tyrosine. Hover over the metabolite rectangles to view their chemical structures.

Tyrosine L-DOPA Betalamic Acid cyclo-DOPA Betanidin Betacyanins (Red/Violet) Amino Acids/Amines Betaxanthins (Yellow/Orange) Tyrosinase (CYP76AD) Tyrosinase (CYP76AD) DODA (DOPA 4,5-dioxygenase) (Spontaneous Condensation) (Spontaneous Condensation) Glucosyl- transferase

Factors Affecting Betalain Colors

  • Specific Betalain Compound: The type of betacyanin or betaxanthin determines the base color.
  • pH: Betalains are generally stable over a wider pH range (pH 3-7) compared to anthocyanins, but extreme pH can cause degradation.
  • Temperature and Light: High temperatures and prolonged light exposure can lead to degradation of betalains.
  • Enzymatic Activity: Enzymes like peroxidases can degrade betalains.

Reference (Betalains - General)

Tanaka Y, Sasaki N, Ohmiya A. Biosynthesis of plant pigments: anthocyanins, betalains and carotenoids. Plant J. 2008;54(4):733-749.

Case Study: The Colors of Stock Flower (Matthiola incana)

A 2025 study in the Plant Biotechnology Journal by Chen et al. provides a fantastic real-world example of how anthocyanin biosynthesis creates color diversity. By studying white, pink, and rose-red varieties of stock flower (Matthiola incana), they pinpointed the exact molecular mechanisms.

1. Phenotypes and Pigments

The study analyzed three distinct color varieties. The primary difference was the accumulation of pelargonidin, a type of anthocyanidin responsible for red/orange hues.

White Matthiola incana

White Flower
Lacks significant anthocyanins.

Pink Matthiola incana

Pink Flower
Accumulates pelargonidin.

Rose-red Matthiola incana

Rose-red Flower
Accumulates high levels of pelargonidin.

2. The Genetic Blueprint

The color change is directly linked to the up-regulation of key genes in the anthocyanin biosynthesis pathway. The pathway branch leading to pelargonidin is activated in the colored flowers.

Anthocyanin pathway in Matthiola

Simplified pathway from Chen et al. (2025).

Key Upregulated Genes

Expression levels of these genes were significantly higher in pink/rose-red flowers compared to white ones.

Gene Function
F3H Structural Gene
DFR Structural Gene
ANS Structural Gene
MYB12 Transcription Factor
MYB111 Transcription Factor
MYB90 (PAP2) Transcription Factor

Case Study Reference

Chen, D., Yang, T., Chen, H., et al. (2025). Largest genome assembly in Brassicaceae: retrotransposon-driven genome expansion and karyotype evolution in Matthiola incana. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.70193.