Metabolomics of Plant Pigmentation: Exploring the Rich Tapestry of Natural Colors

The natural world boasts a dazzling spectrum of colors, extending far beyond the ubiquitous green we associate with plant life. From the vibrant reds and oranges to the calming blues and regal purples, as well as the enigmatic black hues, nature's palette is remarkably diverse. Given that color is perhaps the most visually striking facet of plant biology, the scientific exploration of pigmentation has delved into profound depths. Presently, three principal categories of compounds stand at the forefront of color-related research.


Anthocyanins: Masters of Red, Blue, Purple, and Black


The first category encompasses anthocyanins, the masterminds behind the creation of red, blue, purple, and black colors in plants. For instance, pelargonidin-3,5-diglucoside, pelargonidin-3-glucoside, and delphinidin-3-glucoside orchestrate the splendid red hues seen in strawberries[1]. In the realm of hyacinth flowers, cyanin takes center stage in producing the mesmerizing blue tones[2]. Meanwhile, substances like cyanidin-3-xylosyl (glucosyl) galactoside and cyanidin 3-xylosyl(coumaroylglucosyl) galactoside are responsible for the captivating purple colors found in radishes[3]. In wild cherries, an array of anthocyanins, including cyanidin-3-galactoside and cyanidin-3-O-arabinoside, and other anthocyanin compounds, collaborate to craft the inky black shade of the fruit's skin[4].


Beyond the direct involvement of anthocyanin compounds in color formation, a secondary category of compounds complements anthocyanins in stabilizing the colors they produce. Flavonols, for instance, play a pivotal role in the formation of color in mature grapes[5], while phenolic compounds contribute significantly to the rich coloration of canola seeds[6]. Organic acids, on the other hand, are instrumental in bestowing the vibrant hues seen in gooseberries[7].


Whether it is anthocyanin compounds directly influencing color formation or auxiliary substances lending support, these processes all hinge upon two fundamental mechanisms of anthocyanin pigmentation:


1. Molecular Modification of Anthocyanins: The color spectrum generated by anthocyanins is intricately tied to molecular modifications. Glycosylation and methylation bestow red hues, while acylation imparts blue tones. The depth of color intensifies with an increase in these modifications.


2. Co-pigmentation: Co-pigments, including flavonoids, polyphenols, alkaloids, amino acids, and organic acids, form non-covalent bonds with anthocyanins. This interaction results in heightened color saturation and a redshift effect, ultimately yielding a broad spectrum of colors, spanning from regal purples to serene blues. In this context, color variations arise from differences in pigment composition, variations in co-pigments, and the cumulative impact of anthocyanin molecular modifications.


Carotenoids: Artistry in Red, Yellow and Orange


The second category of compounds, carotenoids, takes the helm in orchestrating the vibrant red, yellows and oranges witnessed in the plant kingdom. Zeaxanthin, for instance, is the virtuoso responsible for the radiant yellow in canola flowers[8]. In contrast to the intricate modifications and co-pigmentation seen in anthocyanins, carotenoids exhibit a remarkable stability and consistency. This remarkable uniformity is primarily attributed to the well-defined synthesis pathways of carotenoids. Variations in color among different species or varieties primarily stem from differences in the metabolic pathways governing carotenoid biosynthesis. Consequently, when investigating color formation linked to carotenoids, the focus predominantly centers on disparities in the content of these compounds along their respective biosynthetic pathways.


Betalains: Infusing Splendor with Red and Yellow


The third category, betalains, lends their artistry to the creation of red and yellow hues in the plant world. Betanin and 2-descarboxy-betanin, for example, are the virtuosos behind the vibrant red hues of beetroot[9]. Meanwhile, indicaxanthin takes the stage to infuse the golden yellows seen in prickly pear fruit[9]. Intriguingly, contemporary research suggests that anthocyanins and betalains tend not to coexist within the same plant. Betalains are predominantly found in the Caryophyllales order, with a special affinity for the Caryophyllaceae family. However, it is imperative to note that in six distinct families within the Caryophyllales order, including Caryophyllaceae, Molluginaceae, Kewaceae, Limeaceae, Macarthuriaceae and Simmondsiaceae, color formation primarily hinges on the presence of anthocyanins. This complexity is further underscored by the discovery of approximately 75 different types of betalains across 17 diverse plant families[9].




Having acquired an in-depth understanding of these three pivotal categories of compounds involved in color formation, we can now embark on preliminary assessments concerning the compounds relevant to our specific color-related inquiries.


If you work with color-related research, we offer:

-          Widely-Targeted Metabolomics for Plants (we have >30,000 plant metabolites in our in-house database)

-          Flavonoids Metabolomics (>3,700 flavonoids for plants research)

-          Targeted Anthocyanin Assay


Have some questions? – We are here to help!



[1] Gao Q, Luo H, Li Y, Liu Z, Kang C. Genetic modulation of RAP alters fruit coloration in both wild and cultivated strawberry. Plant Biotechnol J. 2020 Jul;18(7):1550-1561.

[2] Lou Q, Liu Y, Qi Y, Jiao S, Tian F, Jiang L, Wang Y. Transcriptome sequencing and metabolite analysis reveals the role of delphinidin metabolism in flower colour in grape hyacinth. J Exp Bot. 2014 Jul;65(12):3157-64.

[3] Xu ZS, Yang QQ, Feng K, Yu X, Xiong AS. DcMYB113, a root-specific R2R3-MYB, conditions anthocyanin biosynthesis and modification in carrot. Plant Biotechnol J. 2020 Jul;18(7):1585-1597.

[4] Klisurova D, Petrova I, Ognyanov M, Georgiev Y, Kratchanova M, Denev P. Co-pigmentation of black chokeberry (Aronia melanocarpa) anthocyanins with phenolic co-pigments and herbal extracts. Food Chem. 2019 May 1;279:162-170.

[5] Malacarne G, Costantini L, Coller E, Battilana J, Velasco R, Vrhovsek U, Grando MS, Moser C. Regulation of flavonol content and composition in (Syrah×Pinot Noir) mature grapes: integration of transcriptional profiling and metabolic quantitative trait locus analyses. J Exp Bot. 2015 Aug;66(15):4441-53.

[6] Qu C, Fu F, Lu K, Zhang K, Wang R, Xu X, Wang M, Lu J, Wan H, Zhanglin T, Li J. Differential accumulation of phenolic compounds and expression of related genes in black- and yellow-seeded Brassica napus. J Exp Bot. 2013 Jul;64(10):2885-98.

[7] Molaeafard S, Jamei R, Poursattar Marjani A. Co-pigmentation of anthocyanins extracted from sour cherry (Prunus cerasus L.) with some organic acids: Color intensity, thermal stability, and thermodynamic parameters. Food Chem. 2021 Mar 1;339:128070.

[8] Liu Y, Ye S, Yuan G, Ma X, Heng S, Yi B, Ma C, Shen J, Tu J, Fu T, Wen J. Gene silencing of BnaA09.ZEP and BnaC09.ZEP confers orange color in Brassica napus flowers. Plant J. 2020 Nov;104(4):932-949.

[9]G Polturak, A Aharoni. "La Vie en Rose": Biosynthesis, Sources, and Applications of Betalain Pigments[J]. molecular plant, 2018, 11(1):16.



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