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Chemotaxonomy: Secondary Metabolites

The chemical substances which have been found very useful in taxonomy are secondary metabolites. Secondary metabolites (secondary plant products) perform non-vital (or at least non- universally vital) functions, and are less widespread in plants. The restricted occurrence of these metabolites among plants renders them valuable as taxonomic information.

Secondary plant products are largely waste substances, food stores, pigments, poisons, scents, structural units or water repellents, etc.

The most well-known groups of secondary metabolites are phenolic compounds, alkaloids, glucosinolates, amino acids, terpenoids, oils and waxes, and carbohydrates.

Phenolic compounds

Among all groups or secondary metabolites phenolic compounds provide the more taxonomic data. These compounds are present in leaves, flowers, seeds etc. Among the phenolic compounds flavonoids are the taxonomically most important.

Harborne (1967) stated that flavonoids are best chemical markers in phytochemistry because of their:

  • structural variability,
  • chemical stability,
  • wide distribution in plant kingdom,
  • easy identification, and
  • can be studied from the herbarium specimens.

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Flower pigment

One of the best example of the taxonomic value of secondary metabolites concern flower pigment.

Presence of Anthocyanins indicates the red, blue and similar colour of flowers (and fruits). Two other similar pigments, named betacyanins and betaxanthins also present in flowers. Betacyanins are red-violet, while betaxanthins are yellow. Betacyanins and betaxanthins are collectively known as betaalains. It is evident that if betacyanins or betaxanthins are present in flowers then anthocyanins are not found in the flowers. This indicates that these chemicals are mutually exclusive. The mutually exclusive chemical character has been used to identify the Centrspermae which consists of 13 families, namely Chenopodiaceae, Portulacaceae, Aizoaceae, Nyctaginaceae, Cactaceae, Phytolaccaceae, Stegnospermaceae, Basellaceae, Amaranthaceae, Didieraceae, Caryophyllaceae, Illecebraceae and Molluginaceae. Among these first 10 families (ie. Chenopodiaceae, Portulacaceae, Aizoaceae, Nyctaginaceae, Cactaceae, Phytolaccaceae, Stegnospermaceae, Basellaceae, Amaranthaceae and Didieraceae) betacyanin or betaxanthin present, but no anthocyanin found in them. On the other hand, Anthocyanin is present in Caryophyllaceae, Illecebraceae and Molluginaceae, but no betacyanin or betaxanthin detected in these three families. Based on this pigment character Caryophyllaceae, llecebraceae and Molluginaceae have been placed under the Order Caryophyllales.

On the basis of characters of ovary the family Gesneriaceae was subdivided into two subfamilies, viz., Cyrtandrioideae and Gesnerioideae. Flavonoid characters of leaves revealed that the separation of Gesneriaceae into two subfamilies are justified.

Leaf pigments

Presence of leuco-anthocyanins pigment in leaves can be detected by paper chromatography. In almost all species of the subfamilies Mimosoideae and Caesalpinioideae under the family Leguminosae leuco-anthocyanins are present, while in papilionoideae this pigment is absent.


The families containing tannins are usually woody and families without tannins are herbaceous. Therefore it can be concluded that families having tannins are primitive.

Water soluble carbohydrates

Recently studies on sugar, oligo-saccharides and water soluble polysaccharides in seeds of 22 species of Poaceae revealed that these characters can be successfully employed in taxonomy.


Alkaloids are nitrogen based chemical compounds which are found in different plant groups. Some alkaloids are very specific, for instance –

  • Morphine – only in Papaver somniferum (Papaveraceae) and this alkaloid is not found in any other species. That means Papaver somniferum can easily be identified by presence of morphine.
  • Serpentine – Rauwolfia serpentina.
  • Aconitine – Aconitum napellus (Ranunculaceae) .

Sometimes a single species may possess several alkaloids, e.g. Rauwolfia contains some 20 alkaloids.

The alkaloid Protopine is found in all species of Papaveraceae, moreover, this alkaloid is also found in the members of Fumariaceae. Presence of the same alkaloid (protopine) between these two families indicate a close relationships between Papaveraceae and Fumariaceae

Paper chromatographic analysis of the family Apocynaceae revealed that the Catharanthus and Vinca genera could be easily distinguished

The family Liliaceae was a large family consisting of the genera Smilax, Yucca, Allium, Colchicum and some other genera. Chemical analysis showed that the alkaloid Colchicine is found only in Colchicum. Using this alkaloid variation along with morphological characters the genus Colchicum has been separated from Liliaceae.

(This article is completely based on lectures Provided by Dr. Md Oliur Rahman, Professor, Department of Botany, University of Dhaka.
Some pictures and info have been added by the author. Any mistake, error, misinformation and other related things found in this article is only author’s to blame)


Revised by

  1. Md. Siddiq Hasan on July 22, 2020
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About Abulais Shomrat

Currently in 4th year (Hons) in the Department of Botany, University of Dhaka. Planned to have multiple careers one by one but promised to be with 'Plantlet' as long as it's primary stage remains unfinished. Email: abulaisshomrat@gmail.com. Minimum monthly resolution - Publish (1), Revise (3), Share (5)

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