Molecules: References

Introduction - Common - Bacteria - Plantae - Chromista - Protozoa - Fungi - Animalia - References


  1. Goodwin (1980). The Biochemistry of the Carotenoids vol. 1: Plants.
  2. Goodwin ed. (1988). Plant Pigments.
  3. Britton (1983). The Biochemistry of Natural Pigments.
  4. Ke (2001). Photosynthesis: photobiochemistry and photobiophysics.
  5. McClintlock & Baker eds. (2001). Marine Chemical Ecology.
  6. Pietra (2002). Biodiversity and Natural Product Diversity.
  7. Bhakuni & Rasat (2005). Bioactive Marine Natural Products.
  8. Bhat, Nagasampagi, Sivakumar (2005). Chemistry of Natural Products.
  9. Grimm, Porra, Rüdiger, Scheer eds. (2006). Chlorophylls and Bacteriochlorophylls.


  1. Achenbach (1987). The Pigments of the Flexirubin-Type. A novel class of natural products. Progress in the Chemistry of Organic Natural Products 52: 73-111.
  2. Takaichi, Tsuji, Matsuura, Shimada (1995). A monocyclic carotenoid glucoside ester is a major carotenoid in the green filamentous bacterium Chloroflexus aurantiacus. Plant Cell Physiology 36(5): 773-778.
  3. Dworkin, Falkow, Rosenberg, Schleifer, Stackebrandt eds. (2006). The Prokaryotes.
  4. Shindo, Kikuta, Suzuki, Katsuta, Kasai, Yasumoto-Hirose, Matsuo, Misawa, Takaichi (2007). Rare carotenoids, (3R)-saproxanthin and (3R,2′S)-myxol, isolated from novel marine bacteria (Flavobacteriaceae) and their antioxidative activities. Applied microbiology and biotechnology 74(6): 1350-1357.
  5. Van Arnam, Currie, Clardy (2018). Defense contracts: molecular protection in insect-microbe synthesis. Chemical Society Reviews 47: 1638-1651.
  6. Kallscheuer, Moreira, Airs, Llewellyn, Wiegand, Jogler, Lage (2019). Pink- and orange-pigmented Planctomycetes produce saproxanthin-type carotenoids including a rare C45 carotenoid. Environmental Microbiology Reports 11(6): 741-748.
  7. Cavalier-Smith & Chao (2020). Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). Protoplasma 257: 621-753.


  1. Takaichi & Mochimaru (2007). Carotenoids and carotenogenesis in cyanobacteria: unique ketocarotenoids and carotenoid glycosides. Cellular and Molecular Life Sciences 64: 2607-2619.
  2. Meriluoto, Spoof, Codd eds. (2017). Handbook of Cyanobacterial Monitoring and Cyanotoxin Analysis.
  3. Ding, Pang, Liang, Goh, Glukhov, Gerwick, Tan (2018). MS/MS-Based molecular networking approach for the detection of aplysiatoxin-related compounds in environmental marine Cyanobacteria. Marine drugs 16(12): 505.
  4. Moss, Leão, Rankin, McCullough, Qu, Korobeynikov, Smith, Gerwick, Gerwick (2018). Ketoreductase domain dysfunction expands chemodiversity: malyngamide biosynthesis in the cyanobacterium Okeania hirsuta. ACS Chemical Biology 13(12): 3385-3395.
  5. Nowicka-Krawczyk, Mühlsteinová, Hauer (2019). Detailed characterization of Arthrospira type species separating commercially grown taxa into the new genus Limnospira (Cyanobacteria). Scientific Reports 9: 694.
  6. Fiore, de Lima, Carmichael, McKinnie, Chekan, Moore (2020). Guanitoxin, renaming a cyanobacterial organophosphate toxin. Harmful Algae 92: 101732.


  1. Mizoguchi, Oh-oka, Tamiaki (2005). Determination of stereochemistry of bacteriochlorophyll gF and 81-hydroxy-chlorophyll aF from Heliobacterium modesticaldum. Photochemistry and Photobiology 81: 666-673.
  2. Garrido-Fernández, Maldonago-Barragán, Caballero-Guerrero, Hornero-Méndez, Ruiz-Barba (2010). Carotenoid production in Lactobacillus plantarum. International Journal of Food Microbiology 140: 34-39.
  3. Li, Barber, Zhang (2019). Natural products from anaerobes. Journal of Industrial Microbiology and Biotechnology 46(3-4): 375-383.
  4. Armistead, Herro-Foncubierta, Coleman, Quach, Whidbey, Justicia, Tapia, Casares, Millán, Haidour, Granger, Vorhagen, Santana-Ufret, Merillat, Waldorf, Cuerva, Rajagopal (2020). Lipid analogs reveal features critical for hemolysis and diminish granadaene mediated Group B Streptococcus infection. Nature Communications 11: 1502.


  1. Starr, Jenkins, Bussey, Andrewes (1977). Chemotaxonomic significance of the xanthomonadins, novel brominated aryl-polyene pigments produced by bacteria of the genus Xanthomonas. Archives of Microbiology 113: 1-9.
  2. Budzikiewicz (1993). Secondary metabolites from fluorescent pseudomonads. FEMS Microbiology Letters 104: 209-228.
  3. Bowman (2007). Bioactive compound synthetic capacity and ecological significance of marine bacterial genus Pseudoalteromonas. Marine Drugs 5(4): 220-241.
  4. Nett & König (2007). The chemistry of gliding bacteria. Natural Product Reports 24(6): 1245-1261.
  5. Gross & Loper (2009). Genomics of secondary metabolite production by Pseudomonas spp. Natural Products Report 29: 1408-1446.
  6. Wietz, Månsson, Vynne, Gram (2013). Small-Molecule antibiotics from marine bacteria and strategies to prevent rediscovery of known compounds. In: Kim ed. Marine Microbiology: Bioactive Compounds and Biotechnological Applications: 127-159.
  7. Hu, Withall, Challis, Thomson (2016). Structure, chemical synthesis, and biosynthesis of prodiginine natural products. Chemical Reviews 116(14): 7818-7853.


  1. Pettus, Wing, Sims (1977). Marine Natural Products XII. Isolation of a family of multihalogenated gamma-methylene lactones from the red seaweed Delisea fimbriata. Tetrahedron Letters 1: 41-44.
  2. Asakawa (1995). Chemical consituents of the bryophytes. Progress in the Chemistry of Organic Natural Products 65: 1-652.
  3. Christophersen (1996). Theory of the origin, function, and evolution of secondary metabolites. In: Atta-ur-Rahman ed. Studies in Natural Product Chemistry vol. 18: 677-737.
  4. Iwashina (2000). The structure and distribution of the flavonoids in plants. Journal of Plant Research 3: 287-299.
  5. Osbourn & Lanzotti eds. (2009). Plant-derived Natural Products.

Vascular plants

  1. Murakami & Tanaka (1988). Occurrence, Structure and Taxonomic Implications of Fern Consituents. Progress in the Chemistry of Organic Natural Products 54: 1-329.
  2. Bauer, Garbe, Surburg (1990). Common Fragrance and Flavor Materials: Preparation, Properties and Uses, 2nd ed.
  3. Bruneton (1999). Toxic Plants Dangerous to Humans and Animals.
  4. Langenheim (2003). Plant Resins: Chemistry, Evolution, Ecology, Ethnobotany.
  5. Keeling & Bohlmann (2006). Diterpene resin acids in conifers. Phytochemistry 67: 2415-2423.


  1. Hostettmann & Marston (1995). Saponins.
  2. Dobson (2006). Relationship between Floral Fragrance Composition and Type of Pollinator. In: Dudareva & Pichersky eds. Biology of Floral Scent: 147-198.
  3. Tanaka & Brugliera (2006). Flower colour. In: Ainsworth ed. Flowering and its Manipulation: 201-239.
  4. Dinda (2019). Pharmacology and Applications of Naturally Occurring Iridoids.

Additional references for the angiosperm page, which is so far very incomplete:

  1. Conn (1981). Cyanogenic glycosides. The Biochemistry of Plants: A Comprehensive Treatise 7: 479-500.
  2. Cronquist (1981). An integrated system of classification of flowering plants.
  3. Rodriguez-Saona & Trumble (2000). Biologically Active Aliphatic Acetogenins from Specialized Idioblast Oil cells. Current Organic Chemistry 4(12): 1249-1260.
  4. Hölscher & Schneider (2000). Phenalenones from Strelitzia reginae. Journal of Natural Products 63(7): 1027-1028.
  5. Sicker & Schulz (2002). Benzoxazinones in plants: occurrence, synthetic access, and biological activity. In: Studies in natural products chemistry 27: 185-232.
  6. Colegate & Molyneux eds. (2008) Bioactive Natural Products 2nd ed.
  7. Takhtajan (2009). Flowering plants.
  8. Chatrou, Pirie, Erkens, Couvreur, Neubig, Abbott, Mols, Maas, Saunders, Chase (2012). A new subfamilial and tribal classification of the pantropical flowering plant family Annonaceae informed by molecular phylogenetics. Botanical journal of the Linnean society 169(1): 5-40.
  9. Norman, Lever, Brkljača, Urban (2019). Distribution, biosynthesis, and biological activity of phenylphenalenone-type compounds derived from the family of plants, Haemodoraceae. Natural Product Reports 36: 753-768.
  10. Kemprai, Mahanta, Sut, Barman, Banik, Lal, Saikia, Haldar (2020). Review on safrole: identity shift of the ‘candy shop’ aroma to a carcinogen and deforester. Flavour and Fragrance Journal 35(1): 5-23.
  11. Neske, Hidalgo, Cabedo, Cortes (2020). Acetogenins from Annonaceae family. Their potential biological applications. Phytochemistry 174: 112332.


  1. Lobban, Hallam, Mukherjee, Petrich (2007). Photophysics and multifunctionality of hypericin-like pigments in heterotrich ciliates: a phylogenetic perspective. Photochemistry and Photobiology 83: 1074-1094.
  2. Guella, Skropetra, Di Giuseppe, Dini (2010). Structures, biological activities and phylogenetic relationships of terpenoids from marine ciliates of the genus Euplotes. Marine Drugs 8: 2080-2116.
  3. Buonanno, Guella, Strim, Ortenzi (2012). Chemical defense by mono-prenyl hydroquinone in a freshwater ciliate, Spirostomum ambiguum. Hydrobiologia 684: 97-107.

Fungi & Amoebozoa

  1. Höfle & Röser (1978). Structure of xanthomegnin and related pigments: reinvestigation by 13C nuclear magnetic resonance spectroscopy. Journal of the Chemical Society, Chemical Communications 14: 611-612.
  2. Gill & Steglich (1987). Pigments of Fungi (Macromycetes). Progress in the Chemistry of Organic Natural Products 51: 1-317.
  3. Gill (1994). Pigments of Fungi (Macromycetes). Natural Product Reports 11: 67-90.
  4. ApSimon (2001). Structure, synthesis, and biosynthesis of fumonisin B1 and related compounds. Environmental Health Perspectives 109 supp 2: 245-249.
  5. Ishibashi (2003). Search for bioactive natural products from unexploited microbial resources. Studies in Natural Products Chemistry 29(10): 223-262.
  6. Hanson (2008). The Chemistry of Fungi.
  7. Põldmaa (2011). Tropical species of Cladobotryum and Hypomyces producing red pigments. Studies in Mycology 68(1): 1-34.
  8. McLaughlin & Spatafora eds. (2015). The Mycota vol. VII: Systematics and Evolution Part B, 2nd ed.
  9. Mérillon & Ramawat eds. (2017). Fungal Metabolites.


  1. Vidari & Vita-Finzi (1995). Sesquiterpenes and other secondary metabolites of genus Lactarius (Basidiomycetes): chemistry and biological activity. Studies in Natural Product Chemistry 17: 153-206.
  2. Davoli, Mucci, Schenetti, Weber (2005). Laetiporic acids, a family of non-carotenoid polyene pigments from fruit-bodies and liquid cultures of Laetiporus sulphureus (Polyporales, Fungi). Phytochemistry 66(7): 817-823.
  3. Yin, Yang, Gao (2019). Mushroom toxins: chemistry and toxicology. Journal of agriculture and food chemistry 67(18): 5053-5071.
  4. Ke & Tsai (2022). Understanding and using fungal bioluminescence – Recent progress and future perspectives. Current Opinion in Green and Sustainable Chemistry 33: 100570.


  1. Rundel (1978). The ecological role of secondary lichen substances. Biochemical Systematics and Technology 6: 157-170.
  2. Brodo, Sharnoff, Sharnoff (2001). Lichens of North America.
  3. Huneck (2001). New results on the chemistry of lichen substances. Progress in the Chemistry of Organic Natural Products 81: 1-276.
  4. Mathey, Spiteller, Steglich (2002). Draculone, a new anthraquinone pigment from the tropical lichen Melanotheca cruenta. Zeitschirft für Naturforschung C 57: 565-567.
  5. Nash III ed. (2008). Lichen Biology, 2nd ed.
  6. Aptroot, Thor, Lücking, Elix, Chaves (2009). The lichen genus Herpothallon reinstated. Bibliotheca Lichenologica 99: 19-66.
  7. Basset, Leslie, Hamprecht, White, Barrett (2010). Studies on the resorcylates: biomimetic total syntheses of (+)-montagnetol and (+)-erythrin. Tetrahedron Letters 51(5): 783-785.
  8. Weerakon, Aptroot, Lumbsch, Wolseley, Wijeyaratne, Gueidan (2012). New molecular data on Pyrenulaceae from Sri Lanka reveal two well-supported groups within this family. The Lichenologist 44(5): 639-647.
  9. Nguyen, Chollet-Krugler, Goualt, Tomasi (2013). UV-protectant metabolites from lichens and their symbiotic partners. Natural Product Reports 30(12): 1490-1508.


  1. Matsuno & Hirao (1989). Marine carotenoids. In: Ackman ed. Marine biogenic lipids, fats, and oils vol. 1: 251-388.
  2. Tanaka, Akase, Yamada (2001). Absolute stereochemistry of two carotenoids, clathriaxanthin and isoclathriaxanthin isolated from the marine sponge Tedania digitata. Fisheries Science 67(2): 378-379.
  3. López-Legentil, Dieckmann, Bontemps-Subielos, Turon, Banaigs (2005). Qualitative variations of alkaloids in color morphs of Cystodytes (Ascidiacea). Biochemical Systematics and Ecology 33: 1107-1119.
  4. Bandaranayake (2006). The nature and role of pigments in marine invertebrates. Natural Product Reports 23(2): 223-255.
  5. Cimino & Gavagnin (2006). Molluscs: From Chemo-ecological Study to Biotechnological Application.
  6. Nakamura, Tachikawa, Uemura (2009). (–)-Complanine, an inflammatory substance of marine fireworm: a synthetic study. Beilstein Journal of Organic Chemistry 5(12).
  7. Kumar & Rawat (2011). Marine natural alkaloids as anticancer agents. In: Tiwari & Mishra eds. Opportunity, challenge, and scope of natural products in medicinal chemistry: 213-268.
  8. Schenk & Hoeger (2011). Glutathionyl-biliverdin IXα, a new heme catabolite in a marine annelid: Sex and cell specific accumulation. Biochimie 93(2): 207-216.


  1. Voloshina, Raabe, Estermeier, Steffan, Fleischhauer (2004). Determination of the absolute configuration of calliactine by quantum chemical calculations. International Journal of Quantum Chemistry 100(6): 1104-1113.
  2. Alieva, Konzen, Field, Meleshkevitch, Hunt, Beltran-Ramirez, Miller, Wiedenmann, Salih, Matz (2008). Diversity and evolution of coral fluorescent proteins. PLOS ONE 3(7): e2680.
  3. Chudakov, Matz, Lukyanov, Lukyanov (2010). Fluorescent proteins and their applications in imaging live cells and tissues. Physiological Reviews 90(3): 1103-1163.
  4. Maia, de Oliveira, Oliveira, Reis, Fleury, Edwards, de Oliveira (2013). Colour diversification in octocorals based on conjugated polyenes: a Raman spectroscopic view. Journal of Raman Spectroscopy 44: 560-566.


  1. Goodwin (1969). Pigments in Echinodermata. In: Florkin & Scheer eds. Chemical Zoology vol. 3: 135-147.
  2. Burnell & Apsimon (1983). Echinoderm Saponins. In: Scheuer ed. Marine Natural products: Chemical and Biological Perspectives vol. 5: 287-389.
  3. Minale, Riccio, Zollo (1995). Structural Studies on chemical constituents of echinoderms. In: Atta-ur-Rahman ed. Studies in Natural Product Chemistry vol. 15: 43-110.
  4. Wolkenstein (2015). Persistent and widespread occurrence of bioactive quinone pigments during post-Paleozoic crinoid diversification. Proceedings of the National Academy of Sciences 112(9): 2794-2799.


  1. Wood, Sollers, Dragoo, Dragoo (2002). Volatile Components in the Defensive Spray of the Hooded Skunk, Mephitis macroura. Journal of Chemical Ecology 28(9): 1865-1870.
  2. Saikawa, Hashimoto, Nakata, Yoshihara, Nagai, Ida, Komiya (2004). The red sweat of the hippopotamus. Nature 429: 363.
  3. Hill & McGraw eds. (2006). Bird Coloration: function and evolution vol. 2.
  4. Boone (2011). Purification and characterization of blue and green chromoprotein pigments from the integument of male darters in the genus Etheostoma. Unpubl. M.S. diss., Duquesney University.
  5. Prum, LaFountain, Berro, Stoddard, Frank (2012). Molecular diversity, metabolic transformation, and evolution of carotenoid feather pigments in cotingas (Aves: Cotingidae). Journal of Comparative Physiology B 182(8): 1095-1116.
  6. Kikuchi, Seymoure, Pfennig (2014). Mimicry’s palette: widespread use of conserved pigments in the aposematic signals of snakes. Evolution & Development 16(2): 61-67.
  7. Gruber, Gaffney, Mehr, DeSalle, Sparks, Platisa, Pieribone (2015). Adaptive evolution of eel fluorescent proteins from fatty acid binding proteins produces bright fluorescence in the marine environment. PLOS ONE 10(11): e0140972.


  1. Obika & Bagnara (1964). Pteridines as pigments in amphibians. Science 143: 485-487.
  2. Witkop & Gössinger (1983). Amphibian alkaloids. The Alkaloids 21: 139-253.
  3. Geyer & Pfleiderer (1995). Stereochemistry of drosopterins. Pteridines 6: 22-23.
  4. Daly, Noimai, Kongkathip, Kongkathip, Wilham, Garraffo, Kaneko, Spande, Nimit, Nabhitabhata, Chan-Ard (2004). Biologically active substances from amphibians: preliminary studies on anurans from twenty-one genera of Thailand. Toxicon 44(8): 805-815.
  5. Gao, Zehl, Leitner, Wu, Wang, Kopp (2010). Comparison of toad venoms from different Bufo species by HPLC and LC-DAD-MS/MS. Journal of ethnopharmacology 131(2): 368-376.


  1. Rudd, Ronci, Johnston, Guinan, Voelcker, Benkendorff (2015). Mass spectrometry imaging reveals new biological roles for choline esters and Tyrian purple precursors in muricid molluscs. Scientific reports 5: 13408.
  2. Williams, Ito, Wakamatsu, Goral, Edwards, Wogelius, Henkel, de Oliveira, Maia, Strekopytov, Jeffries, Speiser, Marsden (2016). Identification of shell colour pigments in marine snails Clanculus pharaonius and C. margaritarius. PLOS ONE 11(7): e0156664.
  3. Bonnard, Cantel, Boury, Parrot (2020). Chemical evidence of rare porphyrins in purple shells of Crassostrea gigas. Scientific reports 10: 12150.
  4. Shiomi (2021). Tetramine in the salivary glands of marine carnivorous snails: analysis, distribution, and toxicological aspects. Journal of Marine Science and Engineering 10(1): 6.


  1. Needham (1970). The integumental pigments of some isopod crustacea. Comparative Biochemistry and Physiology 35: 509-534.
  2. Duffey & Towers (1973). On the biochemical basis of HCN production in the millipede Harpaphe haydeniana (Xystodesmidae: Polydesmida). Canadian Journal of Zoology 56(1): 7-16.
  3. Bettini ed. (1978). Arthropod Venoms.
  4. Saporito, Donnelly, Hoffman, Garraffo, Daly (2003). A siphonotid millipede (Rhinotus) as the source of spiropyrrolizidine oximes of dendrobatid frogs. Journal of Chemical Ecology 29(12): 2781-2786.
  5. Oakey (2005). Myodocopa (Crustacea: Ostracoda) as models for evolutionary studies of light and vision: multiple origins of bioluminescence and extreme sexual dimorphism. Hydrobiologia 538: 179-192.
  6. Wilson & Hastings (2013). Bioluminescence: Living Lights, Lights for Living.


  1. Oxford & Gillespie (1998). Evolution and ecology of spider coloration. Annual Review of Entomology 43(1): 619-643.
  2. Sakata & Norton (2001). Opisthonotal gland chemistry of early-derivative oribatid mites (Acari) and its relevance to systematic relationships of Astigmata. International Journal of Acarology 27(4): 281-292.
  3. Takada, Sakata, Shimano, Enami, Mori, Nishida, Kuwahara (2005). Scheloribatid mites as the source of pumiliotoxins in dendrobatid frogs. Journal of Chemical Ecology 31(10): 2403-2415.
  4. Gnaspini & Hara (2007). Defensive Mechanisms. In: Pinto-da-Rocha, Machado, Giribet eds. Harvestmen: the biology of Opiliones 374-399.
  5. Olsen, Kristensen, Strømgaard (2011). Small molecules from spiders used as chemical probes. Angewandte Chemie International Edition 50(48): 11296-11311.


  1. Fiecchi, Anastasia, Galli, Gariboldi (1981). Assignment of the β Configuration to the C-glycosyl bond in carminic acid. The Journal of Organic Chemistry 46(7): 1511.
  2. Hori & Riddiford (1981). Isolation of ommochromes and 3-hydroxykynurenine from the tobacco hornworm, Manduca sexta. Insect Biochemistry 11(5): 507-513.
  3. Allyn, Rothschild, Smith (1982). Microstructure of the blue/green and yellow pigmented wing membranes in Lepidoptera. 1. Genus Graphium. Bulletin of the Allyn Museum 75: 1-20.
  4. Numata & Ibuka (1987). Alkaloids from ants and other insects. The Alkaloids 31: 193-315.
  5. Horikawa, Hoshiyama, Matsuzawa, Shugyo, Tanaka, Suzuki, Sato, Ito, Kaku, Nishii, Inai, Takahashi, Tsunoda (2011). Viridaphin A1 glucoside, a green pigment possessing cytotoxic and antibacterial activity from the aphid Megoura crassicauda. Journal of Natural Products 74(8): 1812-1816.
  6. Futahashi, Kurita, Mano, Fukatsu (2012). Redox alters yellow dragonflies into red. Proceedings of the National Academy of Science 109(31): 12626-12631.
  7. Henze, Lind, Wilts, Kelber (2019). Pterin-pigmented nanospheres create the colours of the polymorphic damselfly Ischnura elegans. Journal of the Royal Society Interface 16(153): 2018075.