Straminipile “Fungi” – Taxonomy


The phylogeny and taxonomy of the mastigonate ‘fungal‐like’ organisms (stramenopiles) are described. The marine Labyrinthulomycota occur in the same stramenopile clade as the bioecids and opalinids, whilst the hyphochytrids and biflagellate oomycetes occur in a sister clade, together with the ochrophyte algae. The uniflagellate hyphochytrids are a small group whose closest relative appears to be the phagotrophic flagellate . The largest and best documented of the straminipile fungi are the oomycetes. There are a number of early diverging oomycete clades (Classes incertae sedis) consisting of mostly holocarpic marine species that are parasites of algae and invertebrates. The more advanced, largely freshwater and terrestrial fungal‐like oomycetes, fall into two main classes, the Saprolegniomycetes and Peronosporomycetes. The former largely encompasses the saprotrophic water moulds, whilst the latter contains the majority of the economically important plant pathogens, including the white blister rusts (Albuginales), and the downy mildews (Peronosporales).

Key Concepts

  • Molecular phylogenetics reveals most bioflagellate fungal‐like organisms traditionally studied by mycologists and occur in the stramenopile (heterokont) clade within the SAR (formerly chromalveolate) superkingdom.
  • These fungal‐like organisms have probably evolved from a photosynthetic flagellate ancestor and there have been several independent plastid loss events.
  • The traditional taxonomy of all of these organisms has had to be substantially re‐evaluated in the light of recent molecular studies.

Keywords: Chromista; Heterokonta; hyphochytrid; labyrinthulid; oomycete; phylogeny; stramenopile; thraustochytrid

Figure 1. Schematic phylogenetic tree summarising the likely phylogenetic relationships between the diverse members of the chromalveolate (including stramenopiles) superkingdom. The photosynthetic lines are shaded in orange and postulated plastid loss events indicated by the red bars. The terminology is taken from Cavalier‐Smith and Chao () and the tree is based on a phylogenetic analysis of conserved protein genes by Tsui et al. (). Reproduced with permission from Beakes et al. () ©Springer.
Figure 2. Labyrinthulomycota. Diagrams summarising representative life cycles in the Thraustochytriaceae (a–c), Aplanochytriaceae (d) and Labyrinthulaceae (e), showing differences in the mode of thallus division and spore formation. Adapted from the original drawings of Daiske Honda. (f) Photograph showing the ultrastructure of the unique membranous plug separating thallus from rhizoid/slime track systems in thraustochytrids and labyrinthulids (Honda, unpublished).
Figure 3. Hyphochytrids. (a–c) Series of drawings showing mature thallus and spore release in the monocentric hyphochytrid Rhizidiomyces inflatus. Note the chytrid‐like appearance and absorpative rhizoid system (a) and release of cytoplasm into a thin‐walled vesicle (b) in which zoospore differentiation takes place (c). Drawings based on photographs of Gauriloff and Fuller in . (d) Line drawing of an electron micrograph of a zoospore of Rhizidiomyces showing single anterior flagellum with mastigoneme hairs. (e, f) Line drawings of developing and mature polycentric thalli of Hyphochytrium catenoides. (d–f) Reproduced with permission from Karling, © Koeltz Scientific Books. Scale bar = 10μm
Figure 4. Oomycota Diagram summarising the evolutionary trends in the morphology of the oomycete thallus mapped onto the proposed evolutionary hierarchy. Adapted from Beakes et al. () © Springer.
Figure 5. Photographic montage summary of the various stages in the asexual and sexual stages of the life cycle of the water mould Saprolegnia. Photographs and micrographs by Gordon Beakes, except for the photographs of zoosporangia by which were taken by the late AD Greenwood.


Anderson OR and Cavalier‐Smith T (2012) Ultrastructure of Diplophyrs parva, a new small freshwater species, and a revised analysis of Labyrinthulea (Heterokonta). Acta Protozoologica 51: 291–304.

Bala K, Robideau G, Lévesque A, et al. (2010) Phytopythium. Persoonia 24: 136–137.

Beakes GW, Glockling SL and Sekimoto S (2011) The evolutionary phylogeny of the oomycete “fungi”. Protoplasma 249: 3–19.

Beakes GW, Honda D and Thines M (2014) Systematics of the Straminipila: Labyrinthulomycota, Hyphochytriomycota and Oomycota. In: McLaughlin J and Spatafora JW, (eds). Mycota VIIA (Systematics and Evolution), 2nd edn. New York: Springer.

Cavalier‐Smith T and Chao EEY (2006, 2007) Phylogeny and megasystematics of phagotrophic heterokonts (Kingdom Chromista). Journal of Molecular Evolution 62: 388–420.

Cook KL, Hudspeth DSS and Hudspeth MES (2001) A cox2 phylogeny of representative marine peronosporomycetes (Oomycetes). Nova Hedwig 122: 231–243.

Cooke DEL, Drenth A, Duncan JM, Wagels G and Brasier CM (2000) A molecular phylogeny of Phytophthora and related oomycetes. Fungal Genetics and Biology 30: 17–32.

Dick MW (2001) Straminipilous fungi. Dordrecht, The Netherlands: Kluwer, Academic Publishers.

Diéguez‐Uribeondo J, Garcia MA, Cerenius LT, et al. (2009) Phylogenetic relationships among plant and animal parasites, and saprotrophs in Aphanomyces (Oomcyetes). Fungal Genetics and Biology 46: 365–376.

Fuller MS (2001) Hyphochytriomycota. In: McLaughlin D, McLaughlin E and Lemke CA, (eds). The Mycota VII Part A. Systematics and Evolution. Berlin, Germany: Springer Verlag; pp. 74–80.

Gauriloff LP and Fuller MS (1978) Rhizidiomyces apophyatus. In: Fuller MS, (ed.) Lower Fungi in the Laboratory. Athens: Department of Botany, University of Georgia; 59–60.

Göker M, Voglmayr H, Riethmüller A and Oberwinkler F (2007) How do obligate parasites evolve? A multi‐gene phylogenetic analysis of downy mildews. Fungal Genetics and Biology 44: 105–122.

Hakariya M, Hirose D and Tokumasu S (2007) A molecular phylogeny of Haptoglossa species, terrestrial peronosporomycetes (oomycetes) endoparasitic on nematodes. Mycoscience 48: 169–175.

Hausner G, Belkhiri A and Klassen GR (2000) Phylogenetic analysis of the small ribosomal subunit RNA gene of the hyphochytrid Rhizidiomyces apophysatus. Canadian Journal of Botany 78: 124–128.

Honda D, Yokochi T, Nakahara T, et al. (1999) Molecular phylogeny of labyrinthulids and thraustochytrids based on the sequencing of the 18S ribosomal RNA gene. Journal of Eukaryotic Microbiology 46: 637–647.

Hulvey JP, Padgett DE and Bailey JC (2007) Species boundaries within the Saprolegnia (Saprolegniales, Oomycota) based on morphological and DNA sequence data. Mycologia 99: 421–429.

Karling JS (1977) Chytridiomycetarum iconographia. Vaduz: Lubrecht and Cramer; 1–414.

Kühn SF, Medlin LK and Eller G (2004) Phylogenetic position of the parasitoid nanoflagellate Pirsonia inferred from nuclear‐encoded small subunit ribosomal DNA and a description of Pseudopirsonia n. gen. and Pseudopirsonia mucosa (Drebes) comb. nov. Protist 155: 143–156.

Leander CA, Porter D and Leander BS (2004) Comparative morphology and molecular phylogeny of aplanochytrids (Labryrinthulomycota). European Journal of Protistology 40: 317–328.

Lévesque CA and de Cock AW (2004) Molecular phylogeny and taxonomy of the genus Pythium. Mycological Research 108: 1363–1383.

Massana R, Terrado R, Forn I, Lovejoy C and Pedró‐Alió C (2006) Distribution and abundance of uncultured heterotrophic flagellates in the world oceans. Environmental Microbiology 8: 1515–1522.

Nakagiri A (2002) Diversity and phylogeny of Halophytophthora (Oomycetes). Abstract 7th International Mycological Congress, Oslo, 55:19.

Perkins FO (1976) Fine structure of lower marine and estuarine fungi. In: Gareth Jones EB, (ed.) Recent Advances in Aquatic Mycology, London, UK: Elek Science; pp. 279–312.

Petersen AB and Rosendahl S (2000) Phylogeny of the peronosporomycetes (Oomycota) based on partial sequences of the large ribosomal subunit (LSU rDNA). Mycological Research 104: 1295–1303.

Porter D (1990) Phylum Labyrinthulomycota. In: Margulis L, Corliss JO, Melkonian M and Chapman DJ, (eds). Handbook of Protoctista. Boston, MA: Jones and Bartlett; 388–398.

Riethmüller A, Voglmayr H, Göker M, Weiss M and Oberwinkler F (2002) Phylogenetic relationships of the downy mildews (Peronosporales) and related groups based on nuclear large subunit ribosomal DNA sequences. Mycologia 94: 834–849.

Runge F, Telle S, Ploch S, et al. (2011) The inclusion of downy mildews in a multi‐locus‐dataset and its reanalysis reveals a high degree of paraphyly in Phytophthora. IMA Fungus 2: 163–171.

Sekimoto S, Hatai K and Honda D (2007) Molecular phylogeny of an unidentified Haliphthoros‐like marine oomycete and Haliphthoros milfordensis inferred from nuclear‐encoded small and large subunit rDNA genes and mitochondrial‐encoded cox2 gene. Mycoscience 48: 212–221.

Sekimoto S, Beakes GW, Gachon CMM, et al. (2008a) The development, ultrastructural cytology, and molecular phylogeny of the basal oomycete Eurychasma dicksonii, infecting the filamentous phaeophyte algae Ectocarpus siliculosus and Pylaiella littoralis. Protist 159: 401–412.

Sekimoto S, Yokoo K, Kawamura Y and Honda D (2008b) Taxonomy, molecular phylogeny, and ultrastructural morphology of Olpidiopsis porphyrae sp. nov. (Oomycetes, stramenopiles), a unicellular obligate endoparasite of Porphyra spp. (Bangiales, Rhodophyta). Mycological Research 112: 361–374.

Sparrow FK (1976) The present status of classification in biflagellate fungi. In: Gareth‐Jones EB, (ed). Recent Advances in Aquatic Mycology. London, UK: Elek Science; pp. 213–222.

Steciow MM, Lara E, Pillonel A, et al. (2014) Incipient loss of flagella in the genus Geolegnia: the emergence of a new clade within Leptolegnia? IMA Fungus 4: 169–175.

Seidl MF, den Ackerveken V, Govers F and Snel B (2012) Reconstruction of oomycete genome evolution identifies differences in evolutionary trajectories leading to present‐day large gene families. Genome Biology and Evolution. DOI: 10.1093/gbe/evs003.

Thines M and Voglmayr H (2009) An introduction to the white blister rusts (Albuginales). In: Lamour K and Kamoun S, (eds). Oomycete Genetics and Genomics: Diversity, Interactions and Research Tools, 77–92. New York: John Wiley & Sons Inc.

Thines M, Voglmayr H and Göker M (2009) Taxonomy and phylogeny of the downy mildews. In: Lamour K and Kamoun S, (eds). Oomycete Genetics and Genomics: Diversity, Interactions and Research Tools. New York: John Wiley & Sons Inc; 47–75.

Tsui CKM, Marshall W, Yokoyama R, et al. (2009) Labryinth‐ulomycetes phylogeny and its implications for the evolutionary loss of chloroplasts and gain of ectoplasmic gliding. Molecular Phylogenetics and Evolution 50: 129–140.

Uzuhashi S, Tojo M and Kakishima M (2010) Phylogeny of the genus Pythium and desription of new genera. Mycoscience 51: 337–365.

Van der Auwera G, Da Baere R, Van der Peer Y, et al. (1995) The phylogeny of the Hyphochytriomycota as deduced from ribosomal RNA sequences of Hyphochytrium catenoides. Molecular Biology and Evolution 12: 671–678.

Yokoyama R, Salleh B and Honda D (2007) Taxonomic rearrangement of the genus Ulkenia sensu lato based on morphology, chemotaxonomical characteristics, and 18S rRNA gene phylogeny (Thraustochytriaceae, Labyrinthulomycetes): emendation for Ulkenia and erection of Botrychytrium, Parietichytrium, and Sicyoidochytrium gen. nov. Mycoscience 48: 329–341.

Further Reading

Adl SM, Simpson AGB, Lane CE, et al. (2012) A revised classification of eukaryotes. Journal of Eukaryotic Microbiology 59: 429–493.

Beakes GW and Glockling SL (2002) A comparative fine‐structural study of dimorphic infection cells in the nematophagous parasite, Haptoglossa erumpens. Fungal Genetics and Biology 37: 250–262.

Jiang RHY and Tyler BM (2012) Mechanisms and evolution of virulence in oomycetes. Annual Review of Phytopathology 50: 14.1–13.24. DOI: 10.1146/annrev-phyto-081211-172912.

Richards TA, Soanes DM, Jones MD, et al. (2011) Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes. Proceedings of the National Academy of Sciences of the United States of America 108: 15258–15263.

Riisberg I, Orr RJ, Kluge R, et al. (2009) Seven gene phylogeny of heterokonts. Protist 160: 191–204.

Richards TA, Jones MD, Leonard G and Bass G (2012) Marine fungi: their ecology and molecular diversity. Annual Review of Marine Science 4: 495–522.

Patterson DJ (1989) Chromophytes from a protistan perspective. In: Green JP, Leadbeater BSC and Diver WL, (eds). The Chromophyte Algae: Problems and Perspectives. Oxford, UK: Clarendon Press; 357–379.

Voglmayr H (2008) Progress and challenges in systematics of downy mildews and white blister rusts: new insights from genes and morphology. European Journal of Plant Pathology 122: 3–18.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Beakes, Gordon W, Thines, Marco, and Honda, Daiske(Feb 2015) Straminipile “Fungi” – Taxonomy. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0001984]