Saccharomycotina

From Palaeos.org

These are the true yeasts, including the Saccharomyces cereviseae of college genetics classes, and the human pathogen Candida. Domestication of Saccharomyces for fermentation of beer goes back at least 9000 years, and probably predates human cultivation of most other plants and animals. This group appears to be monophyletic and to have abandoned multicellularity independently of the yeast-like genera in Taphrinomycotina. Basal members of Saccharomycotina still retain a mycelial growth habit. However, none of the Saccharomycotina produces an ascocarp.

Saccharomyces became the first eukaryote to have its genome completely sequenced in 1996. Shortly afterwards, a dozen other saccharomycotine genomes were partially sequenced, creating the first opportunity to look seriously at the comparative genomics and evolution of an entire eukaryotic class. So far as we know, this remains the only study of this scope as of this date (041231). The results of this analysis were reported in a series of papers published in FEBS Letters in 2000, all of which are now available at the Génolevures website. See, especially, Gaillardin et al. (2000), Llorente et al. (2000a, b), and Malpertuy et al. (2000). A brief diversity summary, such as the present section, is not the place to take on such a massive body of data. However, we cannot resist the temptation to mention a few of the gems to be found in this gigantic dragon-hoard of information.

First, it appears that yeast evolution is driven by a dynamic balance between gene duplication and deletion. It appears that genes are constantly being shuffled around the genome, with chromosome fragments frequently being duplicated and inserted elsewhere, often as additions to the ends of chromosomes -- the peculiarly labile regions near the telomeres. In most cases, the resulting copies are simply deleted. However, over geological time, the entire genome is shuffled with considerable regularity.

Second, the number of orthologs (copies, but not necessarilly exact copies) of each gene is more stable than one might expect from this mode of evolution. It seems that unnecessary gene copies are deleted rather quickly. This conclusion is also fortified by the observation that genes involved in unused metabolic pathways are almost entirely absent. Thus, for example, Saccharomyces, which feeds solely by fermentation, has no genes orthologous to those coding for enzymes involved in oxidative metabolism.

Finally, and most significantly, yeasts show a strong correlation between the age of a gene and its stability. So, for example, the ancient genes coding for proteins involved in the basic work of transcription and translation are quite stable. By contrast, genes related to cell wall synthesis -- functions unique to the fungi and to particular groups within the fungi -- change quite quickly. This particular study needs to be done at a much higher level of resolution, but the tentative conclusion one may draw is that long-term selective pressures are a significant part of the evolutionary picture. If so, this data may settle an important and contentious point about the process of evolution.

[edit] Phylogeny

Usually (e. g., Eriksson et al., 2003b) the Saccharomycotina are treated as a single order, the Saccharomycetales. However, as I feel that this redundancy in taxa is not particularly helpful, I here use a less popular classification that divides the class into four orders (Cavalier-Smith, 1998; Schweigkofler, Lopandic et al., 2002).

<==Saccharomycotina [Endomycetes, Hemiascomycetes, Saccharomycetes]
  |  i. s.: Brettanomyces nanus
  |         Cliteromyces matritensis
  |         Geotrichum
  |           |--G. candidans
  |           `--G. fermentans
  |         Schizoblastosporion starkeyihenrici
  |         Ascoidea [Ascoideaceae]
  |         Cephaloascus [Cephaloascaceae]
  |--Saccharomycetidae
  |    |--Saccharomycetales
  |    `--+--Stephanoascales
  |       `--Dipodascales
  `--Lipomycetaceae [Dipomycetidae, Lipomycetales]
       |--Dipodascopsis uninucleata
       |--Babjevia
       |--Kawasakia
       |--Zygozyma
       `--Lipomyces [incl. Smithiozyma, Waltomyces]
            |--L. lipofer
            `--L. starkeyi

* Type species of genus indicated

[edit] References

Cavalier-Smith, T. 1998. A revised six-kingdom system of life. Biological Reviews 73: 203-266.

Eriksson, O. E. (ed.) 1999. Notes on ascomycete systematics. Nos 2440-2755. Myconet 2: 1-41.

Eriksson, O. E., H. O. Barah, R. S. Currah, K. Hansen, C. P. Kurtzman, T. Laessøe & G. Rambold (eds.) 2003a. Notes on ascomycete systematics. Nos 3580-3623. Myconet 9: 91-103.

Eriksson, O. E., H. O. Barah, R. S. Currah, K. Hansen, C. P. Kurtzman, G. Rambold & T. Laessøe (eds.) 2003b. Outline of Ascomycota – 2003. Myconet 9: 1-89.

Gaillardin, C., G. Duchateau-Nguyen, F. Tekaia, B. Llorente, S. Casaregola, C. Toffano-Nioche, M. Aigle, F. Artiguenave, G. Blandin, M. Bolotin-Fukuhara, E. Bon, P. Brottier, J. deMontigny, B. Dujon, P. Durrens, A. Lépingle, A. Malpertuy, C. Neuvéglise, O. Ozier-Kalogéropoulos, S. Potier, W. Saurin, M. Termier, M. Wésolowski-Louvel, P. Wincker, J.-L. Souciet & J. Weissenbach. 2000. Genomic exploration of the hemiascomycetous yeasts: 21. Comparative functional classification of genes. FEBS Letters 487: 134-149.

Jacobs, A., M. P. A. Coetzee, B. D. Wingfield, K. Jacobs & M. J. Wingfield. 2003. Phylogenetic relationships among Phialocephala species and other ascomycetes. Mycologia 95 (4): 637-645.

Lang, B. F., C. O’Kelly, T. Nerad, M. W. Gray & G. Burger. 2002. The closest unicellular relatives of animals. Current Biology 12: 1773-1778.

Llorente, B., A. Malpertuy, C. Neuvéglise, J. deMontigny, M. Aigle, F. Artiguenave, G. Blandin, M. Bolotin-Fukuhara, E. Bon, P. Brottier, S. Casaregola, P. Durrens, C. Gaillardin, A. Lépingle, O. Ozier-Kalogéropoulos, S. Potier, W. Saurin, F. Tekaia, C. Toffano-Nioche, M. Wésolowski-Louvel, P. Wincker, J. Weissenbach, J.-L. Souciet & B. Dujon. 2000a. Genomic exploration of the hemiascomycetous yeasts: 18. Comparative analysis of chromosome maps and synteny with Saccharomyces cerevisiae. FEBS Letters 487: 101-112.

Llorente, B., P. Durrens, A. Malpertuy, M. Aigle, F. Artiguenave, G. Blandin, M. Bolotin-Fukuhara, E. Bon, P. Brottier, S. Casaregola, B. Dujon, J. deMontigny, A. Lépingle, C. Neuvéglise, O. Ozier-Kalogeropoulos, S. Potier, W. Saurin, F. Tekaia, C. Toffano-Nioche, M. Wésolowski-Louvel, P. Wincker, J. Weissenbach, J.-L. Souciet & C. Gaillardin. 2000b. Genomic exploration of the hemiascomycetous yeasts: 20. Evolution of gene redundancy compared to Saccharomyces cerevisiae. FEBS Letters 487: 122-133.

Lücking, R., & A. Vězda. 1998. Taxonomic status in foliicolous species of the genus Porina (lichenized Ascomycotina: Trichotheliaceae) - II. The Porina epiphylla group. Willdenowia 28: 181-226.

Lumbsch, H. T., I. Schmitt, H. Döring & M. Wedin. 2001. Molecular systematics supports the recognition of an additional order of Ascomycota: The Agyriales. Mycological Research 105 (1): 16-23.

Malpertuy, A., F. Tekaia, S. Casarégola, M. Aigle, F. Artiguenave, G. Blandin, M. Bolotin-Fukuhara, E. Bon, P. Brottier, J. deMontigny, P. Durrens, C. Gaillardin, A. Lépingle, B. Llorente, C. Neuvéglise, O. Ozier-Kalogeropoulos, S. Potier, W. Saurin, C. Toffano-Nioche, M. Wésolowski-Louvel, P. Wincker, J. Weissenbach, J.-L. Souciet & B. Dujon. 2000. Genomic exploration of the hemiascomycetous yeasts: 19. Ascomycetes-specific genes. FEBS Letters 487: 113-121.

Prescott, L. M., J. P. Harley & D. A. Klein. 1996. Microbiology (3rd ed.) Wm. C. Brown Publishers: Dubuque (Iowa).

Rossman, A. Y., G. J. Samuels, C. T. Rogerson & R. Lowen. 1999. Genera of Bionectriaceae, Hypocreaceae and Nectriaceae (Hypocreales, Ascomycetes). Studies in Mycology 42: 1-248.

Schweigkofler, W., K. Lopandic, O. Molnár & H. Prillinger. 2002. Analysis of phylogenetic relationships among Ascomycota with yeast phases using ribosomal DNA sequences and cell wall sugars. Organisms Diversity & Evolution 2: 1-17.

Credits

intro ATW041231, phylogeny CKT061008