1) General considerations

a) Marker description

b) Strain status

c) Strain name

d) Sequence file

e) Homepage

2) Authentication tool

3) Sequence search tool

4) Phylogeny tool

a) Marker table

b) Concatenation

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Marker choices

DNA markers do not provide the same information in taxonomy and phylogeny. While D1/D2 is the most widely used marker to describe species, it is not very reliable for phylogeny because of its small size. Other markers are good performers in phylogenetic analysis, but they are not available for a large number of species. Markers typically used for barcoding (ITS1-5.8S-ITS2, mtCOX II…) are not reliable markers for phylogeny: for instance the size of ITS1-5.8S-ITS2 can be very variable, and mitochondrial markers such as mtCOX II may be misleading because of the peculiar inheritance and the mode of evolution of mitochondrial DNA. Concatenation of coding sequences like ACT1, RPB1, RPB2 or TEF1-alpha provide good robust phylogeny.

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Most of the oligonucleotide primers used to amplify DNA and generate sequences present in the database can be found in the work by:

Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics.Taylor et al., 1990, PCR Protocols: a Guide to Methods and Applications, (ed. M.A. Innis, D.H. Gelfand, J. Sninsky, T.J. White), pp. 315–322. Academic press, San Diego).

Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Kurtzman C.P. and Robnett C.J., 1998, Antonie van Leeuwenhoek , 73:331-371.

Partial sequence analysis of the actin gene and its potential for studying the phylogeny of Candida species and their teleomorphs. Daniel H.M., Sorell T.C. and Meyer W., 2001, Int. J. Syst. Evol. Microbiol., 51:1593-1606.

Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analysis. Kurtzman C.P. and Robnett C.J., 2003, FEMS Yeast Res., 3:417-432.

Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. Kurztman C.P., 2003, FEMS Yeast Res., 4:233-245.

Evaluation of ribosomal RNA and actin gene sequences for the identification of ascomycetous yeasts. Daniel H.M. and Meyer W., 2003, Int. J. Food Microbiol., 86:71-78.

Multigene phylogenetic analysis of Trichomonascus, Wickerhamiella and Zygoascus yeast clade, and the proposal of Sugiyamaella gen. nov. and fourteen new species combinations. Kurtzman C.P. and Robnett C.J., 2007, FEMS Yeast Res., 7:141-154.

Re-examining the phylogeny of clinically relevant Candida species and allied genera based on multigene analysis. Tsui C.K.M., Daniel H.M., Robert V. and Meyer W., 2008, FEMS Yeast Res., 8:651-659.

Phylogeny and evolution of medical species of Candida and related taxa: a multigenic analysis.Diezman et al., 200), J. Clin. Microbiol. 42: 5624-5635.

Phylogenetic relationships among species of Pichia, Issatchenkia and Williopsis determined from multigene sequence analysis, and the proposal of Barnettozyma gen. nov., Lindnera gen. nov. and Wickerhamomyces gen. nov.Kurtzman C.P. et al., 2008, FEMS Yeast Res. 8: 939-954.

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Phylogeny of yeast clades

The genus Candida contains species that have no sexual state. The Candida genus is not monophyletic, therefore Candida species may be closely related to various species that have a sexual state. A clade is a taxon, which is made of a genus containing species with a sexual state and phylogenetically related Candida species.

The establishment of a taxonomic position of a definite species is best done with clades. A phylogenetic tree derived from various publications by Kurtzman and his collaborators is shown below.

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Most of the information on the taxonomy of hemiascomycetous yeast can be found in the 5th edition of "The Yeast, a Taxonomical study" by Kurtzman C.P., Boekhout T. and Fell J. (2011), Elsevier Amsterdam. The most recent changes in yeast taxonomy can be found in Kurtzmann C.P. (2010), Phylogeny of the ascomycetous yeasts and the renaming of Pichia anomala to Wickerhamomyces anomalus. Antonie Van Leeuwenhoek, 99: 13-23. The impact of genomics on yeast taxonomy has been recently reviewed by Casaregola S., Weiss S. and Morel G. (2011), New perspectives in hemiascomycetous yeast taxonomy. C. R. Biol. Aug-Sep; (8-9):590-8. In this publication, all the changes of species names since 1998 have also been reviewed.

Dereeper A., Guignon V., Blanc G., Audic S., Buffet S., Chevenet F., Dufayard J.-F., Guindon S., Lefort V., Lescot M., Claverie J.-M., Gascuel O. robust phylogenetic analysis for the non-specialist. Nucleic Acids Research. 2008 Jul 1; 36 (Web Server Issue):W465-9. Epub 2008 Apr 19.

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