Genomes in Sequencing and Annotation Progress

S. commune is used as a model system for white rot fungi, sexual reproduction and fruit-ing body development (Palmer & Horton, 2006). Moreover, S. commune is a pathogen attacking wounded trees of all kind (Peddireddi, 2008). Genetical tools such as a trans-formation method of S. commune are long established (Mu˜noz Rivas et al., 1986) and optimized (Specht et al., 1991) and gene-knock-outs are possible in this fungus (Mu˜noz Rivas et al., 1986; Specht et al., 1991). The genome release of this species could give rise to large scale genetic and proteomic analysis of this model organism.

P. ostreatus is an edible white rot fungus and likeP. chrysosporium already well stud-ied for the use in bioremediation and concerning extracellular oxidative enzymes (Cohen et al., 2002). But also on the genetic level, P. ostreatus is not totally unknown. The genome size of the dikaryotic strain N001 was determined by pulsed field electrophoresis and a genetic linkage map was created (Larraya et al., 1999; Park et al., 2006; Santoyo et al., 2008). Transformation protocols were developed for P. ostreatus using polyethy-lene glycol and protoplasts (Li et al., 2006) and this was already used for the expression of green fluorescence protein (GFp) in P. ostreatus (Lin et al., 2008). For P. ostreatus, two monokaryotic strains are in sequencing and annotation progress, PC9 and PC15.

They were produced from the commercial dikaryotic strain N001 by de-dikaryotization

(Park et al., 2006). The availability of two monokaryotic strains developed from one dikaryon reveals great possibilities for comparative genomic studies.

P. carnosa andH. annosum are severe pathogenic white rot fungi causing high finan-cial losses to forest owners (http://chem-eng.utoronto.ca/˜bioproducts/research.htm).

H. annosum causes root and butt rot of conifers in the Northern temperate regions of the world but especially in Europe. The preferred host of H. annosum is pine. The disease itself has been intensively studied already since decades (Asiegbu et al., 2005;

Hodges, 1969) but genetics, biochemistry, and molecular aspects of the pathogenicity are less well understood (Asiegbu et al., 2005). However, recently, advances in molecu-lar characterization of pathogenicity factors and application ofAgrobacterium-mediated DNA transformation system have been made (Karlsson et al., 2003; Samils et al., 2006).

The genome sequences of H. annosum (North American P-type) and P. carnosa can be important tools for an insight into pathogenicity of those fungi and may give rise to an effective combat of the diseases.

Also the brown rot fungus S. lacrymans causes enormous damage by the attack of mainly coniferous wood, indoor and outdoor, every year (Schmidt, 2007). S. lacrymans is a true dry rot fungus, meaning that the wood decay occurs even under dry condi-tions. A remarkable fact is that S. lacrymans is divided into two main species, one nonaggressive occurring naturally in North America and Asia (var. shastensis), and another aggressive lineage spread over all continents, in natural environments as well as in buildings (var. lacrymans) (Kauserud et al., 2007). This feature and the great damage the fungi are causing especially in the Northern hemisphere, where coniferous wood is mainly used as construction material, makes obvious why these fungi are cho-sen for sequencing. Techniques of molecular biology are little applied up to date to of S. lacrymans but sequencing of the genome and availability of molecular methods for other basidiomycetes could give rise to extensive studies ofS. lacrymans on the genomic level. The genome sequence could reveal possibilities for the effective combat of this fungus.

P. involutus is the second ectomycorrhizal fungus in pipeline for sequencing. In symbiosis with birch (Betula pendula), transcriptional studies of expressed genes were already performed as well as microarray studies (Johansson et al., 2004). Several genes regulated by symbiosis and genes relevant for mycorrhizal development were identified within these studies [reviewed by (Breakspear & Momany, 2007)]. The genome was already characterized concerning complexity and size indicating a genome size of 23 Mbp

(Le Qu´er´e et al., 2002) which is far smaller than that ofL. bicolor. The relatively small genome size could be due to the fact that only low proportions of non-coding sequences and possibly only low fractions of repetitive DNA are present in the genome (Le Qu´er´e et al., 2002). P. involutus provides a perfect organism for genome comparison with the ectomycorrhizal fungus L. bicolor.

Last but not least the commercially relevant, edible fungusA. bisporus is in sequenc-ing progress. A. bisporus is commonly known as button mushroom and is the most widely cultivated mushroom all over the world and therefore already relatively well studied (Stoop & Mooibroek, 1999). As a saprotrophic fungus growing on compost (Stoop & Mooibroek, 1999), A. bisporus has a different substrate spectrum than the wood-degrading species. Already a large number of genes potentially relevant for fruit-ing body development and substrate usage, as well as genes encodfruit-ing proteins involved in basic biochemical pathways were cloned and characterized in expression patterns (De Groot et al., 1998b; Stoop & Mooibroek, 1999). Breeding of A. bisporus is chal-lenging because of its unusual secondary homothallic life-cycle (Raper et al., 1972).

Instead of forming upon meiosis basidia with four basidiospores with one type of hap-loid nuclei resulting upon spore germination in a sterile monokaryotic mycelium, most basidia produce only two spores containing two nuclei of opposite mating type. Thus, after germination of such basidiospores a fertile dikaryotic mycelium, able to produce mushrooms with the meiotic basidiospores, is directly formed. Such dikaryotic off-spring is not directly usable for crossing experiments. Still, approximately 2% of the produced basidia from A. bisporus carry three or four spores of which those with only one type of haploid nuclei are able to form monokaryotic mycelia upon germination which can be further used for mating with other strains (Summerbell et al., 1989).

This is the reason for the small genetic diversity of available A. bisporus strains. Most of the commercially available strains are derived from only two strains HorstU1 and HorstU3 (Fritsche, 1983). Lack of genetic diversity makes the commercially cultivated strains of the fungus A. bisporus an easy target for fungal and bacterial infections as well as for spontaneous degeneration leading to crop losses and malformed mushrooms (Fritsche, 1983). Within the last decade, effort was made to overcome these problems, which makes the fungus also interesting for the scientific community. Transformation of A. bisporus usingA. tumefaciens was developed (De Groot et al., 1998a) and optimized (Burns et al., 2006; Chen et al., 2000). This rose considerable interest for the applica-tion of A. bisporus for bio-manufacturing and molecular pharming (Kothe, 2001). A sequenced genome can play a crucial role in this process.