Efficient lignin depolymerization is unique to the wood decay basidiomycetes, collectively referred to as white rot fungi. Phanerochaete chrysosporium simultaneously degrades lignin and cellulose, whereas the closely related species, Ceriporiopsis subvermispora, also depolymerizes lignin but may do so with relatively little cellulose degradation. To investigate the basis for selective ligninolysis, we conducted comparative genome analysis of C. subvermispora and P. chrysosporium . Genes encoding manganese peroxidase numbered 13 and five in C. subvermispora and P. chrysosporium , respectively. In addition, the C. subvermispora genome contains at least seven genes predicted to encode laccases, whereas the P. chrysosporium genome contains none. We also observed expansion of the number of C. subvermispora desaturase-encoding genes putatively involved in lipid metabolism. Microarray-based transcriptome analysis showed substantial up-regulation of several desaturase and MnP genes in wood-containing medium. MS identified MnP proteins in C. subvermispora culture filtrates, but none in P. chrysosporium cultures. These results support the importance of MnP and a lignin degradation mechanism whereby cleavage of the dominant nonphenolic structures is mediated by lipid peroxidation products. Two C. subvermispora genes were predicted to encode peroxidases structurally similar to P. chrysosporium lignin peroxidase and, following heterologous expression in Escherichia coli , the enzymes were shown to oxidize high redox potential substrates, but not Mn 2+ . Apart from oxidative lignin degradation, we also examined cellulolytic and hemicellulolytic systems in both fungi. In summary, the C. subvermispora genetic inventory and expression patterns exhibit increased oxidoreductase potential and diminished cellulolytic capability relative to P. chrysosporium .

Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Class I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.

We have constructed a genetic linkage map of the edible basidiomycete Pleurotus ostreatus (var. Florida). The map is based on the segregation of 178 random amplified polymorphic DNA and 23 restriction fragment length polymorphism markers; four hydrophobin, two laccase, and two manganese peroxidase genes; both mating type loci; one isozyme locus (est1); the rRNA gene sequence; and a repetitive DNA sequence in a population of 80 sibling monokaryons. The map identifies 11 linkage groups corresponding to the chromosomes of P. ostreatus, and it has a total length of 1,000.7 centimorgans (cM) with an average of 35.1 kbp/cM. The map shows a high correlation (0.76) between physical and genetic chromosome sizes. The number of crossovers observed per chromosome per individual cell is 0.89. This map covers nearly the whole genome of P. ostreatus.Pleurotus ostreatus (oyster mushroom) is an edible mushroom that occupies the second most important position in the world mushroom market, led by the button mushroom Agaricus bisporus (5, 49). Besides its importance for food production, P. ostreatus is interesting for applications such as paper pulp bleaching, cosmetics, and the pharmaceutical industry. These different applications have fueled research on specific aspects of Pleurotus biochemistry and molecular biology (4,8,20,(31)(32)(33)(34)42).Despite its economic importance, only a limited number of genetic studies of P. ostreatus have been done because of the difficulty in performing directed crosses between strains, contradictory data about the size and organization of its genetic material, and the lack of a genetic linkage map for it. Moreover, breeding of new P. ostreatus strains with a higher agricultural or industrial value has been traditionally carried out by trial and error because of the aforementioned reasons (2).In order to facilitate the design of programs aimed to improve the strains currently available, it is important to increase our knowledge of the genome organization of this fungus. However, the study of the organization of the P. ostreatus genome has been hampered by the small size of fungal chromosomes and by the occurrence of intranuclear mitosis (15). Different authors have reported different chromosome numbers for this species (15,41,51), and only recently has this number been determined using pulsed-field gel electrophoresis (32). This species contains 11 chromosomes that account for a total genomic size of about 35.1 Mbp per haploid genome. Furthermore, chromosome length polymorphisms occur between the homologous chromosomes present in each of the two nuclei in the dikaryon. Electrophoretic separation of P. ostreatus chromosomes allowed the physical mapping of some genes or phenotypic markers on specific chromosomes (for instance, the A mating locus physically mapped on chromosome III and the B locus was on chromosome IX) (32).The use of molecular markers combined with the construction of linkage maps is a potent strategy for designing breeding strategies and for attempting positional cloning of genes ...

ABSTRACTThe genome of the white rot basidiomycetePleurotus ostreatusincludes 12 phenol oxidase (laccase) genes. In this study, we examined their expression profiles in different fungal strains under different culture conditions (submerged and solid cultures) and in the presence of a wheat straw extract, which was used as an inducer of the laccase gene family. We used a reverse transcription-quantitative PCR (RT-qPCR)-based approach and focused on determining the reaction parameters (in particular, the reference gene set for the normalization and reaction efficiency determinations) used to achieve an accurate estimation of the relative gene expression values. The results suggested that (i) laccase gene transcription is upregulated in the induced submerged fermentation (iSmF) cultures but downregulated in the solid fermentation (SSF) cultures, (ii) theLacc2andLacc10genes are the main sources of laccase activity in the iSmF cultures upon induction with water-soluble wheat straw extracts, and (iii) an additional, as-yet-uncharacterized activity (Unk1) is specifically induced in SSF cultures that complements the activity of Lacc2 and Lacc10. Moreover, both the enzymatic laccase activities and theLaccgene family transcription profiles greatly differ between closely related strains. These differences can be targeted for biotechnological breeding programs for enzyme production in submerged fermentation reactors.

Pleurotus ostreatus is a hetertothallic homobasidiomycete whose mating is controlled by a bifactorial tetrapolar genetic system. Although this mechanism is well accepted, there is a lack of knowledge about its molecular basis, as the incompatibility loci have not been cloned and sequenced. As a first step towards the elucidation of the molecular structure of the A-type incompatibility locus, molecular markers have been isolated which correspond to genomic sequences present in different strains of P. ostreatus but not in other higher basidiomycetae. These markers reveal single-copy genetic regions in which some degree of genetic variability can be detected.