Physical mapping of the mitochondrial genome of the cultivated mushroom Agaricus brunnescens (= A. bisporus)

Mitochondrial recombination in natural populations of the button mushroom Agaricus bisporus

In the majority of sexual eukaryotes, the mitochondrial genomes are inherited uniparentally and have predominantly clonal population structures. In clonally evolving genomes, alleles at different loci will be in significant linkage disequilibrium. In this study, the associations among alleles at nine mitochondrial loci were analyzed for 379 isolates in four natural populations of the button mushroom Agaricus bisporus. The results indicated that the mitochondrial genome in the Desert California population was not significantly different from random recombination. In contrast, the three other populations all showed predominantly clonal mitochondrial population structure. While no evidence of recombination was found in the Alberta, Canada A. bisporus population, signatures of recombination were evident in the Coastal Californian and the French populations. We discuss the potential mechanisms that could have contributed to the observed mitochondrial recombination and to the differences in allelic associations among the geographic populations in this economically important mushroom.

Mitochondrial inheritance and the detection of non-parental mitochondrial DNA haplotypes in crosses of Agaricus bisporus homokaryons

This study evaluates mtDNA transmission in Agaricus bisporus, as well as the occurrence of non-parental haplotypes in heterokaryons produced by controlled crosses. Sixteen crosses were performed with blended liquid cultures, using different combinations of 13 homokaryotic strains. For each cross, different mtDNA haplotypes were present in each homokaryon. Heterokaryons generated from these crosses were subject to genetic analysis with RFLP markers to identify (i). karyotic status, (ii). mtDNA haplotype, and (iii). the occurrence of non-parental mtDNA haplotypes. These analyses generally supported the occurrence of uniparental mitochondrial (mt) inheritance in A. bisporus, with one mtDNA haplotype usually favoured in the new heterokaryon. The preponderance of one mtDNA haplotype in a new heterokaryon did not necessarily show a correlation with a greater mycelial growth rate for the parent homokaryon possessing that haplotype. Mixed mtDNA haplotypes and non-parental haplotypes were also identified in the heterokaryons from some crosses. Evidence for the occurrence of two mtDNA haplotypes in one heterokaryotic mycelium was observed in 8 of 16 crosses, suggesting the maintenance of true heteroplasmons after three successive subculturing steps. Non-parental mtDNA haplotypes were seen in heterokaryons produced from 7 of 16 crosses. The mating protocol described can be utilized to generate novel mtDNA haplotypes for strain improvement and the development of strain-specific markers. Mechanisms of mt selection and inheritance are discussed.

Organization of mitochondrial DNA in the basidiomycetous Dioszegia hungarica (Cryptococcus hungaricus) species

The organization of mitochondrial DNA was investigated in the six collection strains of the basidiomycetous yeast Dioszegia hungarica (Cryptococcus hungaricus) isolated so far. Physical and partial functional maps were constructed. Two strains (CBS 6324 and 6576) were identical while three others (CBS 4214, 5124, 6953) differed not only in the distribution of restriction sites but in gene order as well. Results confirm the hypothesis that these five strains are representatives of different closely related species. The sixth strain CBS 6569 revealed a unique mitochondrial genome organization. Its mtDNA separated into eight bands on agarose gel without enzymatic digestion. These molecules carried mitochondrial genes, and RFLP analysis of the four largest molecules using frequently-cutting restriction enzymes (KpnI and SmaI) showed them to have strongly homologous sequences. This unique mtDNA organization was also observed in a strain of Cystofilobasidium capitatum, providing evidence that CBS 6569 belongs to the Cystofilobasidium clade.

Fine-scale genetic analyses reveal unexpected spatial-temporal heterogeneity in two natural populations of the commercial mushroom Agaricus bisporus

This study examined the fine-scale genetic variation of the commercial mushroom, Agaricus bisporus, over 2 years at two sites in France. One site was a meadow fertilized with horse manure and disturbed regularly by humans; the other was a Monterey cypress forest free of human disturbance. Altogether, 50 mushrooms were collected and analysed for mitochondrial and nuclear genetic variation marked by RFLPs and multilocus enzyme electrophoretic polymorphisms. Population samples from these two sites were genetically different and both sites contained high levels of genetic diversity. No identical genotypes were found at either site between the 2 years and there was little evidence for extensive vegetative clonality for this species. Contrary to expectations, very limited evidence of pseudohomothallic reproduction was found. Results from tests of Hardy-Weinberg equilibrium and genotypic equilibrium showed that outcrossing and recombination have played significant roles in both populations. The results demonstrated spatial-temporal genetic heterogeneity of A. bisporus in natural populations.

Development of a molecular typing method for Pneumocystis carinii sp.f. hominis

We are developing a typing method for Pneumocystis carinii sp.f. hominis consisting in the PCR amplification of four variable regions of the genome from bronchoalveolar lavages, followed by the detection of their variation by the single-strand conformation polymorphism technique (SSCP). Most samples of each region from eleven unrelated patients showed two SSCP bands. Six patients were probably infected by a single strain since they showed a single sequence morph of each region. The combinations of the four sequence morphs of these patients were all different so that six different strains were distinguished. Other samples generated three or four SSCP bands which were found to correspond to the presence of two sequence morphs, possibly due to co-infections. Five patients could have been co-infected since they showed two sequence morphs of at least one of the regions. The combinations of sequence morphs of the possible co-infecting strains were different from all other combinations, except that three possible strains in two patients might have been present in other patients. Two BALs from the same patient, which were collected at an interval of 2.5 weeks, gave the same pattern for each of the four regions suggesting that these regions of the genome are stable. These results suggest a great diversity of P. carinii sp.f. hominis strains. Thus, the method should be suitable for epidemiological studies.

Organization, generation and replication of amphimeric genomes: a review

Genomes comprising a pair of separated inverted repeats and called 'amphimers' are reviewed. Amphimeric genomes are observed in a large variety of different organisms, ranging from archaebacteria to mammals. The widespread existence of amphimeric genomes in nature could be due to their particular dynamic structure. Amphimeric genomes containing long inverted segments may provide the only form in which a duplicated segment is stably retained in genomes. Amphimers are often found in amplified subgenomes, indicating that they could promote a special mechanism of DNA replication and amplification. The possible mechanisms of generation, isomerization and replication/amplification of different types of amphimeric genomes are discussed. The study of amphimeric mitochondrial petite genomes of yeast could be a good model system for the study of the role of inverted repeat sequences in genome dynamics.

Plasmid RNA polymerase-like mitochondrial sequences in Agaricus bitorquis

A linear mitochondrial plasmid, pEM, found in certain isolates of the basidiomycete Agaricus bitorquis, potentially encodes virus-like DNA and RNA polymerases. Mitochondrial DNA from Agaricus bisporus that hybridizes to an internal region of pEM contains a fragmented and potentially non-functional version of the carboxy terminal end of the plasmid RNA polymerase. In this study, we present the sequence of the corresponding region of mitochondrial DNA from A. bitorquis. This sequence contained the same region of the plasmid RNA polymerase gene as was reported for the mitochondrial DNA of A. bisporus, and the level of similarity between the A. bisporus and A. bitorquis mitochondrial sequences was much higher than the level of similarity between either mitochondrial sequence and the plasmid. We propose that this plasmid RNA polymerase-like sequence was present in the Agaricus mitochondrial genome before the divergence of A. bisporus and A. bitorquis, and thus is unlikely to be a recent derivative of the plasmid pEM.

Indigenous and introduced populations ofAgaricus bisporus, the cultivated button mushroom, in eastern and western Canada: implications for population biology, resource management, and conservation of genetic diversity

Agaricus bisporus is known from field collections in several parts of southern Canada and the border states of Washington and Idaho. In Ontario, the species is associated with urban horticultural sites, agricultural areas, and thoroughfares. In British Columbia, Washington, and Idaho, the species is less well documented but occurs in habitats similar to those in Ontario. All studied isolates from these two regions were genotypically similar to those collected in Europe and also to a representative sample of cultivar isolates believed to be of European origin. In contrast, a population from forests of Picea in the Rocky Mountains of Alberta had genotypes that are very different from European and cultivar groups, including the putatively introduced populations in other parts of Canada. To a lesser extent, the Albertan individuals also differed from three other isolated natural populations, two in California and one in Israel. Two of 35 isolates from Alberta had nuclear genotypes that were partially or entirely consistent with European ancestry, indicating that foreign (probably cultivar) germ plasm has become established in the native habitat. Thirty of 35 isolates from the Alberta field sample had one of six mitochondrial DNA (mtDNA) haplotypes known only from Alberta; the remaining five had an mtDNA type known from cultivar strains. However, nuclear genotypic similarity to other Albertan or European-cultivar isolates was not significantly correlated with presence or absence of this latter mtDNA type. The genetic diversity represented by the previously unknown Albertan population, and to a lesser extent by the heirloom varietal lineages and their derivatives that have become established in Ontario, British Columbia, Washington, and Idaho, is an important resource for breeders of this valuable fungal crop species. Threats to resource populations of this species, and possible responses, are discussed. Key words: Agaricus bisporus, mushroom population biology, resource management, germ plasm conservation, genetic diversity, microphylogeny.

Molecular systematics of the genus Pleurotus: analysis of restriction polymorphisms in ribosomal DNA

Part of the nuclear ribosomal DNA unit of Pleurotus cornucopiae, including most of the intergenic sequences, was used as a probe to hybridize with DNA from eleven Pleurotus taxa (29 isolates), digested with nine restriction endonucleases. For all digests, a high level of rDNA heterogeneity between and within species was detected, which is in agreement with the phenetic variability already reported in previous studies on Pleurotus taxa. Numerical analysis of the results, performed by use of two different tree-making methods, clearly distinguished among well-defined species, i.e. P. dryinus, P. eryngii and P. flabellatus, which presented large phenetic distances with the rest of the taxa tested. P. abalonus, despite morphological similarity and interfertility with P. cystidiosus, appears to be a discrete taxon. Although they showed relative affinity, P. cornucopiae, P. columbinus and P. ostreatus presented large distances among their representative isolates, supporting the idea that they correspond to distinct taxa. All strains of P. pulmonarius, P. sajor-caju and P. sapidus having small phenetic distances were closely positioned on dendrograms; in relation to results from recent interfertility and isozyme studies, these results support the common genetic background of P. pulmonarius and P. sajor-caju; the position of P. sapidus remains controversial. Furthermore, the rDNA analysis identified ten fragments suitable for species identification: eight allowed the characterization of five taxa (P. cornucopiae. P. ostreatus, P. sajor-caju, P. abalonus and P. columbinus) and two distinguished among clusters including related taxa. By a combination of just two restriction enzymes, the rDNA probe used seems to be the appropriate tool for both varietal characterization and protection of commercially valuable strains.

Wide Distribution of Mitochondrial Genome Rearrangements in Wild Strains of the Cultivated Basidiomycete Agrocybe aegerita

We used restriction fragment length polymorphisms to examine mitochondrial genome rearrangements in 36 wild strains of the cultivated basidiomycete Agrocybe aegerita, collected from widely distributed locations in Europe. We identified two polymorphic regions within the mitochondrial DNA which varied independently: one carrying the Cox II coding sequence and the other carrying the Cox I, ATP6, and ATP8 coding sequences. Two types of mutations were responsible for the restriction fragment length polymorphisms that we observed and, accordingly, were involved in the A. aegerita mitochondrial genome evolution: (i) point mutations, which resulted in strain-specific mitochondrial markers, and (ii) length mutations due to genome rearrangements, such as deletions, insertions, or duplications. Within each polymorphic region, the length differences defined only two mitochondrial types, suggesting that these length mutations were not randomly generated but resulted from a precise rearrangement mechanism. For each of the two polymorphic regions, the two molecular types were distributed among the 36 strains without obvious correlation with their geographic origin. On the basis of these two polymorphisms, it is possible to define four mitochondrial haplotypes. The four mitochondrial haplotypes could be the result of intermolecular recombination between allelic forms present in the population long enough to reach linkage equilibrium. All of the 36 dikaryotic strains contained only a single mitochondrial type, confirming the previously described mitochondrial sorting out after cytoplasmic mixing in basidiomycetes.

Uniparental Mitochondrial Transmission in the Cultivated Button Mushroom, Agaricus bisporus

A uniparental mitochondrial (mt) transmission pattern has been previously observed in laboratory matings of the cultivated mushroom Agaricus bisporus on petri dishes. In this study, four sets of specific matings were further examined by taking mycelial plugs from the confluent zone of mated homokaryons and inoculating these plugs into rye grain for laboratory fruiting and for fruiting under industrial conditions. Examination of the mt genotype of each individual fruit body for mt-specific restriction fragment length polymorphisms further confirmed that the mt genome was inherited uniparentally. The vegetative radial growth and the fruiting activity of two pairs of intraspecific heterokaryons, each pair carrying the same combination of nuclear genomes but different mt genotypes, were compared. Our results suggested that the mt genotype did not appreciably affect radial growth or fruiting activity. The failure to recover both heterokaryons, each carrying either parental mt genotype in any given cross, therefore clearly indicated that in matings of A. bisporus , the mt genome from one of the parental homokaryons is either selectively excluded in the newly formed heterokaryon or selectively eliminated in the immediate heterokaryotic mitotic progeny of the newly formed heterokaryon.

Mitochondrial DNAs of the fungus Armillaria ostoyae: restriction map and length variation

A restriction-enzyme-site map is presented for the 147-kb mtDNA of North American Armillaria ostoyae. The locations of five structural genes, atp6, atp8, coxI, coxIII, and cob, along with the location and orientation of the large and small ribosomal RNA genes, were determined through Southern hybridizations with cloned genes from other fungal mtDNAs. Based on this map, the variation in mtDNA suggested geographic structure at two different levels. On a large geographic scale, 17 mtDNA types from North America were distinct, with respect to both size and restriction maps, from three mtDNA types from Europe. At the local scale, identical mtDNA types were evident among several different genetic individuals located no more than 1 km apart at a site in Michigan. No mtDNA type occurred more than once among genetic individuals from different regions of North America, although the occurrence of similar mtDNAs in isolates from distant regions suggested that this may occur at a low frequency with large sample sizes. Among the North American mtDNA types, analysis of discrete length variants was inconsistent with the hypothesis that the mtDNA of A. ostoyae evolves as a clonal lineage in which each length mutation represents a unique event. The two remaining hypotheses, that similar mutational events have occurred independently and that genetic exchange and recombination occurs among mtDNAs in natural populations of this species, remain to be tested.

Further characterization of a large inverted repeat in the mitochondrial genomes of Agaricus bisporus (= A. brunnescens) and related species

The mitochondrial (mt) genome of Agaricus bisporus Ag50 (a heterokaryon) is a 136-kilobase (kb) circular molecule which contains a pair of large inverted repeats (IRs). Two large BAMHI fragments (B1 and B2) which contain the IR regions were further mapped. The repeated regions were determined to be approximately 7.7 kb in length. The mt small ribosomal RNA (S rRNA) gene is located adjacent to one of the repeated regions. Orientational isomers, generated by homologous recombination between the repeated regions, were not observed in mtDNA extractions from Ag50 mycelium (liquid culture) or from Ag50 fruit bodies. We also did not observe any orientational isomers in Ag50HA or Ag50HB, two homokaryons somatically isolated from Ag50. DNA homologous to the Ag50 mt repeated regions was observed in ten other isolates of Agaricus including four isolates of A. bisporus, two isolates of A. subperonatus, two isolates of A. subfloccosus, one isolate of A. bitorquis, and one isolate of A. pattersonae. The repeated regions and the small unique regions in two other heterokaryotic strains of A. bisporus, Ag2 and Ag85, were physically mapped. The repeated regions in these two strains are also in the inverted forms. Restriction endonuclease mapping indicated that the two copies of the IR in Ag85 were not identical.

Mitochondrial DNA of Schizophyllum commune: restriction map, genetic map, and mode of inheritance

Mitochondrial DNA (mtDNA) found in the basidiomycete Schizophyllum commune (strain 4-40) is a circular molecule 49.75 kbp in length. A physical map containing 61 restriction sites revealed no repeat structures. Cloned genes from Neurospora crassa, Aspergillus nidulans, and Saccharomyces cerevisiae were used in Southern hybridizations to locate nine mitochondrial genes, including a possible pseudogene of ATPase 9, on the restriction map. A probe from a functional ATPase 9 gene identified homologous fragments only in the nuclear genome of S. commune. Restriction fragment length polymorphisms (RFLPs) between mtDNA isolated from different strains of S. commune were used to show that mitochondria do not migrate with nuclei during dikaryosis.

Investigation of Mitochondrial Transmission in Selected Matings between Homokaryons from Commercial and Wild-Collected Isolates of Agaricus bisporus (= Agaricus brunnescens )

Ten heterokaryons of Agaricus bisporus (= Agaricus brunnescens ) were shown to carry four different mitochondrial (mt) genotypes by analysis of mt restriction fragment length polymorphisms (RFLPs). Fifteen homokaryons derived from these strains were used to investigate mt inheritance in A. bisporus. One hundred eighty-nine pairings were performed in 25 different combinations. Pairings in 15 different combinations produced heterokaryons on the basis of nuclear RFLP analyses and/or fruiting trials. The mt genotype of each new intraspecies hybrid was examined by using mt RFLPs as genetic markers. Our results suggest the following. (i) Recombination between the mt genomes was not a common event. (ii) From most individual pairings, all heterokaryons carried the same mt genotype. (iii) Heterokaryons carrying either of the two possible mt genotypes were observed in certain crosses after modification of the pairing procedure. A biparental transmission pattern was demonstrated for some crosses, but there appears to be a preference for one of the mt genotypes to predominate in any specific pairing.

Involvement of a large inverted repeated sequence in a recombinational rearrangement of the mitochondrial genome of the higher fungus Agrocybe aegerita

Southern hybridization of the total DNA of Agrocybe aegerita with cloned mitochondrial (mt) probes revealed a sequence homology between two distant mitochondrial restriction fragments. From the mtDNA restriction map and the distribution of restriction sites on the cross-hybridizing mitochondrial fragments, two copies of a large inverted repeated sequence (IR) of 3 kbp were located on the mitochondrial genome. These IR sequences divided the 80 kbp mtDNA into two single-copy regions of 24 kbp (SSC) and 50 kbp (LSC). For the first time in higher fungi, this IR sequence has been shown to be involved in an intramolecular homologous recombinational event. Such a rearrangement led to an inversion of the orientation of the two unique-copy regions, without any change in mtDNA complexity. The location of the recombinational event was compared with previously reported plant and fungal mitochondrial rearrangements and the potential role of the IR sequence was discussed.

The mitochondrial genome of the basidiomycete Agrocybe aegerita: molecular cloning, physical mapping and gene location

The mtDNA of a wild-type strain of Agrocybe aegerita was purified from mitochondria isolated by cellular fractionation. A representative library was constructed in E. coli by molecular cloning at the HindIII restriction site of pBR322. Southern hybridizations between total DNA of the fungal strain and cloned mitochondrial insert probes were used to establish the restriction map of the mtDNA molecule. Its size was assessed at about 80,500 bp. Four structural genes (for Cox 1, Cox 2, Atp 6, and Atp 8) were located on the map by heterologous hybridizations with oligonucleote probes specific for yeast mitochondrial genes. The location of the genes coding for the large and the small RNAs of the mitochondrial ribosome was determined by hybridization with the E. coli rrnB operon. A comparison of A. aegerita mtDNA organization with that of both phylogenetically close and distant fungi is discussed.

Homology between mitochondrial DNA of Agaricus bisporus and an internal portion of a linear mitochondrial plasmid of Agaricus bitorquis

Agaricus bisporus, the cultivated mushroom, contains a mitochondrial fragment (50H) which was previously demonstrated by Southern hybridization to have sequence similarity to an internal region of pEM, a linear mitochondrial plasmid of Agaricus bitorquis. The nucleotide sequence of 50H was determined and compared to the sequence of the corresponding pEM fragment. The region of sequence homology on pEM is contained within an open reading frame (ORF) that may encode an RNA polymerase, but 50H is neither an intact nor a complete copy of the ORF. pEM also contains an ORF with characteristics of genes for virus-encoded DNA polymerases. pEM appears to be very similar to other linear mitochondrial plasmids (in fungi and higher plants) reported to contain ORFs that may encode the same types of polymerases. The potential functionality of the pEM sequence suggests that it has diverged less than the mitochondrial fragment from a common ancestor.