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

Insight into the evolutionary and domesticated history of the most widely cultivated mushroom Agaricus bisporus via mitogenome sequences of 361 global strains

Agaricus bisporus is the most widely cultivated edible mushroom in the world with a only around three hundred years known history of cultivation. Therefore, it represents an ideal organism not only to investigate the natural evolutionary history but also the understanding on the evolution going back to the early era of domestication. In this study, we generated the mitochondrial genome sequences of 352 A. bisporus strains and 9 strains from 4 closely related species around the world. The population mitogenomic study revealed all A. bisporus strains can be divided into seven clades, and all domesticated cultivars present only in two of those clades. The molecular dating analysis showed this species origin in Europe on 4.6 Ma and we proposed the main dispersal routes. The detailed mitogenome structure studies showed that the insertion of the plasmid-derived dpo gene caused a long fragment (MIR) inversion, and the distributions of the fragments of dpo gene were strictly in correspondence with these seven clades. Our studies also showed A. bisporus population contains 30 intron distribution patterns (IDPs), while all cultivars contain only two IDPs, which clearly exhibit intron loss compared to the others. Either the loss occurred before or after domestication, that could suggest that the change facilitates their adaptation to the cultivated environment.

Evidence of Extensive Intraspecific Noncoding Reshuffling in a 169-kb Mitochondrial Genome of a Basidiomycetous Fungus

Comparative genomics of fungal mitochondrial genomes (mitogenomes) have revealed a remarkable pattern of rearrangement between and within major phyla owing to horizontal gene transfer and recombination. The role of recombination was exemplified at a finer evolutionary time scale in basidiomycetes group of fungi as they display a diversity of mitochondrial DNA inheritance patterns. Here, we assembled mitogenomes of six species from the Hymenochaetales order of basidiomycetes and examined 59 mitogenomes from 2 genetic lineages of Phellinus noxius. Gene order is largely collinear, while intergene regions are major determinants of mitogenome size variation. Substantial sequence divergence was found in shared introns consistent with high horizontal gene transfer frequency observed in yeasts, but we also identified a rare case where an intron was retained in five species since speciation. In contrast to the hyperdiversity observed in nuclear genomes of Phellinus noxius, mitogenomes’ intraspecific polymorphisms at protein-coding sequences are extremely low. Phylogeny network based on introns revealed turnover as well as exchange of introns between two lineages. Strikingly, some strains harbor a mosaic origin of introns from both lineages. Analysis of intergenic sequence indicated substantial differences between and within lineages, and an expansion may be ongoing as a result of exchange between distal intergenes. These findings suggest that the evolution in mitochondrial DNAs is usually lineage specific but chimeric mitotypes are frequently observed, thus capturing the possible evolutionary processes shaping mitogenomes in a basidiomycete. The large mitogenome sizes reported in various basidiomycetes appear to be a result of interspecific reshuffling of intergenes.

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 Haplotype Influences Mycelial Growth of Agaricus bisporus Heterokaryons

We evaluated the influence of mitochondrial haplotype on growth of the common button mushroom Agaricus bisporus. Ten pairs of heterokaryon strains, each pair having the same nuclear genome but different mitochondrial genomes, were produced by controlled crosses among a group of homokaryons of both wild and commercial origins. Seven genetically distinct mitochondrial DNA (mtDNA) haplotypes were evaluated in different nuclear backgrounds. The growth of heterokaryon pairs differing only in their mtDNA haplotypes was compared by measuring mycelial radial growth rate on solid complete yeast medium (CYM) and compost extract medium and by measuring mycelial dry weight accumulation in liquid CYM. All A. bisporus strains were incubated at temperatures similar to those utilized in commercial production facilities (18, 22, and 26(deg)C). Statistically significant differences were detected in 8 of the 10 heterokaryon pairs evaluated for one or two of the three growth parameters measured. Some heterokaryon pairs showed differences in a single growth parameter at all three temperatures of incubation, suggesting a temperature-independent difference. Others showed differences at only a single temperature, suggesting a temperature-dependent difference. The influence of some mtDNA haplotypes on growth was dependent on the nuclear genetic background. Our results show that mtDNA haplotype can influence growth of A. bisporus heterokaryons in some nuclear backgrounds. These observations demonstrate the importance of including a number of mitochondrial genotypes and evaluating different nuclear-mitochondrial combinations of A. bisporus in strain improvement programs.

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.

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.

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.

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.