Recent genome sequencing efforts in the marasmioid clade revealed diverse genomic and life history traits, including genome expansion and pathogenicity in Armillaria spp. Armillaria and Omphalotus belong to the marasmioid clade, whereas Mycena was recently found to be sister of the marasmioid clade ( 8). Phylogeny reconstruction suggested that luciferase originated in early Agaricales. This cluster was found to be conserved across bioluminescent fungi of three lineages: Armillaria, mycenoid, and Omphalotus ( 7). have identified the fungal luciferase, which is physically adjacent to these enzymes and forms a gene cluster containing luciferase, hispidin synthase, and H3H ( 7). Oxygen is then added to the luciferin by luciferase, producing a high-energy intermediate which is subsequently decomposed, yielding light emission. First, a luciferin precursor of hispidin is hydroxylated by hispidin-3-hydroxylase (H3H) into 3-hydroxyhispidin (luciferin) ( 6). Repeats including TEs are LTRs, long interspersed nuclear elements (LINES), short interspersed nuclear elements (SINEs), DNA transposons (DNA), and other types of repeats, such as small RNA (small), simple repeats (simple), and low complexity repeats (low).įungal light emission involves two main steps. ( E) Haploid genome sizes for mycenoid species broken down by repeat types and gene features. Blue dot on a branch indicates a bootstrap value >90. ( D) Reconciliated phylogeny of fungal luciferase. ( C) Gene copy number in the OGs associated with luciferin biosynthesis pathway including luciferase ( luz), hispidin-3-hydroxylase ( h3h), hispidin synthase ( hisps), cytochrome P450 ( cyp450), and caffeylpyruvate hydrolase ( cph). Green horizontal bars indicate the percentage of bioluminescent fungi found in either the mycenoid or the Armillaria lineage. The x axis denotes divergence time estimates. ( B) Species trees inferred from a concatenated supermatrix of the gene alignments using the 360 single-copy orthogroups. ( A) The five species sequenced in this study. Phylogenomic analysis of Mycena and related fungi. Our results contribute to understanding a de novo origin of bioluminescence and the corresponding gene cluster in a diverse group of enigmatic fungal species.įig. Luciferase cluster members were coexpressed across developmental stages, with the highest expression in fruiting body caps and stipes, suggesting fruiting-related adaptive functions. Analyses of synteny across genomes of bioluminescent species resolved how the luciferase cluster was derived by duplication and translocation, frequently rearranged and lost in most Mycena species, but conserved in the Armillaria lineage. We show that bioluminescence evolved in the last common ancestor of mycenoid and the marasmioid clade of Agaricales and was maintained through at least 160 million years of evolution. Two species with haploid genome assemblies ∼150 Mb are among the largest in Agaricales, and we found that a variety of repeats between Mycena species were differentially mediated by DNA methylation.
We sequenced the genomes and transcriptomes of five bonnet mushroom species ( Mycena spp.), a diverse lineage comprising the majority of bioluminescent fungi. bisporus strains.Mushroom-forming fungi in the order Agaricales represent an independent origin of bioluminescence in the tree of life yet the diversity, evolutionary history, and timing of the origin of fungal luciferases remain elusive. Typically, 3–6% of primordia developed into mature sporophores, but significant differences in this proportion, as well as in the numbers of primordia produced, were recorded between 12 A. In larger-scale, nonaxenic culture, strain B430 produced severely malformed but mature sporophores in similar numbers to those of other strains. However, none of these rudimentary primordia developed differentiated tissues or beyond 4 mm diameter, either on axenic casing material in the microcosms or in larger-scale culture. Of six strains tested, only the developmental variant mutant, B430, produced rudimentary primordia on axenic peat-based casing material.
bisporus (commercial strain A15) was capable of producing primordia and mature sporophores on charcoal (wood and activated), anthracite coal, lignite and zeolite, but not on bark, coir, peat, rockwool, silica or vermiculite. bisporus were cultured in axenic and nonaxenic microcosms, using a rye grain substrate covered by a range of organic and inorganic casing materials. Some of these primordia then may develop further into sporophores, involving differentiation of tissue. The mushroom ( Agaricus bisporus) has a requirement for a “casing layer” that has specific physical, chemical and microbiological properties which stimulate and promote the initiation of primordia.
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