Occurrence of double-stranded RNA species in champignon and their relation to Mushroom Virus X symptoms

Mycoviruses are known to infect fungi of different habitats and life style. Some of them, like the Mushroom Virus X (MVX) complex, cause abnormal development of fruiting bodies and severe yield losses in mushroom cultivation. Most mycoviruses have a double-stranded RNA (dsRNA) genome, therefore dsRNA-detection is frequently used as a first step to identify virus infection. In relation with MVX 23 dsRNAs species have been described, occurring in variable number and combination in diseased mushrooms. The aim of our experiments was to find out whether dsRNA-immunoblotting can be used to detect dsRNA in small samples of cultivated A. bisporus varieties and of wild growing Agaricus species. We found that by immunoblotting, the same dsRNA species were detected in apparently healthy cultivated champignon fruiting bodies and in MVX-infected reference samples, respectively, as by conventional CF11 chromatography, but for immunoblotting a much smaller sample size was needed. In two out of three deformed fruit bodies of cultivated A. bisporus from Hungary we detected a 4.1 kbp dsRNA species which was also present in the MVX infected reference samples. Diverse and variable dsRNA patterns were observed in apparently healthy samples of 12 wild growing Agaricus species, indicating that extreme care should be taken when non-cultivated Agaricus is used for breeding new varieties. Non-sterile cultures and environmental mushroom specimens are fairly often mixed with parasitic and endofungal organisms, therefore, we also tested fungi isolated from mushroom cultures. Here again, 1–7 dsRNA species were found in extracts of Trichoderma and Dactylium isolates and of Mycogone-infected sporophores. Our results demonstrate clearly that dsRNAs from very different origins can be present in cultivated champignon and support the view that the MVX symptom-associated dsRNAs are probably of polyphyletic origin and do not represent one defined virus

Comparative genomics reveals the origin of fungal hyphae and multicellularity

Hyphae represent a hallmark structure of multicellular fungi. The evolutionary origins of hyphae and of the underlying genes are, however, hardly known. By systematically analyzing 72 complete genomes, we here show that hyphae evolved early in fungal evolution probably via diverse genetic changes, including co-option and exaptation of ancient eukaryotic (e.g. phagocytosis-related) genes, the origin of new gene families, gene duplications and alterations of gene structure, among others. Contrary to most multicellular lineages, the origin of filamentous fungi did not correlate with expansions of kinases, receptors or adhesive proteins. Co-option was probably the dominant mechanism for recruiting genes for hypha morphogenesis, while gene duplication was apparently less prevalent, except in transcriptional regulators and cell wall - related genes. We identified 414 novel gene families that show correlated evolution with hyphae and that may have contributed to its evolution. Our results suggest that hyphae represent a unique multicellular organization that evolved by limited fungal-specific innovations and gene duplication but pervasive co-option and modification of ancient eukaryotic functions

Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes.

Fruiting bodies (sporocarps, sporophores or basidiomata) of mushroom-forming fungi ( Agaricomycetes) are among the most complex structures produced by fungi. Unlike vegetative hyphae, fruiting bodies grow determinately and follow a genetically encoded developmental program that orchestrates their growth, tissue differentiation and sexual sporulation. In spite of more than a century of research, our understanding of the molecular details of fruiting body morphogenesis is still limited and a general synthesis on the genetics of this complex process is lacking. In this paper, we aim at a comprehensive identification of conserved genes related to fruiting body morphogenesis and distil novel functional hypotheses for functionally poorly characterised ones. As a result of this analysis, we report 921 conserved developmentally expressed gene families, only a few dozens of which have previously been reported to be involved in fruiting body development. Based on literature data, conserved expression patterns and functional annotations, we provide hypotheses on the potential role of these gene families in fruiting body development, yielding the most complete description of molecular processes in fruiting body morphogenesis to date. We discuss genes related to the initiation of fruiting, differentiation, growth, cell surface and cell wall, defence, transcriptional regulation as well as signal transduction. Based on these data we derive a general model of fruiting body development, which includes an early, proliferative phase that is mostly concerned with laying out the mushroom body plan (via cell division and differentiation), and a second phase of growth via cell expansion as well as meiotic events and sporulation. Altogether, our discussions cover 1 480 genes of Coprinopsis cinerea, and their orthologs in Agaricus bisporus, Cyclocybe aegerita, Armillaria ostoyae, Auriculariopsis ampla, Laccaria bicolor, Lentinula edodes, Lentinus tigrinus, Mycena kentingensis, Phanerochaete chrysosporium, Pleurotus ostreatus, and Schizophyllum commune, providing functional hypotheses for ~10 % of genes in the genomes of these species. Although experimental evidence for the role of these genes will need to be established in the future, our data provide a roadmap for guiding functional analyses of fruiting related genes in the Agaricomycetes. We anticipate that the gene compendium presented here, combined with developments in functional genomics approaches will contribute to uncovering the genetic bases of one of the most spectacular multicellular developmental processes in fungi. Citation: Nagy LG, Vonk PJ, Künzler M, Földi C, Virágh M, Ohm RA, Hennicke F, Bálint B, Csernetics Á, Hegedüs B, Hou Z, Liu XB, Nan S, M. Pareek M, Sahu N, Szathmári B, Varga T, Wu W, Yang X, Merényi Z (2023). Lessons on fruiting body morphogenesis from genomes and transcriptomes of Agaricomycetes. Studies in Mycology 104: 1-85. doi: 10.3114/sim.2022.104.01