Pezizomycetes genomes reveal the molecular basis of ectomycorrhizal truffle lifestyle

Newly Designed Fluorescence In Situ Hybridization Probes Reveal Previously Unknown Endophytic Abilities of Tuber magnatum in Herbaceous Plants

Tuber magnatum Picco (the Italian white truffle) is the most valuable and widely appreciated truffle. It is an ectomycorrhizal fungus known to associate with many broadleaf tree species. However, its mycorrhizae are rarely observed in the field, suggesting possible alternative symbiotic strategies, such as endophytism with non-ectomycorrhizal plants. In order to test potential endophytic interactions of T. magnatum with wild plants, a combination of polymerase chain reaction (PCR) and Fluorescence In Situ Hybridization (FISH) approaches were used. Specific FISH probes for T. magnatum were designed, tested in vitro on hyphae and/or ectomycorrhizae, and selected for their specificity. These probes were then used on a wide variety root samples of wild plants collected from three T. magnatum production areas in Italy and previously tested for the presence of T. magnatum mycelium using PCR-specific primers. Molecular analyses detected the presence of T. magnatum in 21 of 100 plant samples analyzed. FISH analysis confirmed the extracellular presence of active T. magnatum hyphae inside the root system of Carex pendula Huds plant. This study provides the first evidence of T. magnatum acting as an endophyte in an herbaceous plant. The newly designed, highly specific T. magnatum FISH probes can be used for further investigations to confirm the endophytic tendencies of T. magnatum and to understand their influence on the life cycle and biology of this fungus.

Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota)

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology. Our phylogenomic tree was supported by high gene tree concordance, facilitating taxonomic revisions in Discinaceae. We recognized 10 genera across two tribes: tribe Discineae (Discina, Maublancomyces, Neogyromitra, Piscidiscina, and Pseudodiscina) and tribe Gyromitreae (Gyromitra, Hydnotrya, Paragyromitra, Pseudorhizina, and Pseudoverpa); Piscidiscina was newly erected and 26 new combinations were formalized. Paradiscina melaleuca and Marcelleina donadinii formed their own family-level clade sister to Morchellaceae, which merits further taxonomic study. Genome size and CAZyme content were consistent with a mycorrhizal lifestyle for the truffle species (Hydnotrya spp.), whereas the other Discinaceae genera possessed genomic properties of a saprotrophic habit. Lorchels were found to be predominantly heterothallic-either MAT1-1 or MAT1-2-but a single occurrence of colocalized mating-type idiomorphs indicative of homothallism was observed in Gyromitra esculenta strain CBS101906 and requires additional confirmation and follow-up study. Lastly, we confirmed that gyromitrin has a phylogenetically discontinuous distribution, having been detected exclusively in two distantly related genera (Gyromitra and Piscidiscina) belonging to separate tribes. Our genomic dataset will facilitate further investigations into the gyromitrin biosynthesis genes and their evolutionary history. With additional sampling of Geomoriaceae and Helvellaceae-two closely related families with no publicly available genomes-these data will enable comprehensive studies on the independent evolution of truffles and ecological diversification in an economically important group of pezizalean fungi.

Whole-Genome Sequence Analysis of Flammulina filiformis and Functional Validation of Gad, a Key Gene for γ-Aminobutyric Acid Synthesis

Flammulina filiformis is one of the widely produced edible fungi worldwide. It is rich in γ-aminobutyric acid (GABA), a non-protein amino acid with important physiological functions in humans. To investigate the functions of key genes in the GABA metabolic pathway of F. filiformis, we isolated the monokaryon Fv-HL23-1 from the factory-cultivated F. filiformis strain Fv-HL23 and then sequenced and assembled the genome using the PacBio Sequel and Illumina NovaSeq sequencing platforms. The results showed that the genome comprised 140 scaffolds with a total length of 40.96 Mb, a GC content of 49.62%, an N50 of 917,125 bp, and 14,256 protein-coding genes. Phylogenetic analysis based on the whole genome revealed a close evolutionary relationship of Fv-HL23-1 with Armillaria mellea, Lentinula edodes, and Schizophyllum commune. A total of 589 carbohydrate-active enzymes were identified in the genome of Fv-HL23-1, suggesting its strong lignocellulose degradation ability, and 108 CYP450 gene family members were identified, suggesting important functions such as resistance to stress, secondary metabolite synthesis, and growth and development. The F. filiformis proteins glutamate decarboxylase 1 (Ff-GAD1) and glutamate decarboxylase 2 (Ff-GAD2), which may be responsible for GABA synthesis, were identified by protein alignment. Molecular docking analysis showed that Ff-GAD2 may have better catalytic activity than Ff-GAD1. To verify the function of Ff-gad2, its heterologous expression in the mycelia of the mononuclear Hypsizigus marmoreus was analyzed. Compared with wild type, the GABA content of mycelia was increased by 85.40-283.90%, the growth rate was increased by 9.39 ± 2.35%, and the fresh weight was increased by 18.44 ± 7.57%. Ff-GAD2 may play a catalytic role in GABA synthesis. In addition, the expression of the full-length Ff-gad2 gene was increased by 7.96 ± 1.39 times compared with the exon expression level in H. marmoreus mycelia, suggesting that the intron may contribute to the heterologous expression of Ff-GAD2. Based on whole-genome sequencing, we analyzed the enzyme system related to the important life activities of F. filiformis, focusing on the function of Ff-GAD, a key enzyme in the GABA synthesis pathway. The results lay a foundation for elucidating the GABA metabolism pathway of edible fungi and developing targeted breeding strategies for GABA-producing edible fungi.

Fungal community characteristics of the last remaining habitat of three paphiopedilum species in China

Paphiopedilum armeniacum, Paphiopedilum wenshanense and Paphiopedilum emersonii are critically endangered wild orchids. Their populations are under severe threat, with a dramatic decline in the number of their natural distribution sites. Ex situ conservation and artificial breeding are the keys to maintaining the population to ensure the success of ex situ conservation and field return in the future. The habitat characteristics and soil nutrient information of the last remaining wild distribution sites of the three species were studied. ITS high-throughput sequencing was used to reveal the composition and structure of the soil fungal community, analyze its diversity and functional characteristics, and reveal its relationship with soil nutrients. The three species preferred to grow on low-lying, ventilated and shaded declivities with good water drainage. There were significant differences in soil alkali-hydrolyzed nitrogen and available phosphorus among the three species. There were 336 fungal species detected in the samples. On average, there were different dominant groups in the soil fungal communities of the three species. The functional groups of soil fungi within their habitats were dominated by saprophytic fungi and ectomycorrhizae, with significant differences in diversity and structure. The co-occurrence network of habitat soil fungi was mainly positive. Soil pH significantly affected soil fungal diversity within their habitats of the three paphiopedilum species. The study confirmed that the dominant groups of soil fungi were significantly correlated with soil nutrients. The three species exhibit comparable habitat inclinations, yet they display substantial variations in the composition, structure, and diversity of soil fungi. The fungal functional group is characterized by a rich presence of saprophytic fungi, a proliferation of ectomycorrhizae, and a modest occurrence of orchid mycorrhizae. The symbiotic interactions among the soil fungi associated with these three species are well-coordinated, enhancing their resilience against challenging environmental conditions. There is a significant correlation between soil environmental factors and the composition of soil fungal communities, with pH emerging as a pivotal factor regulating fungal diversity. Our research into the habitat traits and soil fungal ecosystems of the three wild Paphiopedilum species has established a cornerstone for prospective ex situ conservation measures and the eventual reestablishment of these species in their native landscapes.

Three New Truffle Species (Tuber, Tuberaceae, Pezizales, and Ascomycota) from Yunnan, China, and Multigen Phylogenetic Arrangement within the Melanosporum Group

Based on a multi-locus phylogeny of a combined dataset of ITS, LSU, tef1-α, and rpb2 and comprehensive morphological analyses, we describe three new species from the Melanosporum group of genus Tuber and synonymize T. pseudobrumale and T. melanoexcavatum. Phylogenetically, the three newly described species, T. yunnanense, T. melanoumbilicatum and T. microexcavatum, differ significantly in genetic distance from any previously known species. Morphologically, T. yunnanense is distinctly different from its closest phylogenetically related species, T. longispinosum, due to its long shuttle-shape spores (average the ratio of spore length to spore width for all spores (Qm) = 1.74). Tuber melanoumbilicatum differs from the other species in having a cavity and long shuttle-shaped spores (Qm = 1.65). Although T. microexcavatum sampled ascomata have relatively low maturity, they can be distinguished from its closely related species T. pseudobrumale by the ascomata size, surface warts, and spore number per asci; additionally, phylogenetic analysis supports it as a new species. In addition, molecular analysis from 22 newly collected specimens and Genebank data indicate that T. pseudobrumale and T. melanoexcavatum are clustered into a single well-supported clade (Bootstrap (BS) = 100, posterior probabilities (PP) = 1.0); and morphological characteristics do not differ. Therefore, based on the above evidence and publication dates, we conclude that T. melanoexcavatum is a synonym of T. pseudobrumale. By taking into account current knowledge and combining the molecular, multigene phylogenetic clade arrangement and morphological data, we propose that the Melanosporum group should be divided into four subgroups. Diagnostic morphological features and an identification key of all known species in the Melanosporum group are also included. Finally, we also provide some additions to the knowledge of the characterization of T. pseudobrumale, T. variabilisporum, and T. pseudohimalayense included in subgroup 1 of the Melanosporum group.

Extreme overall mushroom genome expansion in Mycena s.s. irrespective of plant hosts or substrate specializations

Mycena s.s. is a ubiquitous mushroom genus whose members degrade multiple dead plant substrates and opportunistically invade living plant roots. Having sequenced the nuclear genomes of 24 Mycena species, we find them to defy the expected patterns for fungi based on both their traditionally perceived saprotrophic ecology and substrate specializations. Mycena displayed massive genome expansions overall affecting all gene families, driven by novel gene family emergence, gene duplications, enlarged secretomes encoding polysaccharide degradation enzymes, transposable element (TE) proliferation, and horizontal gene transfers. Mainly due to TE proliferation, Arctic Mycena species display genomes of up to 502 Mbp (2-8× the temperate Mycena), the largest among mushroom-forming Agaricomycetes, indicating a possible evolutionary convergence to genomic expansions sometimes seen in Arctic plants. Overall, Mycena show highly unusual, varied mosaic-like genomic structures adaptable to multiple lifestyles, providing genomic illustration for the growing realization that fungal niche adaptations can be far more fluid than traditionally believed.

Phytotoxic Strains of Fusarium commune Isolated from Truffles

Most Fusarium species are known as endophytes and/or phytopathogens of higher plants and have a worldwide distribution. Recently, information discovered with molecular tools has been also published about the presence of these fungi in the microbiome of truffle fruiting bodies. In the present work, we isolated and identified three Fusarium strains from truffle fruiting bodies. All isolates were assigned to the same species, F. commune, and the strains were deposited in the All-Russian Collection of Microorganisms under accession numbers VKM F-5020, VKM F-5021, and VKM F-5022. To check the possible effects of the isolated strains on the plants, the isolates were used to infect sterile seedlings of Sarepta mustard (Brassica juncea L.). This model infection led to a moderate suppression of the photosynthetic apparatus activity and plant growth. Here, we present characteristics of the F. commune isolates: description of the conidial morphology, pigmentation, and composition of the mycelium fatty acids. Overall, this is the first description of the Fusarium cultures isolated from truffle fruiting bodies. Possible symbiosis of the F. commune strains with truffles and their involvement in the cooperative fatty acid production are proposed.

Label-free based comparative proteomics approach revealed the changes in proteomic profiles driven by different maturities in two Chinese white truffles, Tuber panzhihuanense and Tuber latisporum

T. panzhihuanense and T. latisporum are white truffle species native to China, of which T. panzhihuanense has significant commercial potential, with high nutritional value and unique flavor. Maturity is an important factor affecting the nutrition and aroma of truffles, which determines their economic status. Here, a label-free-based comparative proteomics method was used to determine the proteomic profiles of T. panzhihuanense and T. latisporum at two different stages of maturity. The results showed that both maturity and species significantly affected the protein expression patterns. T. panzhihuanense responded stronger to maturity than T. latisporum, accompanied by a more complex interaction network between proteins. Some critical proteins were regulated by maturity and variety, including those involved in aroma formation, e.g., S-adenosyl-methionine synthetase. The enrichment of oxidation-reduction processes, glycolysis, and SNARE interactions in vesicular transport were driven by species and maturity. This study provides the first insights into the proteomic profiles of T. panzhihuanense and T. latisporum, revealing the roles of key proteins and biological processes in their maturation.

Genome assembly of M. spongiola and comparative genomics of the genus Morchella provide initial insights into taxonomy and adaptive evolution

Morchella spongiola is a highly prized mushroom for its delicious flavor and medical value and is one of the most flourishing, representative, and dominant macrofungi in the Qilian Mountains of the Qinghai-Tibet Plateau subkingdoms (QTPs). However, the understanding of M. spongiola remains largely unknown, and its taxonomy is ambiguous. In this study, we redescribed a unique species of M. spongiola, i.e., micromorphology, molecular data, genomics, and comparative genomics, and the historical biogeography of M. spongiola were estimated for 182 single-copy homologous genes. A high-quality chromosome-level reference genome of M. spongiola M12-10 was obtained by combining PacBio HiFi data and Illumina sequencing technologies; it was approximately 57.1 Mb (contig N50 of 18.14 Mb) and contained 9775 protein-coding genes. Comparative genome analysis revealed considerable conservation and unique characteristics between M. spongiola M12-10 and 32 other Morchella species. Molecular phylogenetic analysis indicated that M. spongiola M12-10 is similar to the M. prava/Mes-7 present in sandy soil near rivers, differentiating from black morels ~ 43.06 Mya (million years ago), and diverged from M. parva/Mes-7 at approximately 12.85 Mya (in the Miocene epoch), which is closely related to the geological activities in the QTPs (in the Neogene). Therefore, M. spongiola is a unique species rather than a synonym of M. vulgaris/Mes-5, which has a distinctive grey-brown sponge-like ascomata. This genome of M. spongiola M12-10 is the first published genome sequence of the species in the genus Morchella from the QTPs, which could aid future studies on functional gene identification, germplasm resource management, and molecular breeding efforts, as well as evolutionary studies on the Morchella taxon in the QTPs.

The mycorrhizal symbiosis: research frontiers in genomics, ecology, and agricultural application

Mycorrhizal symbioses between plants and fungi are vital for the soil structure, nutrient cycling, plant diversity, and ecosystem sustainability. More than 250 000 plant species are associated with mycorrhizal fungi. Recent advances in genomics and related approaches have revolutionized our understanding of the biology and ecology of mycorrhizal associations. The genomes of 250+ mycorrhizal fungi have been released and hundreds of genes that play pivotal roles in regulating symbiosis development and metabolism have been characterized. rDNA metabarcoding and metatranscriptomics provide novel insights into the ecological cues driving mycorrhizal communities and functions expressed by these associations, linking genes to ecological traits such as nutrient acquisition and soil organic matter decomposition. Here, we review genomic studies that have revealed genes involved in nutrient uptake and symbiosis development, and discuss adaptations that are fundamental to the evolution of mycorrhizal lifestyles. We also evaluated the ecosystem services provided by mycorrhizal networks and discuss how mycorrhizal symbioses hold promise for sustainable agriculture and forestry by enhancing nutrient acquisition and stress tolerance. Overall, unraveling the intricate dynamics of mycorrhizal symbioses is paramount for promoting ecological sustainability and addressing current pressing environmental concerns. This review ends with major frontiers for further research.

Whole-genome sequencing and evolutionary analysis of the wild edible mushroom, Morchella eohespera

Morels (Morchella, Ascomycota) are an extremely desired group of edible mushrooms with worldwide distribution. Morchella eohespera is a typical black morel species, belonging to the Elata clade of Morchella species. The biological and genetic studies of this mushroom are rare, largely hindering the studies of molecular breeding and evolutionary aspects. In this study, we performed de novo sequencing and assembly of the M. eohespera strain m200 genome using the third-generation nanopore sequencing platform. The whole-genome size of M. eohespera was 53.81 Mb with a contig N50 of 1.93 Mb, and the GC content was 47.70%. A total of 9,189 protein-coding genes were annotated. Molecular dating showed that M. eohespera differentiated from its relative M. conica at ~19.03 Mya (million years ago) in Burdigalian. Evolutionary analysis showed that 657 gene families were contracted and 244 gene families expanded in M. eohespera versus the related morel species. The non-coding RNA prediction results showed that there were 336 tRNAs, 76 rRNAs, and 45 snRNAs in the M. eohespera genome. Interestingly, there was a high degree of repetition (20.93%) in the M. eohespera genome, and the sizes of long interspersed nuclear elements, short interspersed nuclear elements, and long terminal repeats were 0.83 Mb, 0.009 Mb, and 4.56 Mb, respectively. Additionally, selection pressure analysis identified that a total of 492 genes in the M. eohespera genome have undergone signatures of positive selection. The results of this study provide new insights into the genome evolution of M. eohespera and lay the foundation for in-depth research into the molecular biology of the genus Morchella in the future.

Transcriptome and metabolome analysis reveals stage-specific metabolite accumulation during maturity of Chinese black truffle Tuber indicum

Tuber indicum is the most economically important member of Tuber, with the highest production and widest distribution in China. However, the overexploitation of immature ascocarps not only has driven wild resources of the species toward extinction, but also has caused enconomic losses and a decline in the reputation of T.indicum quality. In this study, stage-specific metabolites of T. indicum in relation to nutritional quality and the mechanism of their accumulations were explored by transcriptome and metabolome analysis at five harvest times, representing four maturation stages. A total of 663 compounds were identified in T. indicum ascocarps by a widely targeted metabolomic approach. Lipid compounds are the most prominent metabolites (18%) in our samples and also are higher accumulation at the immature stage than at mature stage, representing 30.16% differential accumulated metabolites in this stage. Levels of some of the amino acids, such as S-(methyl) glutathione, S-adenosylmethionine, which are known truffle aroma precursors, were increased at the mature stage. The gene expression level related to the biosynthesis of volatile organic compounds were verified by qPCR. This study contributes to the preliminary understanding of metabolites variations in T. indicum ascocarps during maturity for quality evaluation and truffle biology.

Sustainable cultivation of the white truffle (Tuber magnatum) requires ecological understanding

The white truffle (Tuber magnatum Picco.; WT) is the most expensive and arguably also the most delicious species within the genus Tuber. Due to its hidden belowground life cycle, complex host symbiosis, and yet unknown distribution, cultivation of the enigmatic species has only recently been achieved at some plantations in France. A sustainable production of WTs under future climate change, however, requires a better ecological understanding of the species' natural occurrence. Here, we combine information from truffle hunters with a literature review to assess the climatic, edaphic, geographic, and symbiotic characteristics of 231 reported WT sites in southeast Europe. Our meta-study shows that 75% of the WT sites are located outside the species' most famous harvest region, the Piedmont in northern Italy. Spanning a wide geographic range from ~ 37° N in Sicily to ~ 47° N in Hungary, and elevations between sea level in the north and 1000 m asl in the south, all WT sites are characterised by mean winter temperatures > 0.4 °C and summer precipitation totals of ~ 50 mm. Often formed during past flood or landslide events, current soil conditions of the WT sites exhibit pH levels between 6.4 and 8.7, high macroporosity, and a cation exchange capacity of ~ 17 meq/100 g. At least 26 potential host species from 12 genera were reported at the WT sites, with Populus alba and Quercus cerris accounting for 23.5% of all plant species. We expect our findings to contribute to a sustainable WT industry under changing environmental and economic conditions.

Large-Scale Field Cultivation of Morchella and Relevance of Basic Knowledge for Its Steady Production

Morels are one of the most highly prized edible and medicinal mushrooms worldwide. Therefore, historically, there has been a large international interest in their cultivation. Numerous ecological, physiological, genetic, taxonomic, and mycochemical studies have been previously developed. At the beginning of this century, China finally achieved artificial cultivation and started a high-scale commercial development in 2012. Due to its international interest, its cultivation scale and area expanded rapidly in this country. However, along with the massive industrial scale, a number of challenges, including the maintenance of steady economic profits, arise. In order to contribute to the solution of these challenges, formal research studying selection, species recognition, strain aging, mating type structure, life cycle, nutrient metabolism, growth and development, and multi-omics has recently been boosted. This paper focuses on discussing current morel cultivation technologies, the industrial status of cultivation in China, and the relevance of basic biological research, including, e.g., the study of strain characteristics, species breeding, mating type structure, and microbial interactions. The main challenges related to the morel cultivation industry on a large scale are also analyzed. It is expected that this review will promote a steady global development of the morel industry based on permanent and robust basic scientific knowledge.

Pezizomycetes Genomes Reveal Diverse P450 Complements Characteristic of Saprotrophic and Ectomycorrhizal Lifestyles

Cytochrome P450 monooxygenases (CYPs/P450s) are heme proteins that play a role in organisms' primary and secondary metabolism. P450s play an important role in organism adaptation since lifestyle influences P450 composition in their genome. This phenomenon is well-documented in bacteria but less so in fungi. This study observed this phenomenon where diverse P450 complements were identified in saprophytic and ectomycorrhizal Pezizomycetes. Genome-wide data mining, annotation, and phylogenetic analysis of P450s in 19 Pezizomycetes revealed 668 P450s that can be grouped into 153 P450 families and 245 P450 subfamilies. Only four P450 families, namely, CYP51, CYP61, CYP5093, and CYP6001, are conserved across 19 Pezizomycetes, indicating their important role in these species. A total of 5 saprophyte Pezizomycetes have 103 P450 families, whereas 14 ectomycorrhizal Pezizomycetes have 89 P450 families. Only 39 P450 families were common, and 50 and 64 P450 families, respectively, were unique to ectomycorrhizal and saprophytic Pezizomycetes. These findings suggest that the switch from a saprophytic to an ectomycorrhizal lifestyle led to both the development of diverse P450 families as well as the loss of P450s, which led to the lowest P450 family diversity, despite the emergence of novel P450 families in ectomycorrhizal Pezizomycetes.

Transcriptome Metabolic Characterization of Tuber borchii SP1-A New Spanish Strain for In Vitro Studies of the Bianchetto Truffle

Truffles are ascomycete hypogeous fungi belonging to the Tuberaceae family of the Pezizales order that grow in ectomycorrhizal symbiosis with tree roots, and they are known for their peculiar aromas and flavors. The axenic culture of truffle mycelium is problematic because it is not possible in many cases, and the growth rate is meager when it is possible. This limitation has prompted searching and characterizing new strains that can be handled in laboratory conditions for basic and applied studies. In this work, a new strain of Tuber borchii (strain SP1) was isolated and cultured, and its transcriptome was analyzed under different in vitro culture conditions. The results showed that the highest growth of T. borchii SP1 was obtained using maltose-enriched cultures made with soft-agar and in static submerged cultures made at 22 °C. We analyzed the transcriptome of this strain cultured in different media to establish a framework for future comparative studies, paying particular attention to the central metabolic pathways, principal secondary metabolite gene clusters, and the genes involved in producing volatile aromatic compounds (VOCs). The results showed a transcription signal for around 80% of the annotated genes. In contrast, most of the transcription effort was concentrated on a limited number of genes (20% of genes account for 80% of the transcription), and the transcription profile of the central metabolism genes was similar in the different conditions analyzed. The gene expression profile suggests that T. borchii uses fermentative rather than respiratory metabolism in these cultures, even in aerobic conditions. Finally, there was a reduced expression of genes belonging to secondary metabolite clusters, whereas there was a significative transcription of those involved in producing volatile aromatic compounds.

The genome of Lyophyllum shimeji provides insight into the initial evolution of ectomycorrhizal fungal genomes

Mycorrhizae are one of the most fundamental symbioses between plants and fungi, with ectomycorrhizae being the most widespread in boreal forest ecosystems. Ectomycorrhizal fungi are hypothesized to have evolved convergently from saprotrophic ancestors in several fungal clades, especially members of the subdivision Agaricomycotina. Studies on fungal genomes have identified several typical characteristics of mycorrhizal fungi, such as genome size expansion and decreases in plant cell-wall degrading enzymes (PCWDEs). However, genomic changes concerning the evolutionary transition to the ectomycorrhizal lifestyle are largely unknown. In this study, we sequenced the genome of Lyophyllum shimeji, an ectomycorrhizal fungus that is phylogenetically related to saprotrophic species and retains some saprotroph-like traits. We found that the genome of Ly. shimeji strain AT787 lacks both incremental increases in genome size and reduced numbers of PCWDEs. Our findings suggest that the previously reported common genomic traits of mycorrhizal fungi are not essential for the ectomycorrhizal lifestyle, but are a result of abolishing saprotrophic activity. Since Ly. shimeji is commercially consumed as an edible mushroom, the newly available genomic information may also impact research designed to enhance the cultivation of this mushroom.

Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes

Ascomycota account for about two-thirds of named fungal species.1 Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.2 Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.3,4,5 However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous "orphan" ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi.

Hidden fairy rings and males-Genetic patterns of natural Burgundy truffle (Tuber aestivum Vittad.) populations reveal new insights into its life cycle

Burgundy truffles are heterothallic ascomycetes that grow in symbiosis with trees. Despite their esteemed belowground fruitbodies, the species' complex lifecycle is still not fully understood. Here, we present the genetic patterns in three natural Burgundy truffle populations based on genotyped fruitbodies, ascospore extracts and ectomycorrhizal root tips using microsatellites and the mating-type locus. Distinct genetic structures with high relatedness in close vicinity were found for females (forming the fruitbodies) and males (fertilizing partner as inferred from ascospore extracts), with high genotypic diversity and annual turnover of males, suggesting that ephemeral male mating partners are germinating ascospores from decaying fruitbodies. The presence of hermaphrodites and the interannual persistence of a few males suggest that persistent mycelia may sporadically also act as males. Only female or hermaphroditic individuals were detected on root tips. At one site, fruitbodies grew in a fairy ring formed by a large female individual that showed an outward growth rate of 30 cm per year, with the mycelium decaying within the ring and being fertilized by over 50 male individuals. While fairy ring structures have never been shown for truffles, the genetics of Burgundy truffle populations support a similar reproductive biology as those of other highly prized truffles.

Construction of nucleus-directed fluorescent reporter systems and its application to verification of heterokaryon formation in Morchella importuna

INTRODUCTION

Morchella importuna (M. importuna) is a rare fungus with high nutrition value and distinct flavor. Despite the successful artificial cultivation, its genetic characteristics and biological processes such as life cycle, reproductive system, and trophic mode remain poorly understood.

METHODS

Considering this, we constructed pEH2B and pMH2B vectors by fusing M. importuna endogenous histone protein H2B with fluorescent proteins eGFP or mCherry, respectively. Based on the constructed pEH2B and pMH2B vectors, nuclear fluorescence localization was performed via Agrobacterium tumefaciens-mediated transformation (ATMT). These two vectors were both driven by two endogenous promoters glyceraldehyde 3-phosphate dehydrogenase (GPD) and ubiquitin (UBI). The vector-based reporter systems were tested by the paired culture of two genetically modified strains pEH2B-labeled M04M24 (24e, MAT1-1-1) and pMH2B-abeled M04M26 (26m, MAT1-2-1).

RESULTS

The fluorescence observation and molecular identification results indicated the successful hyphal fusion and heterokaryon formation. We found that the expression of the reporter genes was stable, and it did not interfere with the growth of the fungus.

DISCUSSION

Our constructed nucleus-directed fluorescent systems in M. importuna can be used for monitoring the dynamic development and reproductive processes in living cells and also for monitoring the interaction between morels and plant roots. Therefore, morels exhibit the potential to be a candidate organism used for the research on basic biology and genetics of ascomycetes.

Diversity of genomic adaptations to the post-fire environment in Pezizales fungi points to crosstalk between charcoal tolerance and sexual development

Wildfires drastically impact the soil environment, altering the soil organic matter, forming pyrolyzed compounds, and markedly reducing the diversity of microorganisms. Pyrophilous fungi, especially the species from the orders Pezizales and Agaricales, are fire-responsive fungal colonizers of post-fire soil that have historically been found fruiting on burned soil and thus may encode mechanisms of processing these compounds in their genomes. Pyrophilous fungi are diverse. In this work, we explored this diversity and sequenced six new genomes of pyrophilous Pezizales fungi isolated after the 2013 Rim Fire near Yosemite Park in California, USA: Pyronema domesticum, Pyronema omphalodes, Tricharina praecox, Geopyxis carbonaria, Morchella snyderi, and Peziza echinospora. A comparative genomics analysis revealed the enrichment of gene families involved in responses to stress and the degradation of pyrolyzed organic matter. In addition, we found that both protein sequence lengths and G + C content in the third base of codons (GC3) in pyrophilous fungi fall between those in mesophilic/nonpyrophilous and thermophilic fungi. A comparative transcriptome analysis of P. domesticum under two conditions - growing on charcoal, and during sexual development - identified modules of genes that are co-expressed in the charcoal and light-induced sexual development conditions. In addition, environmental sensors such as transcription factors STE12, LreA, LreB, VosA, and EsdC were upregulated in the charcoal condition. Taken together, these results highlight genomic adaptations of pyrophilous fungi and indicate a potential connection between charcoal tolerance and fruiting body formation in P. domesticum.

The Microbiome Structure of the Symbiosis between the Desert Truffle Terfezia boudieri and Its Host Plant Helianthemum sessiliflorum

The desert truffle Terfezia boudieri is an ascomycete fungus that forms ect-endomycorrhiza in the roots of plants belonging to Cistaceae. The fungus forms hypogeous edible fruit bodies, appreciated as gourmet food. Truffles and host plants are colonized by various microbes, which may contribute to their development. However, the diversity and composition of the bacterial community under field conditions in the Negev desert are still unknown. The overall goal of this research was to identify the rhizosphere microbial community supporting the establishment of a symbiotic association between T. boudieri and Helianthemum sessiliflorum. The bacterial community was characterized by fruiting bodies, mycorrhized roots, and rhizosphere soil. Based on next-generation sequencing meta-analyses of the 16S rRNA gene, we discovered diverse bacterial communities of fruit bodies that differed from those found in the roots and rhizosphere. Families of Proteobacteria, Planctomycetes, and Actinobacteria were present in all four samples. Alpha diversity analysis revealed that the rhizosphere and roots contain significantly higher bacterial species numbers compared to the fruit. Additionally, ANOSIM and PCoA provided a comparative analysis of the bacterial taxa associated with fruiting bodies, roots, and rhizosphere. The core microbiome described consists of groups whose biological role triggers important traits supporting plant growth and fruit body development.

Role of Sulfur Compounds in Vegetable and Mushroom Aroma

At the base of the food pyramid is vegetables, which should be consumed most often of all food products, especially in raw and unprocessed form. Vegetables and mushrooms are rich sources of bioactive compounds that can fulfill various functions in plants, starting from protection against herbivores and being natural insecticides to pro-health functions in human nutrition. Many of these compounds contain sulfur in their structure. From the point of view of food producers, it is extremely important to know that some of them have flavor properties. Volatile sulfur compounds are often potent odorants, and in many vegetables, belonging mainly to Brassicaeae and Allium (Amaryllidaceae), sulfur compounds determine their specific flavor. Interestingly, some of the pathways that form volatile sulfur compounds in vegetables are also found in selected edible mushrooms. The most important odor-active organosulfur compounds can be divided into isothiocyanates, nitriles, epithionitriles, thiols, sulfides, and polysulfides, as well as others, such as sulfur containing carbonyl compounds and esters, R-L-cysteine sulfoxides, and finally heterocyclic sulfur compounds found in shiitake mushrooms or truffles. This review paper summarizes their precursors and biosynthesis, as well as their sensory properties and changes in selected technological processes.

Genetic Diversity of Phymatotrichopsis omnivora Based on Mating Type and Microsatellite Markers Reveals Heterothallic Mating System

Phymatotrichopsis omnivora is a member of Pezizomycetes and causes root rot disease on a broad range of dicotyledonous plants. Using recently generated draft genome sequence data from four P. omnivora isolates, we developed simple sequence repeat (SSR) markers and identified both mating type genes (MAT1-1-1 and MAT1-2-1) in this fungus. To understand the genetic diversity of P. omnivora isolates (n = 43) and spore mats (n = 29) collected from four locations (Oklahoma, Texas, Arizona, and Mexico) and four host crops (cotton, alfalfa, peach, and soybean), we applied 24 SSR markers and showed that of the 72 P. omnivora isolates and spore mats tested, 41 were distinct genotypes. Furthermore, the developed SSR markers did not show cross-transferability to other close relatives of P. omnivora in the class Pezizomycetes. A multiplex PCR detecting both mating type idiomorphs and a reference gene (TUB2) was developed to screen P. omnivora isolates. Based on the dataset we tested, P. omnivora is a heterothallic fungus with both mating types present in the United States in a ratio close to 1:1. We tested P. omnivora spore mats obtained from spatially distinct disease rings that developed in a center-pivot alfalfa field and showed that both mating types can be present not only in the same field but also within a single spore mat. This study shows that P. omnivora has the genetic toolkit for generating sexually diverse progeny, providing impetus for future studies that focus on identifying sexual morphs in nature.

Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk-cap (Lactarius) mushrooms

Ectomycorrhizal fungi play a key role in forests by establishing mutualistic symbioses with woody plants. Genome analyses have identified conserved symbiosis-related traits among ectomycorrhizal fungal species, but the molecular mechanisms underlying host specificity remain poorly known. We sequenced and compared the genomes of seven species of milk-cap fungi (Lactarius, Russulales) with contrasting host specificity. We also compared these genomes with those of symbiotic and saprotrophic Russulales species, aiming to identify genes involved in their ecology and host specificity. The size of Lactarius genomes is significantly larger than other Russulales species, owing to a massive accumulation of transposable elements and duplication of dispensable genes. As expected, their repertoire of genes coding for plant cell wall-degrading enzymes is restricted, but they retained a substantial set of genes involved in microbial cell wall degradation. Notably, Lactarius species showed a striking expansion of genes encoding proteases, such as secreted ectomycorrhiza-induced sedolisins. A high copy number of genes coding for small secreted LysM proteins and Lactarius-specific lectins were detected, which may be linked to host specificity. This study revealed a large diversity in the genome landscapes and gene repertoires within Russulaceae. The known host specificity of Lactarius symbionts may be related to mycorrhiza-induced species-specific genes, including secreted sedolisins.

Bacterial Communities in the Fruiting Bodies and Background Soils of the White Truffle Tuber magnatum

Tuber magnatum Picco is a greatly appreciated truffle species mainly distributed in Italy. Its price and characteristics mostly depend on its geographical origin. Truffles represent a fundamental step of the life cycle of Tuber species promoting spore dissemination. They consist of two main parts, gleba, the inner part, and peridium, which is in direct contact with ground soil. Within the truffle and around in the growing soil, both the occurrence and abundance of different microbial species seem to play an essential role in truffle production. The development of the next-generation sequencing (NGS) based technology has greatly improved to deepen the role of the composition of microbial communities, thus improving the knowledge of the existing relationships between microbial taxa in a specific condition. Here, we applied a metabarcoding approach to assess the differences in T. magnatum samples collected from three areas in Tuscany (Italy). Peridium and gleba were analyzed separately with the aim to distinguish them based on their microbial composition. Also, soil samples were collected and analyzed to compare productive and unproductive truffle grounds to confirm the presence of specific patterns linked to truffle production. Results indicate that differences occurred between truffle compartments (gleba and peridium) as well as between analyzed soils (productive and unproductive), with distinctive taxa associated. Furthermore, findings also demonstrated specific characteristics associated with truffle collection areas, thus indicating a degree of microbial selection related to different environments.

Mating-Type Genes Play an Important Role in Fruiting Body Development in Morchella sextelata

True morels (Morchella spp.) are edible mushrooms that are commercially important worldwide due to their rich nutrition and unique appearance. In recent years, outdoor cultivation has been achieved and expanded on a large scale in China. However, the mechanisms of fruiting body development in morels are poorly understood. In this study, the role of mating-type genes in fruiting body development was researched. Fruiting bodies cultivated with different mating-type strains showed no difference in appearance, but the ascus and ascospores were slightly malformed in fruiting bodies obtained from the MAT1-1 strains. The transcript levels of mating-type genes and their target genes revealed that the regulatory mechanisms were conserved in ascomycetes fungi. The silencing of mat1-2-1 by RNA interference verified the direct regulatory effect of mat1-2-1 on its target genes at the asexual stage. When cultivated with the spawn of single mating-type strains of MAT1-1 or MAT1-2, only one corresponding mating-type gene was detected in the mycelial and conidial samples, but both mat1-1-1 and mat1-2-1 were detected in the samples of primordium, pileus, and stipe. An understanding of the mating-type genes’ role in fruiting body development in M. sextelata may help to understand the life cycle and facilitate artificial cultivation.

Phylogenetic and ecological reevaluation of the order Onygenales

The order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina. Families in this order have classically been isolated from soil and dung, and two lineages contain causative agents of superficial, cutaneous and systemic infections in mammals. The ecology and habitat choices of the species are driven mainly by the keratin and cellulose degradation abilities. The present study aimed to investigate whether the ecological trends of the members of Onygenales can be interpreted in an evolutionary sense, linking phylogenetic parameters with habitat preferences, to achieve polyphasic definitions of the main taxonomic groups. Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis. Previously described families, namely, Arthrodermataceae, Ajellomycetaceae, Ascosphaeraceae, Eremascaceae, Gymnoascaceae, Onygenaceae and Spiromastigoidaceae, were accepted in Onygenales, and two new families, Malbrancheaceae and Neogymnomycetaceae, were introduced. A number of species could not be assigned to any of the defined families. Our study provides a revised overview of the main lines of taxonomy of Onygenales, supported by multilocus analyses of ITS, LSU, TUB, TEF1, TEF3, RPB1, RPB2, and ribosomal protein 60S L10 (L1) (RP60S) sequences, combined with available data on ecology, physiology, morphology, and genomics.

Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales

We aimed to identify genomic traits of transitions to ectomycorrhizal ecology within the Boletales by comparing the genomes of 21 symbiotrophic species with their saprotrophic brown-rot relatives. Gene duplication rate is constant along the backbone of Boletales phylogeny with large loss events in several lineages, while gene family expansion sharply increased in the late Miocene, mostly in the Boletaceae. Ectomycorrhizal Boletales have a reduced set of plant cell-wall-degrading enzymes (PCWDEs) compared with their brown-rot relatives. However, the various lineages retain distinct sets of PCWDEs, suggesting that, over their evolutionary history, symbiotic Boletales have become functionally diverse. A smaller PCWDE repertoire was found in Sclerodermatineae. The gene repertoire of several lignocellulose oxidoreductases (e.g. laccases) is similar in brown-rot and ectomycorrhizal species, suggesting that symbiotic Boletales are capable of mild lignocellulose decomposition. Transposable element (TE) proliferation contributed to the higher evolutionary rate of genes encoding effector-like small secreted proteins, proteases, and lipases. On the other hand, we showed that the loss of secreted CAZymes was not related to TE activity but to DNA decay. This study provides novel insights on our understanding of the mechanisms influencing the evolutionary diversification of symbiotic boletes.

Life Cycle and Phylogeography of True Truffles

True truffle (Tuber spp.) is one group of ascomycetes with great economic importance. During the last 30 years, numerous fine-scale population genetics studies were conducted on different truffle species, aiming to answer several key questions regarding their life cycles; these questions are important for their cultivation. It is now evident that truffles are heterothallic, but with a prevalent haploid lifestyle. Strains forming ectomycorrhizas and germinating ascospores act as maternal and paternal partners respectively. At the same time, a number of large-scale studies were carried out, highlighting the influences of the last glaciation and river isolations on the genetic structure of truffles. A retreat to southern refugia during glaciation, and a northward expansion post glaciation, were revealed in all studied European truffles. The Mediterranean Sea, acting as a barrier, has led to the existence of several refugia in different peninsulas for a single species. Similarly, large rivers in southwestern China act as physical barriers to gene flow for truffles in this region. Further studies can pay special attention to population genetics of species with a wide distribution range, such as T. himalayense, and the correlation between truffle genetic structure and the community composition of truffle-associated bacteria.

A Transcriptomic Atlas of the Ectomycorrhizal Fungus Laccaria bicolor

Trees are able to colonize, establish and survive in a wide range of soils through associations with ectomycorrhizal (EcM) fungi. Proper functioning of EcM fungi implies the differentiation of structures within the fungal colony. A symbiotic structure is dedicated to nutrient exchange and the extramatricular mycelium explores soil for nutrients. Eventually, basidiocarps develop to assure last stages of sexual reproduction. The aim of this study is to understand how an EcM fungus uses its gene set to support functional differentiation and development of specialized morphological structures. We examined the transcriptomes of Laccaria bicolor under a series of experimental setups, including the growth with Populus tremula x alba at different developmental stages, basidiocarps and free-living mycelium, under various conditions of N, P and C supply. In particular, N supply induced global transcriptional changes, whereas responses to P supply seemed to be independent from it. Symbiosis development with poplar is characterized by transcriptional waves. Basidiocarp development shares transcriptional signatures with other basidiomycetes. Overlaps in transcriptional responses of L. bicolor hyphae to a host plant and N/C supply next to co-regulation of genes in basidiocarps and mature mycorrhiza were detected. Few genes are induced in a single condition only, but functional and morphological differentiation rather involves fine tuning of larger gene sets. Overall, this transcriptomic atlas builds a reference to study the function and stability of EcM symbiosis in distinct conditions using L. bicolor as a model and indicates both similarities and differences with other ectomycorrhizal fungi, allowing researchers to distinguish conserved processes such as basidiocarp development from nutrient homeostasis.

Investigation of the Proteomes of the Truffles Tuber albidum pico, T. aestivum, T. indicum, T. magnatum, and T. melanosporum

Truffles of the Tuber species are known as expensive foods, mainly for their distinct aroma and taste. This high price makes them a profitable target of food fraud, e.g., the misdeclaration of cheaper truffle species as expensive ones. While many studies investigated truffles on the metabolomic level or the volatile organic compounds extruded by them, research at the proteome level as a phenotype determining basis is limited. In this study, a bottom-up proteomic approach based on LC-MS/MS measurements in data-independent acquisition mode was performed to analyze the truffle species Tuber aestivum, Tuber albidum pico, Tuber indicum, Tuber magnatum, and Tuber melanosporum, and a protein atlas of the investigated species was obtained. The yielded proteomic fingerprints are unique for each of the of the five truffle species and can now be used in case of suspected food fraud. First, a comprehensive spectral library containing 9000 proteins and 50,000 peptides was generated by two-dimensional liquid chromatography coupled to tandem mass spectrometry (2D-LC-MS/MS). Then, samples of the truffle species were analyzed in data-independent acquisition (DIA) proteomics mode yielding 2715 quantified proteins present in all truffle samples. Individual species were clearly distinguishable by principal component analysis (PCA). Quantitative proteome fingerprints were generated from 2066 ANOVA significant proteins, and side-by-side comparisons of truffles were done by T-tests. A further aim of this study was the annotation of functions for the identified proteins. For Tuber magnatum and Tuber melanosporum conclusive links to their superior aroma were found by enrichment of proteins responsible for sulfur-metabolic processes in comparison with other truffles. The obtained data in this study may serve as a reference library for food analysis laboratories in the future to tackle food fraud by misdeclaration of truffles. Further identified proteins with their corresponding abundance values in the different truffle species may serve as potential protein markers in the establishment of targeted analysis methods. Lastly, the obtained data may serve in the future as a basis for deciphering the biochemistry of truffles more deeply as well, when protein databases of the different truffle species will be more complete.

Eco-archaeological excavation techniques reveal snapshots of subterranean truffle growth

Despite its status as a highly-prized and coveted fungi in gastronomy, many aspects of the subterranean life cycle of the Burgundy truffle (Tuber aestivum) are still unknown, because in situ observations of the formation and maturation of truffle fruitbodies remain difficult. Here, we adopted a suite of archaeological fine-scale excavating techniques to provide unique spatiotemporal snapshots of Burgundy truffle growth at three sites in southern Germany. We also recorded the relative position, fresh weight, maturity level and genotype composition of all excavated fruitbodies. Varying by a factor of thousand, the fresh weight of 73 truffle ranged from 0.1 to 103.2 g, with individual maturity levels likely representing different life cycle stages from completely unripe to fully ripe and even decaying. While only a slightly positive relationship between fruitbody weight and maturity level was found, our results suggest that genetically distinct specimens can exhibit different life cycle stages at the same period of time and under the same environmental conditions. We therefore argue that truffles are likely able to grow, mature and ripe simultaneously between early summer and late winter of the following year. Our case study should encourage further eco-archaeological truffle excavations under different biogeographic settings and at different seasons of the year to gain deeper insights into the fungi's subterranean ecology. The expected cross-disciplinary findings will help truffle hunters and farmers to improve their harvest practices and management strategies.

Evolution of the Mode of Nutrition in Symbiotic and Saprotrophic Fungi in Forest Ecosystems

In this review, we highlight the main insights that have been gathered from recent developments using large-scale genomics of fungal saprotrophs and symbiotrophs (including ectomycorrhizal and orchid and ericoid mycorrhizal fungi) inhabiting forest ecosystems. After assessing the goals and motivations underlying our approach, we explore our current understanding of the limits and future potential of using genomics to understand the ecological roles of these forest fungi. Comparative genomics unraveled the molecular machineries involved in lignocellulose decomposition in wood decayers, soil and litter saprotrophs, and mycorrhizal symbionts. They also showed that transitions from saprotrophy to mutualism entailed widespread losses of lignocellulose-degrading enzymes; diversification of novel, lineage-specific symbiosis-induced genes; and convergent evolution of genetic innovations that facilitate the accommodationof mutualistic symbionts within their plant hosts. We also identify the major questions that remain unanswered and propose new avenues of genome-based research to understand the role of soil fungi in sustainable forest ecosystems.

The First Genomic Resources for Phymatotrichopsis omnivora, a Soilborne Pezizomycete Pathogen with a Broad Host Range

Phymatotrichopsis omnivora is a destructive plant pathogen causing root rot disease of alfalfa, cotton, pecan, grape, and many other important dicotyledonous species. A member of the family Rhizinaceae, in the class Pezizomycetes, P. omnivora is a soilborne ascomycete fungus that is difficult to maintain in culture, currently genetically intractable, and for which there are no publicly available genomic resources. We have generated draft genome sequences of four P. omnivora isolates obtained from cotton and alfalfa, growing in Texas and Oklahoma. These genome sequences will provide new insights into the biology of the fungus, including the factors responsible for its broad host range and pathogenicity.

FunOrder: A robust and semi-automated method for the identification of essential biosynthetic genes through computational molecular co-evolution

Secondary metabolites (SMs) are a vast group of compounds with different structures and properties that have been utilized as drugs, food additives, dyes, and as monomers for novel plastics. In many cases, the biosynthesis of SMs is catalysed by enzymes whose corresponding genes are co-localized in the genome in biosynthetic gene clusters (BGCs). Notably, BGCs may contain so-called gap genes, that are not involved in the biosynthesis of the SM. Current genome mining tools can identify BGCs, but they have problems with distinguishing essential genes from gap genes. This can and must be done by expensive, laborious, and time-consuming comparative genomic approaches or transcriptome analyses. In this study, we developed a method that allows semi-automated identification of essential genes in a BGC based on co-evolution analysis. To this end, the protein sequences of a BGC are blasted against a suitable proteome database. For each protein, a phylogenetic tree is created. The trees are compared by treeKO to detect co-evolution. The results of this comparison are visualized in different output formats, which are compared visually. Our results suggest that co-evolution is commonly occurring within BGCs, albeit not all, and that especially those genes that encode for enzymes of the biosynthetic pathway are co-evolutionary linked and can be identified with FunOrder. In light of the growing number of genomic data available, this will contribute to the studies of BGCs in native hosts and facilitate heterologous expression in other organisms with the aim of the discovery of novel SMs.

The discovery and description of novel fungal secondary metabolites promises novel antibiotics, pharmaceuticals, and other useful compounds. A way to identify novel secondary metabolites is to express the corresponding genes in a suitable expression host. Consequently, a detailed knowledge or an accurate prediction of these genes is necessary. In fungi, the genes are co-localized in so-called biosynthetic gene clusters. Notably, the clusters may also contain genes that are not necessary for the biosynthesis of the secondary metabolites, so-called gap genes. We developed a method to detect co-evolved genes within the clusters and demonstrated that essential genes are co-evolving and can thus be differentiated from the gap genes. This adds an additional layer of information, which can support researchers with their decisions on which genes to study and express for the discovery of novel secondary metabolites.

De Novo Gene Birth, Horizontal Gene Transfer, and Gene Duplication as Sources of New Gene Families Associated with the Origin of Symbiosis in Amanita

By introducing novel capacities and functions, new genes and gene families may play a crucial role in ecological transitions. Mechanisms generating new gene families include de novo gene birth, horizontal gene transfer, and neofunctionalization following a duplication event. The ectomycorrhizal (ECM) symbiosis is a ubiquitous mutualism and the association has evolved repeatedly and independently many times among the fungi, but the evolutionary dynamics enabling its emergence remain elusive. We developed a phylogenetic workflow to first understand if gene families unique to ECM Amanita fungi and absent from closely related asymbiotic species are functionally relevant to the symbiosis, and then to systematically infer their origins. We identified 109 gene families unique to ECM Amanita species. Genes belonging to unique gene families are under strong purifying selection and are upregulated during symbiosis, compared with genes of conserved or orphan gene families. The origins of seven of the unique gene families are strongly supported as either de novo gene birth (two gene families), horizontal gene transfer (four), or gene duplication (one). An additional 34 families appear new because of their selective retention within symbiotic species. Among the 109 unique gene families, the most upregulated gene in symbiotic cultures encodes a 1-aminocyclopropane-1-carboxylate deaminase, an enzyme capable of downregulating the synthesis of the plant hormone ethylene, a common negative regulator of plant-microbial mutualisms.

A Critical Review on Communication Mechanism within Plant-Endophytic Fungi Interactions to Cope with Biotic and Abiotic Stresses

Endophytic fungi infect plant tissues by evading the immune response, potentially stimulating stress-tolerant plant growth. The plant selectively allows microbial colonization to carve endophyte structures through phenotypic genes and metabolic signals. Correspondingly, fungi develop various adaptations through symbiotic signal transduction to thrive in mycorrhiza. Over the past decade, the regulatory mechanism of plant-endophyte interaction has been uncovered. Currently, great progress has been made on plant endosphere, especially in endophytic fungi. Here, we systematically summarize the current understanding of endophytic fungi colonization, molecular recognition signal pathways, and immune evasion mechanisms to clarify the transboundary communication that allows endophytic fungi colonization and homeostatic phytobiome. In this work, we focus on immune signaling and recognition mechanisms, summarizing current research progress in plant-endophyte communication that converge to improve our understanding of endophytic fungi.

Comparative Transcriptome and Endophytic Bacterial Community Analysis of Morchella conica SH

The precious rare edible fungus Morchella conica is popular worldwide for its rich nutrition, savory flavor, and varieties of bioactive components. Due to its high commercial, nutritional, and medicinal value, it has always been a hot spot. However, the molecular mechanism and endophytic bacterial communities in M. conica were poorly understood. In this study, we sequenced, assembled, and analyzed the genome of M. conica SH. Transcriptome analysis reveals significant differences between the mycelia and fruiting body. As shown in this study, 1,329 and 2,796 genes were specifically expressed in the mycelia and fruiting body, respectively. The Gene Ontology (GO) enrichment showed that RNA polymerase II transcription activity-related genes were enriched in the mycelium-specific gene cluster, and nucleotide binding-related genes were enriched in the fruiting body-specific gene cluster. Further analysis of differentially expressed genes in different development stages resulted in finding two groups with distinct expression patterns. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment displays that glycan degradation and ABC transporters were enriched in the group 1 with low expressed level in the mycelia, while taurine and hypotaurine metabolismand tyrosine metabolism-related genes were significantly enriched in the group 2 with high expressed level in mycelia. Moreover, a dynamic shift of bacterial communities in the developing fruiting body was detected by 16S rRNA sequencing, and co-expression analysis suggested that bacterial communities might play an important role in regulating gene expression. Taken together, our study provided a better understanding of the molecular biology of M. conica SH and direction for future research on artificial cultivation.

Draft Genome Sequence of the Ectomycorrhizal Fungus Astraeus odoratus from Northern Thailand

We report the draft genome sequence of Astraeus odoratus, an edible ectomycorrhizal fungus from northern Thailand. The assembled genome has a size of 45.1 Mb and 13,403 annotated protein-coding genes. This reference genome will provide a better understanding of the biology of mushroom-forming ectomycorrhizal fungi in the family Diplocystidiaceae.

A Comprehensive Phylogenetic and Bioinformatics Survey of Lectins in the Fungal Kingdom

Fungal lectins are a large family of carbohydrate-binding proteins with no enzymatic activity. They play fundamental biological roles in the interactions of fungi with their environment and are found in many different species across the fungal kingdom. In particular, their contribution to defense against feeders has been emphasized, and when secreted, lectins may be involved in the recognition of bacteria, fungal competitors and specific host plants. Carbohydrate specificities and quaternary structures vary widely, but evidence for an evolutionary relationship within the different classes of fungal lectins is supported by a high degree of amino acid sequence identity. The UniLectin3D database contains 194 fungal lectin 3D structures, of which 129 are characterized with a carbohydrate ligand. Using the UniLectin3D lectin classification system, 109 lectin sequence motifs were defined to screen 1223 species deposited in the genomic portal MycoCosm of the Joint Genome Institute. The resulting 33,485 putative lectin sequences are organized in MycoLec, a publicly available and searchable database. These results shed light on the evolution of the lectin gene families in fungi.

Distribution of methionine sulfoxide reductases in fungi and conservation of the free-methionine-R-sulfoxide reductase in multicellular eukaryotes

Methionine, either as a free amino acid or included in proteins, can be oxidized into methionine sulfoxide (MetO), which exists as R and S diastereomers. Almost all characterized organisms possess thiol-oxidoreductases named methionine sulfoxide reductase (Msr) enzymes to reduce MetO back to Met. MsrA and MsrB reduce the S and R diastereomers of MetO, respectively, with strict stereospecificity and are found in almost all organisms. Another type of thiol-oxidoreductase, the free-methionine-R-sulfoxide reductase (fRMsr), identified so far in prokaryotes and a few unicellular eukaryotes, reduces the R MetO diastereomer of the free amino acid. Moreover, some bacteria possess molybdenum-containing enzymes that reduce MetO, either in the free or protein-bound forms. All these Msrs play important roles in the protection of organisms against oxidative stress. Fungi are heterotrophic eukaryotes that colonize all niches on Earth and play fundamental functions, in organic matter recycling, as symbionts, or as pathogens of numerous organisms. However, our knowledge on fungal Msrs is still limited. Here, we performed a survey of msr genes in almost 700 genomes across the fungal kingdom. We show that most fungi possess one gene coding for each type of methionine sulfoxide reductase: MsrA, MsrB, and fRMsr. However, several fungi living in anaerobic environments or as obligate intracellular parasites were devoid of msr genes. Sequence inspection and phylogenetic analyses allowed us to identify non-canonical sequences with potentially novel enzymatic properties. Finaly, we identified several ocurences of msr horizontal gene transfer from bacteria to fungi.

Build Your Own Mushroom Soil: Microbiota Succession and Nutritional Accumulation in Semi-Synthetic Substratum Drive the Fructification of a Soil-Saprotrophic Morel

Black morel, a widely prized culinary delicacy, was once an uncultivable soil-saprotrophic ascomycete mushroom that can now be cultivated routinely in farmland soils. It acquires carbon nutrients from an aboveground nutritional supplementation, while it remains unknown how the morel mycelium together with associated microbiota in the substratum metabolizes and accumulates specific nutrients to support the fructification. In this study, a semi-synthetic substratum of quartz particles mixed with compost was used as a replacement and mimic of the soil. Two types of composts (C1 and C2) were used, respectively, plus a bare-quartz substratum (NC) as a blank reference. Microbiota succession, substrate transformation as well as the activity level of key enzymes were compared between the three types of substrata that produced quite divergent yields of morel fruiting bodies. The C1 substratum, with the highest yield, possessed higher abundances of Actinobacteria and Chloroflexi. In comparison with C2 and NC, the microbiota in C1 could limit over-expansion of microorganisms harboring N-fixing genes, such as Cyanobacteria, during the fructification period. Driven by the microbiota, the C1 substratum had advantages in accumulating lipids to supply morel fructification and maintaining appropriate forms of nitrogenous substances. Our findings contribute to an increasingly detailed portrait of microbial ecological mechanisms triggering morel fructification.

Comparative transcriptome analysis of cells from different areas reveals ROS responsive mechanism at sclerotial initiation stage in Morchella importuna

Morels are some of the most highly prized edible and medicinal mushrooms, with great economic and scientific value. Outdoor cultivation has been achieved and expanded on a large scale in China in recent years. Sclerotial formation is one of the most important phases during the morel life cycle, and previous reports indicated that reactive oxygen species (ROS) play an important role. However, ROS response mechanisms at sclerotial initiation (SI) stage are poorly understood. In this study, comparative transcriptome analyses were performed with sclerotial and hyphal cells at different areas in the same plate at SI stage. Gene expression was significantly different at SI stage between sclerotial formation and mycelia growth areas. GO and KEGG analyses indicated more vigorous metabolic characteristics in the hyphae area, while transcription process, DNA repair, and protein processing were enriched in sclerotial cells. Gene expression related to H₂O₂ production was high in the hyphae area, while expression of H₂O₂-scavenging genes was high in sclerotial cells, leading to a higher H₂O₂ concentration in the hyphal region than in the sclerotium. Minor differences were observed in gene expression of H₂O₂-induced signaling pathway in sclerotial and hyphal cells; however, expression levels of the target genes of transcription factor MSN2, important in the H₂O₂-induced signaling pathways, were significantly different. MSN2 enhanced stress response regulation in sclerotia by regulating these target genes. Small molecular HSPs were also found upregulated in sclerotial cells. This study indicated that sclerotial cells are more resistant to ROS stress than hyphal cells through transcriptional regulation of related genes.

Geographical-based variations in white truffle Tuber magnatum aroma is explained by quantitative differences in key volatile compounds

The factors that vary the aroma of Tuber magnatum fruiting bodies are poorly understood. The study determined the headspace aroma composition, sensory aroma profiles, maturity and bacterial communities from T. magnatum originating from Italy, Croatia, Hungary, and Serbia, and tested if truffle aroma is dependent on provenance and if fruiting body volatiles are explained by maturity and/or bacterial communities. Headspace volatile profiles were determined using gas chromatography-mass spectrometry-olfactometry (GC-MS-O) and aroma of fruiting body extracts were sensorially assessed. Fruiting body maturity was estimated through spore melanisation. Bacterial community was determined using 16S rRNA amplicon sequencing. Main odour active compounds were present in all truffles but varied in concentration. Aroma of truffle extracts were sensorially discriminated by sites. However, volatile profiles of individual fruiting bodies varied more within sites than across geographic area, while maturity level did not play a role. Bacterial communities varied highly and were partially explained by provenance. A few rare bacterial operational taxonomical units associated with a select few nonodour active volatile compounds. Specificities of the aroma of T. magnatum truffles are more likely to be linked to individual properties than provenance. Some constituents of bacteria may provide biomarkers of provenance and be linked to nonodour active volatiles.

Desert truffle genomes reveal their reproductive modes and new insights into plant-fungal interaction and ectendomycorrhizal lifestyle

Desert truffles are edible hypogeous fungi forming ectendomycorrhizal symbiosis with plants of Cistaceae family. Knowledge about the reproductive modes of these fungi and the molecular mechanisms driving the ectendomycorrhizal interaction is lacking. Genomes of the highly appreciated edible desert truffles Terfezia claveryi Chatin and Tirmania nivea Trappe have been sequenced and compared with other Pezizomycetes. Transcriptomes of T. claveryi × Helianthemum almeriense mycorrhiza from well-watered and drought-stressed plants, when intracellular colonizations is promoted, were investigated. We have identified the fungal genes related to sexual reproduction in desert truffles and desert-truffles-specific genomic and secretomic features with respect to other Pezizomycetes, such as the expansion of a large set of gene families with unknown Pfam domains and a number of species or desert-truffle-specific small secreted proteins differentially regulated in symbiosis. A core set of plant genes, including carbohydrate, lipid-metabolism, and defence-related genes, differentially expressed in mycorrhiza under both conditions was found. Our results highlight the singularities of desert truffles with respect to other mycorrhizal fungi while providing a first glimpse on plant and fungal determinants involved in ecto to endo symbiotic switch that occurs in desert truffle under dry conditions.