Phylogenetic Analyses of Armillaria Reveal at Least 15 Phylogenetic Lineages in China, Seven of Which Are Associated with Cultivated Gastrodia elata

Draft genome sequence of Armillaria calvescens strain YAFA0618 associated with Gastrodia elata

Armillaria calvescens is a symbiotic fungus of Gastrodia elata. Here, we present a draft genome sequence of A. calvescens strain YAFA0618. The genome resource will support subsequent research into the relationship between A. calvescens and G. elata.

Characteristics and functions of volatile organic compounds in the tripartite symbiotic system of Gastrodia elata-Armillaria gallica-Rahnella aceris HPDA25

Tripartite interactions among plants, fungi, and bacteria are critical for maintaining plant growth and fitness, and volatile organic compounds (VOCs) play a significant role in these interactions. However, the functions of VOCs within the niche of mycoheterotrophic plants, which represent unique types of interactions, remain poorly understood. Gastrodia elata, a mycoheterotrophic orchid species, forms a symbiotic relationship with specific Armillaria species, serving as a model system to investigate this intriguing issue. Rahnella aceris HPDA25 is a plant growth-promoting bacteria isolated from G. elata, which has been found to facilitate the establishment of G. elata-Armillaria symbiosis. In this study, using the tripartite symbiotic system of G. elata-Armillaria gallica-R. aceris HPDA25, we investigate the role of VOCs in the interaction among mycoheterotrophic plants, fungi, and bacteria. Our results showed that 33 VOCs of HPDA25-inducible symbiotic G. elata elevated compared to non-symbiotic G. elata, indicating that VOCs indeed play a role in the symbiotic process. Among these, 21 VOCs were accessible, and six active VOCs showed complete growth inhibition activities against A. gallica, while R. aceris HPDA25 had no significant effect. In addition, three key genes of G. elata have been identified that may contribute to the increased concentration of six active VOCs. These results revealed for the first time the VOCs profile of G. elata and demonstrated its regulatory role in the tripartite symbiotic system involving G. elata, Armillaria, and bacteria.

Establishment of an efficient Agrobacterium tumefaciens-mediated transformation system for an Armillaria species, a host of the fully mycoheterotrophic plant Gastrodia elata

The genus Armillaria (Basidiomycota, Agaricales, Physalacriaceae) comprises pathogenic fungi that cause root-rot disease in plants, as well as species with low pathogenicity, some of which are hosts of the fully mycoheterotrophic orchid plant Gastrodia elata (Orchidaceae). To investigate the mechanisms underlying such special interactions between Armillaria fungi and G. elata, it is crucial to establish genetic transformation platforms for the Armillaria fungi and G. elata. In this study, an Armillaria strain Arm37 was isolated from G. elata, which can form symbiosis with G. elata in axenic culture under laboratory conditions. A vector pYT-EV containing a cassette for hygromycin-resistance selection and a cassette for expressing or silencing target genes was constructed. An Agrobacterium tumefaciens-mediated transformation (ATMT) system for Arm37 was successfully developed and optimized to achieve a transformation efficiency of 32%. The ATMT system was successfully used to express the reporter genes eGFP encoding enhanced green fluorescent protein and GUS encoding β-glucuronidase and to effectively silence the endogenous gene URA3 encoding orotidine-5'-phosphate decarboxylase in Arm37. This ATMT system established for Arm37 provides an efficient genetic tool for exploring the Arm37 genes that are involved in the unique interaction between the Armillaria fungi and fully mycoheterotrophic plant G. elata.

Variation in SSRs at different genomic regions and implications for the evolution and identification of Armillaria gallica

Armillaria spp. are devastating forest pathogens. Due to its low pathogenicity and abundant genetic variation, Armillaria gallica exhibited a unique and beneficial symbiosis with Gastrodia elata, which was used as a traditional Chinese medicine. However, the variation and population structure of A. gallica populations have rarely been investigated. Hence, we analyzed the evolution and variation in simple sequence repeats (SSRs) in three Armillaria genomes: A. gallica, A. cepistipes, and A. ostoyae to assess the genetic diversity and population structure of 14 A. gallica strains. Genome analysis revealed that SSRs were more abundant in the intergenic region than the intron and exon region, as was the SSR density. Compared with other two genomes, SSR density was the lowest in exon region and largest in the intron region of A. gallica, with significant variation in genic region. There were 17 polymorphic markers in A. gallica genome was identified, with 26.7% in genic region, which is higher than that of 18.8% in the intergenic region. Moreover, a total of 50 alleles and 42 polymorphic loci were detected among these A. gallica strains. The averaged polymorphism information content (PIC) was 0.4487, ranged from 0.2577 to 0.6786. Both principal coordinate analysis (PCoA) and population structure analyses based on the genotype data of SSRs divided the strains into two clusters. The cluster I included all the strains from high-altitude G. elata producing areas and some low-altitude areas, while the strains in Cluster II originated from low-altitude G. elata producing areas. These results indicated that substantial genome-specific variation in SSRs within the genic region of A. gallica and provide new insights for further studies on the evolution and breeding of A. gallica.

Fungal communities associated with early immature tubers of wild Gastrodia elata

Full myco-heterotrophic orchid Gastrodia elata Bl. is widely distributed in Northeast Asia, and previous research has not fully investigated the symbiotic fungal community of its early immature tubers. This study utilized Illumina sequencing to compare symbiotic fungal communities in natural G. elata immature tubers and their habitats. LEfSe (Linear Discriminant Analysis Effect Size) was used to screen for Biomarkers that could explain variations among different fungal communities, and correlation analyses were performed among Biomarkers and other common orchid mycorrhizal fungi. Our results illustrate that the symbiotic fungal communities of immature G. elata tubers cannot be simply interpreted as subsets of the environmental fungal communities because some key members cannot be traced back to the environment. The early growth of G. elata was related to a small group of fungi, such as Sebacina, Thelephora, and Inocybe, which were also common mycorrhizal fungi from other orchids. In addition, Mycena, Auricularia, and Cryptococcus were unique fungal partners of G. elata, and many new species have yet to be discovered. Possible symbiotic Mycena should be M. plumipes and its sibling species in this case. Our results provide insight into the symbiotic partner switch and trophic pattern change during the development and maturation of G. elata.

The role of symbiotic fungi in the life cycle of Gastrodia elata Blume (Orchidaceae): a comprehensive review

Gastrodia elata Blume, a fully mycoheterotrophic perennial plant of the family Orchidaceae, is a traditional Chinese herb with medicinal and edible value. Interestingly, G. elata requires symbiotic relationships with Mycena and Armillaria strains for seed germination and plant growth, respectively. However, there is no comprehensive summary of the symbiotic mechanism between fungi and G. elata. Here, the colonization and digestion of hyphae, the bidirectional exchange of nutrients, the adaptation of fungi and G. elata to symbiosis, and the role of microorganisms and secondary metabolites in the symbiotic relationship between fungi and G. elata are summarized. We comprehensively and deeply analyzed the mechanism of symbiosis between G. elata and fungi from three perspectives: morphology, nutrition, and molecules. The aim of this review was to enrich the understanding of the mutualistic symbiosis mechanisms between plants and fungi and lay a theoretical foundation for the ecological cultivation of G. elata.

Global metabolic profile and multiple phytometabolites in the different varieties of Gastrodia elata Blume

Gastrodia elata Blume (Tianma in Chinese), a myco-heterotrophic orchid, is widely distributed in China. Tubers derived from this orchid are traditionally used as both medicinal and edible materials. At present, five primary varieties of G. elata are recorded in the "Flora of China." Among them, the three main varieties currently in artificial cultivation are G. elata f. elata (GR, red stem), G. elata f. glauca (GB, black stem), and G. elata f. viridis (GG, green stem). In our study, the metabolic profiles and chemical composition of these three varieties were determined via UPLC-MS/MS and HPLC-UV. In total, 11,132 metabolites were detected, from which multiple phytometabolites were identified as aromatic compounds, heteroatomic compounds, furans, carbohydrates, organic acids, and their derivatives. A number of differentially expressed metabolites (DEMs) were annotated as bioactive ingredients. Overall, parishins, vanilloloside, and gastrodin A/B in the GB group were markedly higher, whereas gastrodin, gastrol, and syringic acid were more enriched in the GG or GR groups. Moreover, HPLC fingerprint analysis also found six metabolites used as markers for the identification of Gastrodiae Rhizoma in the Chinese Pharmacopoeia, which were also typical DEMs in metabolomics. Of these, gastrodin, 4-hydroxybenzyl alcohol, citric acid, and adenosine were quantitatively detected, showing a similar result with the metabolomic data. In summary, our findings provide novel insights into the phytochemical ingredients of different G. elata varieties, highlighting diverse biological activities and healthcare value.

Armillaria altimontana in North America: Biology and Ecology

Armillaria altimontana is a fungus (Basidiomycota, Agaricomycetes, Agaricales, and Physalacriaceae) that is generally considered as a weak/opportunistic pathogen or saprophyte on many tree hosts. It widely occurs across the northwestern USA to southern British Columbia, Canada, but relatively little is known about its ecological role in the diverse forest ecosystems where it occurs. This review summarizes the biology and ecology of A. altimontana, including its identification, life cycle, distribution, host associations, and bioclimatic models under climate change.

Characterization of the transcriptional responses of Armillaria gallica 012m to GA3

Gastrodia elata needs to establish a symbiotic relationship with Armillaria strains to obtain nutrients and energy. However, the signaling cross talk between G. elata and Armillaria strains is still unclear. During our experiment, we found that the vegetative mycelium of Armillaria gallica 012m grew significantly better in the media containing gibberellic acid (GA3) than the blank control group (BK). To explore the response mechanism, we performed an RNA-sequencing experiment to profile the transcriptome changes of A. gallica 012m cultured in the medium with exogenous GA3. The transcriptome-guided differential expression genes (DEGs) analysis of GA3 and BK showed that a total of 1309 genes were differentially expressed, including 361 upregulated genes and 948 downregulated genes. Some of those DEGs correlated with the biological process, including positive regulation of chromosome segregation, mitotic metaphase/anaphase transition, attachment of mitotic spindle microtubules to kinetochore, mitotic cytokinesis, and nuclear division. These analyses explained that GA3 actively promoted the growth of A. gallica to some extent. Further analysis of protein domain features showed that the deduced polypeptide contained 41 candidate genes of GA receptor, and 27 of them were expressed in our samples. We speculate that GA receptors exist in A. gallica 012m. Comparative studies of proteins showed that the postulated GA receptor domains of A. gallica 012m have a higher homologous correlation with fungi than others based on cluster analysis.

Whole genome sequencing and analysis of Armillaria gallica Jzi34 symbiotic with Gastrodia elata

BACKGROUND

Armillaria species are plant pathogens, but a few Armillaria species can establish a symbiotic relationship with Gastrodia elata, a rootless and leafless orchid, that is used as a Chinese herbal medicine. Armillaria is a nutrient source for the growth of G. elata. However, there are few reports on the molecular mechanism of symbiosis between Armillaria species and G. elata. The genome sequencing and analysis of Armillaria symbiotic with G. elata would provide genomic information for further studying the molecular mechanism of symbiosis.

RESULTS

The de novo genome assembly was performed with the PacBio Sequel platform and Illumina NovaSeq PE150 for the A. gallica Jzi34 strain, which was symbiotic with G. elata. Its genome assembly contained ~ 79.9 Mbp and consisted of 60 contigs with an N50 of 2,535,910 bp. There were only 4.1% repetitive sequences in the genome assembly. Functional annotation analysis revealed a total of 16,280 protein coding genes. Compared with the other five genomes of Armillaria, the carbohydrate enzyme gene family of the genome was significantly contracted, while it had the largest set of glycosyl transferase (GT) genes. It also had an expansion of auxiliary activity enzymes AA3-2 gene subfamily and cytochrome P450 genes. The synteny analysis result of P450 genes reveals that the evolutionary relationship of P450 proteins between A. gallica Jzi34 and other four Armillaria was complex.

CONCLUSIONS

These characteristics may be beneficial for establishing a symbiotic relationship with G. elata. These results explore the characteristics of A. gallica Jzi34 from a genomic perspective and provide an important genomic resource for further detailed study of Armillaria. This will help to further study the symbiotic mechanism between A. gallica and G. elata.

Genomic and Transcriptomic Approaches Provide a Predictive Framework for Sesquiterpenes Biosynthesis in Desarmillaria tabescens CPCC 401429

Terpenoids constitute a structurally diverse class of secondary metabolites with wide applications in the pharmaceutical, fragrance and flavor industries. Desarmillaria tabescens CPCC 401429 is a basidiomycetous mushroom that could produce anti-tumor melleolides. To date, no studies have been conducted to thoroughly investigate the sesquiterpenes biosynthetic potential in Desarmillaria or related genus. This study aims to unravel the phylogeny, terpenome, and functional characterization of unique sesquiterpene biosynthetic genes of the strain CPCC 401429. Herein, we report the genome of the fungus containing 15,145 protein-encoding genes. MLST-based phylogeny and comparative genomic analyses shed light on the precise reclassification of D. tabescens suggesting that it belongs to the genus Desarmillaria. Gene ontology enrichment and pathway analyses uncover the hidden capacity for producing polyketides and terpenoids. Genome mining directed predictive framework reveals a diverse network of sesquiterpene synthases (STSs). Among twelve putative STSs encoded in the genome, six ones are belonging to the novel minor group: diverse Clade IV. In addition, RNA-sequencing based transcriptomic profiling revealed differentially expressed genes (DEGs) of the fungus CPCC 401429 in three different fermentation conditions, that of which enable us to identify noteworthy genes exemplified as STSs coding genes. Among the ten sesquiterpene biosynthetic DEGs, two genes including DtSTS9 and DtSTS10 were selected for functional characterization. Yeast cells expressing DtSTS9 and DtSTS10 could produce diverse sesquiterpene compounds, reinforced that STSs in the group Clade IV might be highly promiscuous producers. This highlights the potential of Desarmillaria in generating novel terpenoids. To summarize, our analyses will facilitate our understanding of phylogeny, STSs diversity and functional significance of Desarmillaria species. These results will encourage the scientific community for further research on uncharacterized STSs of Basidiomycota phylum, biological functions, and potential application of this vast source of secondary metabolites.

Comparative transcriptome analysis of Armillaria gallica 012m in response to ethephon treatment

Background

Gastrodia elata, known as a rootless, leafless, achlorophyllous and fully mycoheterotrophic orchid, needs to establish symbionts with particular Armillaria species to acquire nutrition and energy. Previous research findings had approved that ethylene (ET) played an important role in plant-fungi interaction and some receptors of ET had been discovered in microorganisms. However, the molecular mechanisms underlying the role of ET in the interaction between G. elata and Armillaria species remain unknown.

Methods

Exiguous ethephon (ETH) was added to agar and liquid media to observe the morphological features of mycelium and count the biomass respectively. Mycelium cultured in liquid media with exiguous ETH (0.1 ppm, 2.0 ppm, 5.0 ppm) were chosen to perform whole-transcriptome profiling through the RNA-seq technology (Illumina NGS sequencing). The DEGs of growth-related genes and candidate ET receptor domains were predicted on SMART.

Results

ETH-0.1 ppm and ETH-2 ppm could significantly improve the mycelium growth of A. gallica 012m, while ETH-5 ppm inhibited the mycelium growth in both solid and liquid media. The number of up-regulated or down-regulated genes increased along with the concentrations of ETH. The growth of mycelia might benefit from the up-regulated expression of Pyr_redox (Pyridine nucleotide-disulphide oxidoreductase), GAL4 (C6 zinc finger) and HMG (High Mobility Group) genes in the ETH-0.1 ppm and ETH-2 ppm. Therefore, the growth of mycelia might be impaired by the down-regulated expression of ZnF_C2H2 and ribosomal protein S4 proteins in the ETH-5 ppm. Seven ET receptor domains were predicted in A. gallica 012m. Based on cluster analysis and comparative studies of proteins, the putative ETH receptor domains of A. gallica 012m have a higher homologous correlation with fungi.

Conclusions

The responses of A. gallica 012m to ETH had a concentration effect similar to the plants’ responses to ET. Therefore, the number of up-regulated or down-regulated genes are increased along with the concentrations of ETH. Seven ET receptor protein domains were predicted in the genome and transcriptome of A. gallica 012m. We speculate that ETH receptors exist in A. gallica 012m and ethylene might play an important role in the plant-fungi interaction.

An exploration of mechanism of high quality and yield of Gastrodia elata Bl. f. glauca by the isolation, identification and evaluation of Armillaria

BACKGROUND

Gastrodia elata Bl. f. glauca, a perennial herb of G.elata Bl. in Orchidaceae, is one of the most valuable traditional Chinese medicines. G. elata Bl. is a chlorophyll-free myco-heterotrophic plant, which must rely on the symbiotic growth of Armillaria, but not all Armillaria strains can play the symbiotic role. Additionally, Armillaria is easy to degenerate after multiple generations, and the compatibility between the strains from other areas and G. elata Bl. f. glauca in Changbai Mountain is unstable. Therefore, it is incredibly significant to isolate, identify and screen the symbiotic Armillaria suitable for the growth of G. elata Bl. f. glauca in Changbai Mountain, and to explore the mechanism by which Armillaria improves the production performance of G. elata Bl. f. glauca.

RESULTS

Firstly, G. elata Bl. f. glauca tubers, and rhizomorphs and fruiting bodies of Armillaria were used for the isolation and identification of Armillaria. Five Armillaria isolates were obtained in our laboratory and named: JMG, JMA, JMB, JMC and JMD. Secondly, Armillaria was selected based on the yield and the effective component content of G. elata Bl. f. glauca. It was concluded that the yield and quality of G. elata Bl. f. glauca co-planted with JMG is the highest. Finally, the mechanism of its high quality and yield was explored by investigating the effects of different Armillaria strains on the soil, its nutrition element contents and the soil microbial diversity around G. elata Bl. f. glauca in Changbai Mountain.

CONCLUSIONS

Compared with commercial strains, JMG significantly increased the content of Na, Al, Si, Mn, Fe, Zn, Rb and the absorption of C, Na, Mg, Ca, Cr, Cu, Zn and Rb in G. elata Bl. f. glauca; it improved the composition, diversity and metabolic functions of soil microbial communities around G. elata Bl. f. glauca at phylum, class and genus levels; it markedly increased the relative abundance of bacteria such as Chthoniobacter and Armillaria in the dominant populations, and enhanced such functions as Cell motility, amino acid metabolism and Lipid metabolism; it dramatically decreased the relative abundance of Bryobacter and other fungi in the dominant populations, and reduced such functions as microbial energy metabolism, translation and carbohydrate metabolism. This is the main reason why excellent Armillaria strains promote the high quality and yield of G. elata Bl. f. glauca in Changbai Mountain.

Transcriptome analysis reveals the regulatory mode by which NAA promotes the growth of Armillaria gallica

A symbiotic relationship is observed between Armillaria and the Chinese herbal medicine Gastrodia elata (G. elata). Armillaria is a nutrient source for the growth of G. elata, and its nutrient metabolism efficiency affects the growth and development of G. elata. Auxin has been reported to stimulate Armillaria species, but the molecular mechanism remains unknown. We found that naphthalene acetic acid (NAA) can also promote the growth of A. gallica. Moreover, we identified a total of 2071 differentially expressed genes (DEGs) by analyzing the transcriptome sequencing data of A. gallica at 5 and 10 hour of NAA treatment. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these unigenes were significantly enriched in the metabolism pathways of arginine, proline, propanoate, phenylalanine and tryptophan. The expression levels of the general amino acid permease (Gap), ammonium transporter (AMT), glutamate dehydrogenase (GDH), glutamine synthetase (GS), Zn(II) 2Cys6 and C2H2 transcription factor genes were upregulated. Our transcriptome analysis showed that the amino acid and nitrogen metabolism pathways in Armillaria were rapidly induced within hours after NAA treatment. These results provide valuable insights into the molecular mechanisms by which NAA promotes the growth of Armillaria species.

Phylogenetic Relationships, Speciation, and Origin of Armillaria in the Northern Hemisphere: A Lesson Based on rRNA and Elongation Factor 1-Alpha

Armillaria species have a global distribution and play various roles in the natural ecosystems, e.g., pathogens, decomposers, and mycorrhizal associates. However, their taxonomic boundaries, speciation processes, and origin are poorly understood. Here, we used a phylogenetic approach with 358 samplings from Europe, East Asia, and North America to delimit the species boundaries and to discern the evolutionary forces underpinning divergence and evolution. Three species delimitation methods indicated multiple unrecognized phylogenetic species, and biological species recognition did not reflect the natural evolutionary relationships within Armillaria; for instance, biological species of A. mellea and D. tabescens are divergent and cryptic species/lineages exist associated with their geographic distributions in Europe, North America, and East Asia. While the species-rich and divergent Gallica superclade might represent three phylogenetic species (PS I, PS II, and A. nabsnona) that undergo speciation. The PS II contained four lineages with cryptic diversity associated with the geographic distribution. The genus Armillaria likely originated from East Asia around 21.8 Mya in early Miocene when Boreotropical flora (56-33.9 Mya) and the Bering land bridge might have facilitated transcontinental dispersal of Armillaria species. The Gallica superclade arose at 9.1 Mya and the concurrent vicariance events of Bering Strait opening and the uplift of the northern Tibetan plateau might be important factors in driving the lineage divergence.

Global Distribution and Richness of Armillaria and Related Species Inferred From Public Databases and Amplicon Sequencing Datasets

Armillaria is a globally distributed fungal genus most notably composed of economically important plant pathogens that are found predominantly in forest and agronomic systems. The genus sensu lato has more recently received attention for its role in woody plant decomposition and in mycorrhizal symbiosis with specific plants. Previous phylogenetic analyses suggest that around 50 species are recognized globally. Despite this previous work, no studies have analyzed the global species richness and distribution of the genus using data derived from fungal community sequencing datasets or barcoding initiatives. To assess the global diversity and species richness of Armillaria, we mined publicly available sequencing datasets derived from numerous primer regions for the ribosomal operon, as well as ITS sequences deposited on Genbank, and clustered them akin to metabarcoding studies. Our estimates reveal that species richness ranges from 50 to 60 species, depending on whether the ITS1 or ITS2 marker is used. Eastern Asia represents the biogeographic region with the highest species richness. We also assess the overlap of species across geographic regions and propose some hypotheses regarding the drivers of variability in species diversity and richness between different biogeographic regions.

Transcriptomics Reveals the Putative Mycoparasitic Strategy of the Mushroom Entoloma abortivum on Species of the Mushroom Genus Armillaria

During mycoparasitism, a fungus—the host—is parasitized by another fungus—the mycoparasite. The genetic underpinnings of these relationships have been best characterized in ascomycete fungi. However, within basidiomycete fungi, there are rare instances of mushroom-forming species parasitizing the reproductive structures, or sporocarps, of other mushroom-forming species, which have been rarely investigated on a genetic level. One of the most enigmatic of these occurs between Entoloma abortivum and species of Armillaria, where hyphae of E. abortivum are hypothesized to disrupt the development of Armillaria sporocarps, resulting in the formation of carpophoroids. However, it remains unknown whether carpophoroids are the direct result of a mycoparasitic relationship. To address the nature of this unique interaction, we analyzed gene expression of field-collected Armillaria and E. abortivum sporocarps and carpophoroids. Transcripts in the carpophoroids are primarily from E. abortivum, supporting the hypothesis that this species is parasitizing Armillaria. Most notably, we identified differentially upregulated E. abortivum β-trefoil-type lectins in the carpophoroid, which we hypothesize bind to Armillaria cell wall galactomannoproteins, thereby mediating recognition between the mycoparasite and the host. The most differentially upregulated E. abortivum transcripts in the carpophoroid code for oxalate decarboxylases—enzymes that degrade oxalic acid. Oxalic acid is a virulence factor in many plant pathogens, including Armillaria species; however, E. abortivum has evolved a sophisticated strategy to overcome this defense mechanism. The number of gene models and genes that code for carbohydrate-active enzymes in the E. abortivum transcriptome was reduced compared to other closely related species, perhaps as a result of the specialized nature of this interaction.

IMPORTANCE By studying fungi that parasitize other fungi, we can understand the basic biology of these unique interactions. Studies focused on the genetic mechanisms regulating mycoparasitism between host and parasite have thus far concentrated on a single fungal lineage within the Ascomycota. The work presented here expands our understanding of mycoparasitic relationships to the Basidiomycota and represents the first transcriptomic study to our knowledge that examines fungal-fungal relationships in their natural setting. The results presented here suggest that even distantly related mycoparasites utilize similar mechanisms to parasitize their host. Given that species of the mushroom-forming pathogen Armillaria cause plant root-rot diseases in many agroecosystems, an enhanced understanding of this interaction may contribute to better control of these diseases through biocontrol applications.

Historical Differentiation and Recent Hybridization in Natural Populations of the Nematode-Trapping Fungus Arthrobotrys oligospora in China

Maintaining the effects of nematode-trapping fungi (NTF) agents in order to control plant-parasitic nematodes (PPNs) in different ecological environments has been a major challenge in biological control applications. To achieve such an objective, it is important to understand how populations of the biocontrol agent NTF are geographically and ecologically structured. A previous study reported evidence for ecological adaptation in the model NTF species Arthrobotrys oligospora. However, their large-scale geographic structure, patterns of gene flow, their potential phenotypic diversification, and host specialization remain largely unknown. In this study, we developed a new panel of 20 polymorphic short tandem repeat (STR) markers and analyzed 239 isolates of A. oligospora from 19 geographic populations in China. In addition, DNA sequences at six nuclear gene loci and strain mating types (MAT) were obtained for these strains. Our analyses suggest historical divergence within the A. oligospora population in China. The genetically differentiated populations also showed phenotypic differences that may be related to their ecological adaptations. Interestingly, our analyses identified evidence for recent dispersion and hybridization among the historically subdivided geographic populations in nature. Together, our results indicate a changing population structure of A. oligospora in China and that care must be taken in selecting the appropriate strains as biocontrol agents that can effectively reproduce in agriculture soil while maintaining their nematode-trapping ability.

Desarmillaria caespitosa, a North American vicariant of D. tabescens

Desarmillaria caespitosa, a North American vicariant species of European D. tabescens, is redescribed in detail based on recent collections from the USA and Mexico. This species is characterized by morphological features and multilocus phylogenetic analyses using portions of nuc rDNA 28S (28S), translation elongation factor 1-alpha (tef1), the second largest subunit of RNA polymerase II (rpb2), actin (act), and glyceraldehyde-3-phosphate dehydrogenase (gpd). A neotype of D. caespitosa is designated here. Morphological and genetic differences between D. caespitosa and D. tabescens were identified. Morphologically, D. caespitosa differs from D. tabescens by having wider basidiospores, narrower cheilocystidia, which are often irregular or mixed (regular, irregular, or coralloid), and narrower caulocystidia. Phylogenetic analyses of five independent gene regions show that D. caespitosa and D. tabescens are separated by nodes with strong support. The new combination, D. caespitosa, is proposed.

Exploring the Species Diversity of Edible Mushrooms in Yunnan, Southwestern China, by DNA Barcoding

Yunnan Province, China, is famous for its abundant wild edible mushroom diversity and a rich source of the world's wild mushroom trade markets. However, much remains unknown about the diversity of edible mushrooms, including the number of wild edible mushroom species and their distributions. In this study, we collected and analyzed 3585 mushroom samples from wild mushroom markets in 35 counties across Yunnan Province from 2010 to 2019. Among these samples, we successfully obtained the DNA barcode sequences from 2198 samples. Sequence comparisons revealed that these 2198 samples likely belonged to 159 known species in 56 different genera, 31 families, 11 orders, 2 classes, and 2 phyla. Significantly, 51.13% of these samples had sequence similarities to known species at lower than 97%, likely representing new taxa. Further phylogenetic analyses on several common mushroom groups including 1536 internal transcribed spacer (ITS) sequences suggested the existence of 20 new (cryptic) species in these groups. The extensive new and cryptic species diversity in wild mushroom markets in Yunnan calls for greater attention for the conservation and utilization of these resources. Our results on both the distinct barcode sequences and the distributions of these sequences should facilitate new mushroom species discovery and forensic authentication of high-valued mushrooms and contribute to the scientific inventory for the management of wild mushroom markets.

Epidemiology, Biotic Interactions and Biological Control of Armillarioids in the Northern Hemisphere

Armillarioids, including the genera Armillaria, Desarmillaria and Guyanagaster, represent white-rot specific fungal saprotrophs with soilborne pathogenic potentials on woody hosts. They propagate in the soil by root-like rhizomorphs, connecting between susceptible root sections of their hosts, and often forming extended colonies in native forests. Pathogenic abilities of Armillaria and Desarmillaria genets can readily manifest in compromised hosts, or hosts with full vigour can be invaded by virulent mycelia when exposed to a larger number of newly formed genets. Armillaria root rot-related symptoms are indicators of ecological imbalances in native forests and plantations at the rhizosphere levels, often related to abiotic environmental threats, and most likely unfavourable changes in the microbiome compositions in the interactive zone of the roots. The less-studied biotic impacts that contribute to armillarioid host infection include fungi and insects, as well as forest conditions. On the other hand, negative biotic impactors, like bacterial communities, antagonistic fungi, nematodes and plant-derived substances may find applications in the environment-friendly, biological control of armillarioid root diseases, which can be used instead of, or in combination with the classical, but frequently problematic silvicultural and chemical control measures.

Evolutionary histories and mycorrhizal associations of mycoheterotrophic plants dependent on saprotrophic fungi

Mycoheterotrophic plants (MHPs) are leafless, achlorophyllous, and completely dependent on mycorrhizal fungi for their carbon supply. Mycorrhizal symbiosis is a mutualistic association with fungi that is undertaken by the majority of land plants, but mycoheterotrophy represents a breakdown of this mutualism in that plants parasitize fungi. Most MHPs are associated with fungi that are mycorrhizal with autotrophic plants, such as arbuscular mycorrhizal (AM) or ectomycorrhizal (ECM) fungi. Although these MHPs gain carbon via the common mycorrhizal network that links the surrounding autotrophic plants, some mycoheterotrophic lineages are associated with saprotrophic (SAP) fungi, which are free-living and decompose leaf litter and wood materials. Such MHPs are dependent on the forest carbon cycle, which involves the decomposition of wood debris and leaf litter, and have a unique biology and evolutionary history. MHPs associated with SAP fungi (SAP-MHPs) have to date been found only in the Orchidaceae and likely evolved independently at least nine times within that family. Phylogenetically divergent SAP Basidiomycota, mostly Agaricales but also Hymenochaetales, Polyporales, and others, are involved in mycoheterotrophy. The fungal specificity of SAP-MHPs varies from a highly specific association with a single fungal species to a broad range of interactions with multiple fungal orders. Establishment of symbiotic culture systems is indispensable for understanding the mechanisms underlying plant-fungus interactions and the conservation of MHPs. Symbiotic culture systems have been established for many SAP-MHP species as a pure culture of free-living SAP fungi is easier than that of biotrophic AM or ECM fungi. Culturable SAP-MHPs are useful research materials and will contribute to the advancement of plant science.

One stop shop IV: taxonomic update with molecular phylogeny for important phytopathogenic genera: 76–100 (2020)

This is a continuation of a series focused on providing a stable platform for the taxonomy of phytopathogenic fungi and fungus-like organisms. This paper focuses on one family: Erysiphaceae and 24 phytopathogenic genera: Armillaria, Barriopsis, Cercospora, Cladosporium, Clinoconidium, Colletotrichum, Cylindrocladiella, Dothidotthia,, Fomitopsis, Ganoderma, Golovinomyces, Heterobasidium, Meliola, Mucor, Neoerysiphe, Nothophoma, Phellinus, Phytophthora, Pseudoseptoria, Pythium, Rhizopus, Stemphylium, Thyrostroma and Wojnowiciella. Each genus is provided with a taxonomic background, distribution, hosts, disease symptoms, and updated backbone trees. Species confirmed with pathogenicity studies are denoted when data are available. Six of the genera are updated from previous entries as many new species have been described.

Draft genomic sequence of Armillaria gallica 012m: insights into its symbiotic relationship with Gastrodia elata

Armillaria species (Basidiomycota, Physalacriaceae) are well known as plant pathogens related to serious root rot disease on various trees in forests and plantations. Interestingly, some Armillaria species are essential symbionts of the rare Chinese medicinal herb Gastrodia elata, a rootless and leafless orchid used for over 2000 years. In this work, an 87.3-M draft genome of Armillaria gallica 012m strain, which was symbiotic with G. elata, was assembled. The genome includes approximately 23.6% repetitive sequences and encodes 26,261 predicted genes. In comparison with other four genomes of Armillaria, the following gene families related to pathogenicity/saprophytic phase, including cytochrome P450 monooxygenases, carbohydrate-active enzyme AA3, and hydrophobins, were significantly contracted in A. gallica 012m. These characteristics may be beneficial for G. elata to get less injuries. The genome-guided analysis of differential expression between rhizomorph (RH) and vegetative mycelium (VM) showed that a total of 2549 genes were differentially expressed, including 632 downregulated genes and 1917 upregulated genes. In the RH, most differentially expressed genes (DEGs) related to pathogenicity were significantly upregulated. To further elucidate gene function, Gene Ontology enrichment analysis showed that the upregulated DEGs significantly grouped into monooxygenase activity, hydrolase activity, glucosidase activity, extracellular region, fungal cell wall, response to xenobiotic stimulus, response to toxic substance, etc. These phenomena indicate that RH had better infection ability than VM. The infection ability of RH may be beneficial for G. elata to obtain nutrition, because the rhizomorph constantly infected the nutritional stems of G. elata and formed the hyphae that can be digested by G. elata. These results clarified the characteristics of A. gallica 012m and the reason why the strain 012m can establish a symbiotic relationship with G. elata in some extent from the perspective of genomics.

Evaluation of five regions as DNA barcodes for identification of Lepista species (Tricholomataceae, Basidiomycota) from China

Background

Distinguishing among species in the genus Lepista is difficult because of their similar morphologies.

Methods

To identify a suitable DNA barcode for identification of Lepista species, we assessed the following five regions: internal transcribed spacer (ITS), the intergenic spacer (IGS), nuclear ribosomal RNA subunit, mitochondrial small subunit rDNA, and tef1. A total of 134 sequences from 34 samples belong to eight Lepista species were analyzed. The utility of each region as a DNA barcode was assessed based on the success rates of its PCR amplification and sequencing, and on its intra- and inter-specific variations.

Results

The results indicated that the ITS region could distinguish all species tested. We therefore propose that the ITS region can be used as a DNA barcode for the genus Lepista. In addition, a phylogenetic tree based on the ITS region showed that the tested eight Lepista species, including two unrecognized species, formed eight separate and well-supported clades.

Mobile genetic elements explain size variation in the mitochondrial genomes of four closely-related Armillaria species

Background

Species in the genus Armillaria (fungi, basidiomycota) are well-known as saprophytes and pathogens on plants. Many of them cause white-rot root disease in diverse woody plants worldwide. Mitochondrial genomes (mitogenomes) are widely used in evolutionary and population studies, but despite the importance and wide distribution of Armillaria, the complete mitogenomes have not previously been reported for this genus. Meanwhile, the well-supported phylogeny of Armillaria species provides an excellent framework in which to study variation in mitogenomes and how they have evolved over time.

Results

Here we completely sequenced, assembled, and annotated the circular mitogenomes of four species: A. borealis, A. gallica, A. sinapina, and A. solidipes (116,443, 98,896, 103,563, and 122,167 bp, respectively). The variation in mitogenome size can be explained by variable numbers of mobile genetic elements, introns, and plasmid-related sequences. Most Armillaria introns contained open reading frames (ORFs) that are related to homing endonucleases of the LAGLIDADG and GIY-YIG families. Insertions of mobile elements were also evident as fragments of plasmid-related sequences in Armillaria mitogenomes. We also found several truncated gene duplications in all four mitogenomes.

Conclusions

Our study showed that fungal mitogenomes have a high degree of variation in size, gene content, and genomic organization even among closely related species of Armillara. We suggest that mobile genetic elements invading introns and intergenic sequences in the Armillaria mitogenomes have played a significant role in shaping their genome structure. The mitogenome changes we describe here are consistent with widely accepted phylogenetic relationships among the four species.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5732-z) contains supplementary material, which is available to authorized users.

Chemometric Analysis of Elemental Fingerprints for GE Authentication of Multiple Geographical Origins

The feasibility of combining elemental fingerprints and chemical pattern recognition methods for authentication of the geographical origins of a Chinese herb, Gastrodia elata BI. (GE), was studied in this paper. A total of 210 GE samples were collected from 7 different producing areas. The levels of 15 mineral elements in GE, including Zn, Cd, Co, Cr, Cu, Ca, Mg, Mn, Mo, Ni, Pb, Sr, Fe, Na, and K, were determined using inductively coupled plasma mass spectrometry (ICP-MS). Using the autoscaled data of elemental fingerprints and partial least-squares discriminant analysis (PLSDA), two chemometrics strategies for multiclass classifications, One-Versus-Rest (OVR) and One-Versus-One (OVO), were studied and compared in discrimination of GE geographical origins. As a result, OVR-PLSDA and OVO-PLSDA could achieve the classification accuracy of 0.672 and 0.925, respectively. The results indicate that mineral elemental fingerprints coupled with chemometrics can provide a useful alternative method for simultaneous discrimination of multiple GE geographical origins.

The genus Heimioporus in China

Species of Heimioporus (Boletaceae, Boletales) in China are investigated on the basis of morphology and molecular phylogenetic analyses of DNA sequences from the nuc rDNA internal transcribed spacer ITS1-5.8S-ITS2 region and nuc 28S rDNA D1-D2 domains (28S) and translation elongation factor 1-α gene (TEF1). Three species are recognized in China: H. conicus, sp. nov., H. gaojiaocong, sp. nov., and the previously described H. japonicus. Heimioporus xerampelinus, originally described from southwestern China, is synonymized with H. japonicus; specimens from China previously regarded as H. retisporus and H. subretisporus are confirmed to represent H. japonicus and H. gaojiaocong, respectively. A key to the Chinese taxa of the genus is provided. A preliminary biogeographical analysis shows that Heimioporus in East Asia and Southeast Asia/Australia are closely related. Heimioporus japonicus is a geographically widespread species occurring in East Asia and Southeast Asia; however, no taxa common to East Asia and Australia were uncovered.

Armillaria Root-Rot Pathogens: Species Boundaries and Global Distribution

This review considers current knowledge surrounding species boundaries of the Armillaria root-rot pathogens and their distribution. In addition, a phylogenetic tree using translation elongation factor subunit 1-alpha (tef-1α) from isolates across the globe are used to present a global phylogenetic framework for the genus. Defining species boundaries based on DNA sequence-inferred phylogenies has been a central focus of contemporary mycology. The results of such studies have in many cases resolved the biogeographic history of species, mechanisms involved in dispersal, the taxonomy of species and how certain phenotypic characteristics have evolved throughout lineage diversification. Such advances have also occurred in the case of Armillaria spp. that include important causal agents of tree root rots. This commenced with the first phylogeny for Armillaria that was based on IGS-1 (intergenic spacer region one) DNA sequence data, published in 1992. Since then phylogenies were produced using alternative loci, either as single gene phylogenies or based on concatenated data. Collectively these phylogenies revealed species clusters in Armillaria linked to their geographic distributions and importantly species complexes that warrant further research.

Armillaria mexicana, a newly described species from Mexico

Armillaria mexicana (Agaricales, Physalacriaceae) is described as a new species based on morphology, DNA sequence data, and phylogenetic analyses. It clearly differs from previously reported Armillaria species in North, Central, and South America. It is characterized by the absence of fibulae in the basidioma, abundant cheilocystidia, and ellipsoidal, hyaline basidiospores that are apparently smooth under light microscope, but slightly to moderately rugulose under scanning electron microscope. It is differentiated from other Armillaria species by macromorphological characters, including annulus structure, pileus and stipe coloration, and other structures. DNA sequence data (nuc rDNA internal transcribed spacers [ITS1-5.8S-ITS2 = ITS], 28S D-domain, 3' end of 28S intergenic spacer 1, and translation elongation factor 1-α [TEF1]) show that A. mexicana sequences are quite distinct from sequences of analogous Armillaria species in GenBank. In addition, sequences of ITS of the A. mexicana ex-type culture reveal an ITS1 of 1299 bp and an ITS2 of 582 bp, the longest ITS regions reported thus far in fungi. Phylogenetic analysis based on TEF1 sequences place A. mexicana in a well-separated, monophyletic clade basal to the polyphyletic A. mellea complex.

Phylogenetic constrains on Polyporus umbellatus-Armillaria associations

It has been well established that some Armillaria species are symbionts of Polyporus umbellatus, However, little is known about the evolutionary history of P. umbellatus-Armillaria associations. In this research, we used an analysis based on the strength of the phylogenetic signal to investigate P. umbellatus-Armillaria associations in 57 sclerotial samples across 11 provinces of China. We isolated Armillaria strains from the invasion cavity inside the sclerotia of P. umbellatus and then phylogenetically analyzed these Armillaria isolates. We also tested the effect of P. umbellatus and Armillaria phylogenies on the P. umbellatus-Armillaria associations. We isolated forty-seven Armillaria strains from 26 P. umbellatus sclerotial samples. All Armillaria isolates were classified into the 5 phylogenetic lineages found in China except for one singleton. Among the 5 phylogenetic lineages, one lineage (lineage 8) was recognized by delimitation of an uncertain phylogenetic lineage in previous study. Results of simple Mantel test implied that phylogenetically related P. umbellatus populations tend to interact with phylogenetically related Armillaria species. Phylogenetic network analyses revealed that the interaction between P. umbellatus and Armillaria is significantly influenced by the phylogenetic relationships between the Armillaria species.

Resolved phylogeny and biogeography of the root pathogen Armillaria and its gasteroid relative, Guyanagaster

Background

Armillaria is a globally distributed mushroom-forming genus composed primarily of plant pathogens. Species in this genus are prolific producers of rhizomorphs, or vegetative structures, which, when found, are often associated with infection. Because of their importance as plant pathogens, understanding the evolutionary origins of this genus and how it gained a worldwide distribution is of interest. The first gasteroid fungus with close affinities to Armillaria—Guyanagaster necrorhizus—was described from the Neotropical rainforests of Guyana. In this study, we conducted phylogenetic analyses to fully resolve the relationship of G. necrorhizus with Armillaria. Data sets containing Guyanagaster from two collecting localities, along with a global sampling of 21 Armillaria species—including newly collected specimens from Guyana and Africa—at six loci (28S, EF1α, RPB2, TUB, actin-1 and gpd) were used. Three loci—28S, EF1α and RPB2—were analyzed in a partitioned nucleotide data set to infer divergence dates and ancestral range estimations for well-supported, monophyletic lineages.

Results

The six-locus phylogenetic analysis resolves Guyanagaster as the earliest diverging lineage in the armillarioid clade. The next lineage to diverge is that composed of species in Armillaria subgenus Desarmillaria. This subgenus is elevated to genus level to accommodate the exannulate mushroom-forming armillarioid species. The final lineage to diverge is that composed of annulate mushroom-forming armillarioid species, in what is now Armillaria sensu stricto. The molecular clock analysis and ancestral range estimation suggest the most recent common ancestor to the armillarioid lineage arose 51 million years ago in Eurasia. A new species, Guyanagaster lucianii sp. nov. from Guyana, is described.

Conclusions

The armillarioid lineage evolved in Eurasia during the height of tropical rainforest expansion about 51 million years ago, a time marked by a warm and wet global climate. Species of Guyanagaster and Desarmillaria represent extant taxa of these early diverging lineages. Desarmillaria represents an armillarioid lineage that was likely much more widespread in the past. Guyanagaster likely evolved from a gilled mushroom ancestor and could represent a highly specialized endemic in the Guiana Shield. Armillaria species represent those that evolved after the shift in climate from warm and tropical to cool and arid during the late Eocene. No species in either Desarmillaria or Guyanagaster are known to produce melanized rhizomorphs in nature, whereas almost all Armillaria species are known to produce them. The production of rhizomorphs is an adaptation to harsh environments, and could be a driver of diversification in Armillaria by conferring a competitive advantage to the species that produce them.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0877-3) contains supplementary material, which is available to authorized users.