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Whole genome sequencing and analysis of the symbiotic Armillaria gallica M3 with Gastrodia elata

BMC Genomics volume 26, Article number: 324 (2025) Cite this article

Abstract

Background

On the one hand, Armillaria is regarded as a plant disease that causes serious root rot of forest trees, on the other hand, Armillaria is also an important symbiotic fungi of the valuable Chinese herb Gastrodia elata. Currently, the whole genome database of Armillaria is relatively limited, and it is expected that a more comprehensive understanding of the symbiotic interactions between Armillaria and G. elata can be achieved through genome-wide comparisons and functional annotations. Whole genome sequencing of Armillaria gallica M3 strain was performed using Oxford Nanopore Technologies sequencing platform, and the sequencing data were used to perform genome assembly, gene prediction and functional annotation, carbohydrate-active enzymes, and host–pathogen interactions using bioinformatics methods.

Results

In this study, we obtained an 83.33 M genome of A. gallica M3 strain, which consisted of 38 overlapping clusters with an N50 of 6,065,498 bp and a GC content of 47.43%. A total of 12,557 genes were identified in the genome of A. gallica M3, and the repetitive sequences accounted for about 44.36% of the genome. 42.26% of the genome was composed of glycoside hydrolases (GHs), 16.15% of the genome was composed of glycosyltransferases (GTs). In addition, 3412 genes in A. gallica M3 were involved in the host–pathogen interaction mechanism.

Conclusions

These results have elucidated the characteristics of A. gallica M3 from a genomic perspective to a certain extent. They help to analyze the inner mechanism of A. gallica M3 being able to symbiosis with G. elata at the genomic level, which is of great significance to the next related research of A. gallica M3.

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Introduction

Gastrodia elata BI., a perennial herb of the Gastrodia in the Orchidaceae, has been used in medicine for more than 2,000 years, and is a traditional and valuable Chinese medicine in China [1]. G. elata has anticonvulsant, hypnotic, sedative, antidepressant effects and other pharmacological effects [2]. G. elata to dried rhizomes into medicine, the main medicinal ingredients for gastrodin [3]. Since G. elata has no roots or leaves and no chloroplasts, it cannot carry out photosynthesis. The growth process of G. elata to Armillaria as the only source of nutrients, through the digestion of Armillaria invasion of rhizomorphs to obtain nutrients [4, 5]. And when the Armillaria source of nutrition is insufficient, it will use the nutrients in the body of G. elata for its growth. Therefore, Armillaria and G. elata to establish a special symbiotic relationship [6].

Most terrestrial plants form symbiotic relationships with fungi, and these mycorrhizal fungi can influence soil structure and regulate soil nutrient and carbon cycling [7]. Armillaria are one of the most globally important genera of fungal root pathogens and one of the largest and oldest organisms on earth [8, 9]. The ability of Armillaria to act as saprophytes, especially white rot fungi, is considered to be beneficial to natural ecosystems because they degrade lignin and therefore play an important role in the carbon cycle [8].

Armillaria gallica, an important plant pathogenic fungus, often causes root rot in many trees. However, it is extremely special that Armillaria is an essential fungus in the growth process of G. elata, which can provide nutrients for G. elata. At present, there are more than 70 known species of Armillaria, but only a few of them can be symbiotic with G. elata [10]. As the ability of different strains of Armillaria to form rhizomorphs and the ability of rhizomorphs to infest the cortical tissue of G. elata differs, the quality of Armillaria will directly affect the yield of G. elata [11]. Liu et al. found that the extracellular secretion of pectinase, xylanase, cellulase, laccase and other enzymes not only provides nutrients for the growth and development of A. gallica, but also provides a material basis for A. gallica to infest the epidermis of G. elata [12]). In other words, the activity of extracellular enzymes of A. gallica is closely related to the yield and quality of G. elata. Meanwhile, Zhao et al. showed that the extracellular enzyme activity was stronger and polysaccharide content was higher in the A. gallica strain [13]. Moreover, A. gallica has strong parasitic ability, and its mycelium is thick and developed, which are beneficial to the cultivation and production of G. elata. [3]. A. gallica polysaccharides have a variety of pharmacological activities, including antioxidant effects, anti-fatigue and anti-inflammatory effects [14,15,16].

Compared to most other seed plants, G. elata's mitochondrial genome significantly enlarged [1]. It was also found that the number of monocotyledonous mannose-binding lectin Gastrodia antifungal protein (GAFP) genes was increased in G. elata, and the GAFP protein could inhibit the growth of ascomycete and basidiomycete, including Armillaria and Ganoderma lucidum, among others [17, 18]. More than 80% of the GAFP genes expressed highly in protocorms and juvenile tubers before G. elata established a stable symbiotic relationship with Armillaria [1]. Strigolactone promotes Armillaria mycelial branching and contributes to the establishment of a symbiotic relationship between G. elata and Armillaria [19]. In G. elata, the number of strigolactone biosynthesis and transport key genes carotenoid cleavage dioxygenases (CCDs) and ABC transporters was increased; the number of calmodulin-dependent protein kinase genes of the does-not-make-infections 3 subfamily (DMI3) genes was also increased, which helped to further regulate the Armillaria colonization in G. elata [1, 20]. Tan et al. conducted transcriptome analysis of the symbiotic region of Armillaria and G. elata, and found that the genes for a variety of extracellular enzymes (cellulase, xylanase, laccase) were in a state of down-regulation after Armillaria invaded the endothelial layer of G. elata [21]. At this time, the infestation of Armillaria on G. elata reached a state of equilibrium, there is no tendency to further invade the G. elata, providing a basis for understanding the symbiotic relationship between Armillaria and G. elata at the level of gene expression.

Currently, studies exploring the symbiotic relationship between Armillaria and G. elata have focused on phenotyping, physiological and biochemical assays, and transcriptome analyses. However, few studies have been reported to explore the symbiotic relationship between Armillaria and G. elata at the genome-wide level. Therefore, carrying out the whole genome analysis of the genus Armillaria is of theoretical significance and applied value for further understanding the role of Armillaria in symbiotic relationships with plants such as G. elata and Polyporus umbellatus. In this study, we present the draft genome of A. gallica M3 strain collected from Xiaocaoba Town, Yiliang County, Zhaotong City, Yunnan Province, and study the genome of A. gallica M3 with 12 other strains of Agaricales. This study helps to analyze the intrinsic mechanism that A. gallica M3 strain can be symbiotic with G. elata at the genomic level, and provides a theoretical basis for the standardization of A. gallica M3 strain accompanied by planting G. elata.

Materials and methods

Strains and culture conditions

Armillaria gallica M3 was provided by Yunnan Senhao Fungi Industry Co., Ltd. Routinely, A. gallica M3 was cultured in PDA solid medium (Huankai Microbial, Guangdong Provence, China.) at 28 °C for 5 days in a dark environment, and reinoculated in fresh PDA solid medium at 28 °C. The strains used in this study are stored at the Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming city, China.

DNA extraction

Total genomic DNA was extracted using the CTAB hexadecyltrimethylammonium bromide method [22]. DNA purity was confirmed spectrophotometrically at 260 nm with NanoDrop One spectrophotometer, and DNA concentration was determined with Qubit 3.0 fluorometer (Life Technologies, Carlsbad, CA. USA) to determine DNA concentration for accurate quantification of DNA (Thermo Fisher Scientific).

Whole-genome sequencing, assembly, and annotation

High-throughput sequencing of the genome was performed using the Illumina NovaSeq 6000 platform and the PromethION P48 sequencer (Oxford Nanopore Technologies, Oxford, UK). Preliminary genome assembly was first performed using the software NECAT (https://github.com/xiaochuanle/NECAT). The initial assembly was corrected by the software Racon (V1.4.11) and Pilon (V1.23) [23]. The error-corrected genome was de-hybridized using the software Purge haplotigs (V1.0.4) to obtain the final assembly (Draft Genome). The software Oxford Nanopore GUPPY (V4.0.2) was used to convert the raw image data files obtained from high-throughput sequencing into fast5 raw data by Base Calling [24]. After filtering low quality sequences, splice sequences, etc., the results were stored in FASTQ (fq) file format and annotated for analysis [25].

To evaluate the completeness of the assembled fungal genome and assess the quality of the gene set, we utilized BUSCO (Benchmarking Universal Single-Copy Orthologs) version 5.2.2. BUSCO provides a quantitative measure of genome and gene set completeness by identifying evolutionarily conserved single-copy orthologs. BUSCO evaluation is generally greater than 90%, and genome annotation is considered to be better. The lineage dataset is: fungi_odb10. BUSCO analysis first obtains data sets, and then provides quantitative measurement of genome and genome integrity by identifying evolutionarily conserved single-copy homologues.

Use RepeatMasker software (version: open-4.0.9) to make repeated comments based on RepBase library (http://www.girinst.org/repbase); Then use RepeatModeler software (version: open-1.0.11) to build a database for denovo prediction based on its own sequence characteristics, and also use RepeatMasker software (version: open-4.0.9) to compare and predict repeated sequences.

The tRNAscan-SE (V1.23) was used to find tRNA sequences in the genome based on the structural features of tRNAs [26]. The rRNA prediction was performed using the rRNA database. INFERNAL (V1.1.2) was used to find ncRNA sequences in the genome based on the Rfam database [27].

We use the following databases for gene function annotation: Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), Pfam and NR. The protein sequences encoded by genes in gene set were compared with existing protein databases Uniprot, NR and metabolic pathway database KEGG by diamond blastp (version: 2.0.11.149; Parameter:–-evalue 1e-5) to obtain the functional information of the sequence and the metabolic pathway information that the protein may participate in. Among them, KEGG annotations are related to KEGG ORTHOLOGY and PATHWAY using Kobas (version: 3.0). Uniprot database records the corresponding relationship between each protein family and the functional nodes in Gene Ontology, and predicts the biological function of the protein sequence encoded by the gene through this system. Protein's conserved sequences, motif and domains were obtained by comparing the Pfam database with InterProScan (version: 5.52–86.0).

Pathogen Host Interactions (PHI) and Carbohydrate-active enzymes (CAZymes) database annotations

Pathogenicity analysis and annotation of target protein sequences using Diamond blastp based on the Pathogenic Host Interaction Database [28]. Using CAZy database to annotate the genome of Armillaria gallica M3 strain, so as to identify and classify CAZYmes (http://www.cazy.org/).

Genome evolution analysis

We selected seven strains belonging to the genus Armillaria from NCBI database: Armillaria gallica Ar21-2, Armillaria gallica 012 m, Armillaria borealis ab13-tr4-ip16, Armillaria ostroyae C18/9, Armillaria solidipes 28–4, Amanita brunnescens Koide BX004, Armillaria gallica M3 and 6 fungal strains, and their protein sequences were obtained from NCBI. The specific information is shown in Table 1. Gene family clustering of 13 fungal strains using orthofinder software (V2.3.12) [29]. Among them, blastp (V2.6.0) software was used to do the comparison [30]. The software muscle (V3.8.31) was used to do multiple sequence alignment of protein sequences for each single-copy gene family. The results were filtered and concatenated into super gene using trimal (V1.4.rev22) [31, 32]. Finally, maximum likelihood (ML) species phylogenetic tree containing 1000 bootstrap was constructed using RAxML (V8.2.10) software (model PROTGAMMAWAG) based on super gene [33].

Table 1 Fungal strains and Genebank registration numbers
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Birth-mortality models in CAFE (V3.1) software was used to predict the contraction and expansion of the A. gallica gene family relative to its ancestors based on species evolutionary trees and gene family clustering results [34].

Comparative genomic analysis of A. gallica M3, A. gallica Ar21-2, A. gallica 012 m

Based on all amino acid sequences of the selected 3 species, gene families were clustered using Orthofinder software. Venn diagrams were drawn based on the statistics of the clustering results of the protein sequences of the three selected species. GO and KEGG analyses were performed using the R package clusterProfiler based on shared gene and uniq gene and functional annotation results, respectively [35,36,37].

Results

General genomic characteristics

The genome size of A. gallica M3 was 86,179,563 bp, with an average GC content of 47.43%. A total of 12,557 protein-coding sequences (CDSs) were identified. The genome completeness was 95.4% based on the BUSCO assessment, while 14 BUSCOs were fragmented and 21 BUSCOs were missing. In addition, 281 tRNAs, 60 rRNA manipulators (15 18S rRNAs, 28 5.8S rRNAs, 17 5S rRNAs) and 25 snRNAs (including 7 CD-boxes and 18 splicing) were predicted in the genome. The whole genome sequence of A. gallica M3 has been submitted to GenBank with the accession number is PRJNA1082085.

Gene annotation

In the GO analysis, a total of 7,671 genes were annotated in A. gallica M3, and were mapped to 18,679 GO terms. These include 4,058 biological process (BP), 5,048 cellular component (CC), and 9,573 molecular function (MF) (Fig. 1A). For the BP domain, carbohydrate metabolic process (153), translation (124), transcription, DNA-templated (109) are the most abundant terms. For the CC domain, genes were significantly enriched in integral component of membrane (2339), nucleus (467), and cytoplasm (308). For the MF domain, ATP binding (721), metal ion binding (505), and oxidoreductase activity (358) are the most abundant terms.

Fig. 1
figure 1

GO functional annotation (A) and KEGG pathway annotation (B) of the A. gallica M3 genome

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In order to further reveal the biological functions of the coding genes in A. gallica M3, the genes were annotated in the KEGG database. 2,557 coding genes of A. gallica M3 were annotated to five major categories through the KEGG database. These include Cellular Processes, Environmental Information Processing, Genetic Information Processing, Metabolism, and Organic Systems. Among these categories, Metabolic pathways had the highest number of annotated genes (1737), with a high number of genes for Carbohydrate metabolism, Amino acid metabolism and Translation (Fig. 1B).

In the Pfam annotation, 7308 genes were annotated. Based on the annotation of Pfam domains, the genes annotated in each domain are statistically summarized, and the top 20 domains with the most gene annotations are shown in Fig. 2. Among them, these genes are significantly enriched in three protein families: Major Facilitator Superfamily, Cytochrome P450 and Protein kinase domain.

Fig. 2
figure 2

Pfam functional annotation of the A. gallica M3 genome

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A total of 12,069 genes were annotated by searching the NR database. Among them, 62.68% of the genes were annotated to Armillaria gallica, 18.65% to Armillaria ostoyae and 16.38% to Armillaria solidipes (Fig. 3), and other species accounted for a small proportion.

Fig. 3
figure 3

NR functional annotation of the A. gallica M3 genome

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The carbohydrate enzyme classification and annotation

A total of 452 CAZymes were annotated in the genome of A. gallica M3, which including 191 Glycoside hydrolases (GHs), 73 Glycosyltransferases (GTs), 22 Polysaccharide lyases (PLs), 119 Auxiliary Activities (AAs), 30 Carbohydrate Esterases (CEs) and 17 Carbohydrate-Binding Modules (CBMs) (Fig. 4A). Among them, GHs are a class of enzymes that hydrolyze glycosidic bonds. GTs are a class of enzymes that transport sugar molecules to other broad-spectrum receptors (Li et al., 2021).

Fig. 4
figure 4

Annotation on the CAZymes and GHs of A. gallica M3. A CAZymes classification chart. B GHs family classification chart. C Functional annotation chart of KEGG of GHs

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According to the statistics, there are 47 GHs families in A. gallica M3, including 22 genes related to chitinase (Fig. 4B). To further reveal the biological functions of GHs in A. gallica M3, we annotated these genes in the KEGG database. 206 GHs of A. gallica M3 were involved in Metabolism in the KEGG database. Of these, 70 GHs were associated with Metabolic pathways, with the highest number of genes for Carbohydrate metabolism, Polysaccharide biosynthesis and metabolism and Lipid metabolism (Fig. 4C).

Pathogen Host Interaction (PHI)

A total of 3,412 genes were associated with PHI in A. gallica M3 by gene annotation. Among the 3,412 predicted genes, they were mainly distributed in Chemical target (0.35%), Reduced virulence (51.91%), Increased virulence (Hypervirulence) (4.63%), Enhanced antagonism (0.03%), Effector (plant avirulence determinant) (0.73%), Unaffected pathogenicity (31.33%), Loss of pathogenicity (6.95%) and Lethal (4.07%) in eight modules (Fig. 5).

Fig. 5
figure 5

Distribution of phenotypic categories of A. gallica M3 gene orthologs using the PHI database

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Genome comparison analyses

A ML phylogenetic tree was constructed based on supergene using RAxML (version: 8.2.10) software (model PROTGAMMAWAG). The phylogenetic relationship between A. gallica M3 and other related species was analyzed. The phylogenetic tree showed that among the three different strains of A. gallica, A. gallica M3 was genetically distant from A. gallica Ar21-2 and was relatively closely related to A. gallica 012 m with 100% bootstrap value (Fig. 6).

Fig. 6
figure 6

Phylogenetic analysis of A. gallica M3

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Evolutionary analysis of gene families of A. gallica M3 was performed using CAFE (V3.1). The results of the expansion and contraction gene family analysis showed that A. gallica M3 had 306 gene family expansions and 856 gene family contractions compared to the other 12 fungal strains. In the GO database, gene families such as oxidoreductase activity, fungal-type cell wall, monooxygenase activity, hydrolase activity, and extracellular region contracted significantly. Gene families such as transmembrane transporter protein activity and iron ion binding expanded significantly. In the KEGG database, gene families such as Glycine, serine and threonine metabolism and Tyrosine metabolism contracted significantly. Gene families such as Ubiquinone and other terpenoid − quinone biosynthesis, Biosynthesis of cofactors were significantly expanded (Fig. 7).

Fig. 7
figure 7

Annotation of the gene family contraction and expansion of A. gallica M3. A contraction and B expansion gene family GO enrichment results. C contraction and D expansion gene family KEGG enrichment results

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Analysis of the shared and unique gene family of A. gallica M3

This study counted and plotted Venn diagrams based on the clustering results of the protein sequences of A. gallica M3, A. gallica Ar21-2 and A. gallica 012 m (Fig. 8). The results showed that there were 7072 gene families in the three species, 719 gene families shared by A. gallica M3 with A. gallica Ar21-2, 624 gene families shared with A. gallica 012 m, and 412 gene families unique to A. gallica M3.

Fig. 8
figure 8

Venn diagram of clustering result statistics of gene families of three species

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In order to further characterize A. gallica and A. gallica M3 strains themselves, GO and KEGG functional annotation analysis was performed on the shared genes of the three strains and the unique gene family of A. gallica M3. A total of 243 shared gene families and 90 unique gene families were coded and annotated in the GO analysis (Fig. 9). Among them, the shared gene families such as carbohydrate metabolic process, flavin adenine dinucleotide binding were significantly enriched, and the unique gene families such as iron ion binding, monooxygenase activity were significantly enriched. In the KEGG analysis, 98 shared gene families and 70 unique gene families were encoded and annotated (Fig. 10). Among them, the shared gene families such as Biosynthesis of secondary metabolites, Biosynthesis of cofactors were significantly enriched, and the unique gene families such as Oxidative phosphorylation, Fatty acid biosynthesis were significantly enriched.

Fig. 9
figure 9

GO enrichment results for shared (A) and unique (B) gene families

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Fig. 10
figure 10

KEGG enrichment results for shared (A) and unique (B) gene families

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Discussion

In this study, we obtained a 83.33 Mbp genome of A. gallica M3, which consisted of 38 contigs with an N50 of 6,065,498 bp and 47.43% GC content. A total of 12,557 genes were identified in the A. gallica M3 genome, and the Repetitive sequences accounted for about 44.36% of the genome. In the GO database, gene families related to monooxygenase activity associated with pathogenicity/saprophytic, hydrolytic enzyme activity associated with infection ability and extracellular region were significantly contracted in the genome of A. gallica M3. Some studies have shown that the contraction of genes related to pathogenicity may enable the Armillaria to not further infect the endothelial layer of G. elata after infesting the epidermis of G. elata, which not only provides essential nutrients for the growth of G. elata but also avoids the pathological damage to G. elata, which is conducive to the symbiotic relationship between Armillaria and G. elata [38].

Carbohydrate-active enzymes (CAZymes) are crucial in the growth and development of plant pathogenic fungi [39]. The results predicted by the CAZy database indicate that there are 452 CAZymes in A. gallica M3 strain. A. gallica M3 had fewer CAZymes compared to the genome annotations of other Armillaria (Table 2). Among the 452 CAZymes, glycoside hydrolase and glycosyltransferase genes were significantly enriched, which are essential for the symbiosis of Armillaria with G. elata.

Table 2 Number of genes encoding CAZymes in Armillaria
Full size table

Glycoside hydrolases (GHs) are the main enzymes in the process of providing nutrients to G. elata or Polyporus umbellatus by Armillaria, which can hydrolyze glycosidic bonds and thus break down polysaccharides [40]. Playing a crucial role in the infestation of the epidermis of G. elata by the hyphae of A. gallica M3 strain, Collins et al. also showed that GHs may be associated with the pathogenicity of Armillaria [41]. Usually, plant symbiotic fungi contain more enzymes that degrade plant cell walls, such as Chitinase and Cellulase [42]. In A. gallica M3 strain containing 22 genes for Chitinase, it was reported that Chitinase, as a GHs, not only provides a material basis for the symbiosis between A. gallica and G. elata, but also senses the signal communication between A. gallica and G. elata [4]. This may facilitate the rhizomorphs to not cause further damage to the host after infestation of G. elata, so that the A. gallica and G. elata can better maintain the balance between infestation and nutrient acquisition in the process of symbiosis.

Glycosyltransferases (GTs) are enzymes that transport sugar molecules to other broad-spectrum receptors, where they complete the glycosylation of other molecules by creating glycosidic bonds [43]. Plants can produce polysaccharides by the action of GTs, including the synthesis and modification of cell wall polysaccharides, glycoproteins, glycolipids, and a number of small molecules, all catalyzed by GTs [44]. GTs within Armillaria have been reported to catalyze the transglycosylation of p-hydroxybenzyl alcohol compounds to produce gastrodin [45]. Tsai et al. also found that after Armillaria infected G. elata, the GTs involved in the gastrodin synthesis pathway appeared in the Armillaria infected G. elata [46]. This suggests that the A. gallica M3 provides nutrients to G. elata while its significantly enriched glycosyltransferase also promotes gastrodin synthesis.

There are nine families of Carbohydrate esterases (CEs) in A. gallica M3 strain, consisting of 30 genes (Table S1). Among them, the CE4 family has acetyl xylan, chitin, chitooligosaccharide and peptidoglycan deacetylase activities. It has been hypothesized that the chitin of pathogens invading plants can trigger recognition by plant defense and induce plant chitinase activity, resulting in the formation of lignin and healing tissue [47]. In addition, deacetylases in CE4 can modify plant chitinase, thereby rendering plant defenses ineffective, and modify chitin to chitosan, thereby enabling fungi to invade plants [41]. White-rot fungi are the only organisms capable of efficiently degrading lignin [48]. Among the carbohydrate active enzymes, GH1, GH3, GH5, GH6, and GH12 families are important enzymes involved in cellulose degradation.CE1, CE15, GH10, and GH43 are enzymes concerning xylan degradation.GH16 family proteins also have amylase and cellulase activities. A. gallica M3 also contains pectin cleavage family PL1 (pectin/pectin lyase), and PL3 (pectin lyase) genes.

Whole genome sequencing of A. gallica M3 strain contributes to the understanding of the function of relevant pathogenic genes of A. gallica during its interaction with G. elata. Previous studies have shown that A. gallica pathogenicity (lower virulence and aggressiveness) is weaker compared with A. mellea, A. borealis and A. ostoyae, a characteristic that may favor the establishment of a symbiotic relationship between A. gallica and G. elata rather than causing G. elata tuber disease [8, 49, 50]. A total of 3,412 PHI-associated genes were identified in the genome of A. gallica M3 by gene annotation, of which genes associated with Reduced virulence, Unaffected pathogenicity and Loss of pathogenicity were significantly enriched. Among them, 51.91% of the genes were enriched to the Reduced virulence module, 6.95% of the genes were Loss of pathogenicity, while the genes related to the Lethal only accounted for 4.07%, which further indicated that A. gallica M3 strain was weak in pathogenicity and was suitable for mixing planting with G. elata. These results elucidate the characterization of A. gallica M3 strain and its ability to establish a symbiotic relationship with G. elata to some extent from a genomic point of view.

Conclusions

In this paper, we analyzed the whole genome information of A. gallica M3, and through gene annotation, we found that there were 3412 genes involved in the host pathogen interaction mechanism in A. gallica M3, 51.91% of the genes were enriched to the Reduced virulence module, and the genes related to the Lethal only accounted for 4.07%, which further indicated that A. gallica M3 strain was weak in pathogenicity and was suitable for mixing planting with G. elata. In addition, 42.26% of the genome was composed of glycoside hydrolases (GHs), 16.15% of the genome was composed of glycosyltransferases (GTs), which is helpful for G. elata to obtain the potential of nutritional application. In general, this study has important theoretical significance and application value for further understanding the diversity of Armillaria, determining the evolutionary history and phylogenetic relationship of Armillaria, and exploring the molecular mechanism of symbiosis between Armillaria and G. elata.”

Data availability

The whole genome sequence of A. gallica M3 has been submitted to GenBank with the accession number is PRJNA1082085.The bioproject is PRJNA1082085. The BioSample is SAMN40199449. (https://www.ncbi.nlm.nih.gov/bioproject/1082085).

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Acknowledgements

We are grateful for the Yunnan Major Scientific and Technological Projects. We acknowledge support by Yunnan Senhao Fungi Industry Co., Ltd.

Funding

This study was supported by the Yunnan Major Scientific and Technological Projects (grant NO. 202202AG050008).

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Author notes

  1. Cheng-Ying Luo and Yao Lu contributed equally to this work.

Authors and Affiliations

  1. Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China

    Cheng-Ying Luo, Yao Lu, Lei Su, Jia-Jia Liu, Yi-Cen Lin & Lian-Bing Lin

  2. Gastrodia Industry Development Center of Yiliang County, Zhaotong, 657000, China

    Cheng-Ying Luo

  3. Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, Kunming, 650500, China

    Yao Lu, Lei Su, Jia-Jia Liu, Yi-Cen Lin & Lian-Bing Lin

  4. Yunnan Senhao Fungi Industry Co., Ltd, Zhaotong, 657600, China

    Jia-Yun Miao

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Contributions

L.C.Y. conducted experiments, data sorting and writing-preparation of original manuscript. L.Y. and S.L. conduct data analysis and review and edit manuscripts. L.J.J. and M.J.Y. assists in the analysis. L.Y.C. reviewed and revised the manuscript. L.L.B. designed the study, provided reagents, materials and revised papers. All authors contributed to the article and approved the submitted version.

Corresponding authors

Correspondence to Yi-Cen Lin or Lian-Bing Lin.

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We collected A. gallica M3 from Yunnan Senhao Fungi Industry Co., Ltd. We collected A. gallica in accordance with relevant institutional, national and international guidelines and legislation.

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The authors declare no competing interests.

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Luo, CY., Lu, Y., Su, L. et al. Whole genome sequencing and analysis of the symbiotic Armillaria gallica M3 with Gastrodia elata. BMC Genomics 26, 324 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12864-024-10897-9

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BMC Genomics

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