The genome of the Tiger Milk mushroom, Lignosus rhinocerotis, provides insights into the genetic basis of its medicinal properties
© Yap et al.; licensee BioMed Central Ltd. 2014
Received: 17 February 2014
Accepted: 23 July 2014
Published: 29 July 2014
The sclerotium of Lignosus rhinocerotis (Cooke) Ryvarden or Tiger milk mushroom (Polyporales, Basidiomycota) is a valuable folk medicine for indigenous peoples in Southeast Asia. Despite the increasing interest in this ethnobotanical mushroom, very little is known about the molecular and genetic basis of its medicinal and nutraceutical properties.
The de novo assembled 34.3 Mb L. rhinocerotis genome encodes 10,742 putative genes with 84.30% of them having detectable sequence similarities to others available in public databases. Phylogenetic analysis revealed a close evolutionary relationship of L. rhinocerotis to Ganoderma lucidum, Dichomitus squalens, and Trametes versicolor in the core polyporoid clade. The L. rhinocerotis genome encodes a repertoire of enzymes engaged in carbohydrate and glycoconjugate metabolism, along with cytochrome P450s, putative bioactive proteins (lectins and fungal immunomodulatory proteins) and laccases. Other genes annotated include those encoding key enzymes for secondary metabolite biosynthesis, including those from polyketide, nonribosomal peptide, and triterpenoid pathways. Among them, the L. rhinocerotis genome is particularly enriched with sesquiterpenoid biosynthesis genes.
The genome content of L. rhinocerotis provides insights into the genetic basis of its reported medicinal properties as well as serving as a platform to further characterize putative bioactive proteins and secondary metabolite pathway enzymes and as a reference for comparative genomics of polyporoid fungi.
This mushroom is rich in carbohydrates and dietary fiber with moderate amounts of protein while being low in fat . Previous research reported the medical benefits of L. rhinocerotis against hypertension, cancer cell cytotoxicity along with enhancement of immunomodulatory activity and antioxidant properties [5–8]. The non-digestible carbohydrates of Polyporus rhinocerus, a synonym for L. rhinocerotis, was also reported as a potential novel prebiotic for gastrointestinal health . The recent interests in the nutrition and biopharmacology of L. rhinocerotis signalled for an immediate need to decipher its biochemical functions, at the genetic level and the identification of its bioactive components.
Rapid advancements in technology has led to the sequencing of numerous fungal genomes with the fungal kingdom becoming one of the most sequenced amongst the eukaryotes . This is not unexpected due to their importance in industry, agriculture, medical, and health. However, the publicly available genome sequences of macrofungi, especially medicinal mushrooms, are still relatively scarce compared to the plant pathogenic and wood-degrading basidiomycetes or to ascomyceteous microfungi. A recent example is the genome sequence of the medicinal mushroom Ganoderma lucidum (lingzhi) by Chen et al. and Liu et al. where the genes in the triterpene biosynthesis and wood degradation pathways were described [11, 12]. Other genomes of edible mushrooms include Volvariella volvacea (straw mushroom) by Bao et al.  and Agaricus bisporus (button mushroom) by Foulongne-Oriol et al. .
In this paper, we present the de novo draft genome sequence of L. rhinocerotis TM02 sclerotium. The recent availability of several genome sequences of polyporaceous fungi, especially from the JGI CSP Saprotrophic Agaricomycotina Project , has allowed us to gain insights into the L. rhinocerotis genome through comparative analyses. We have also surveyed its secondary metabolite production capabilities and identified putative genes that may be involved in the biosynthesis of bioactive proteins and polysaccharides. To our knowledge, this is the first detailed description of the genomic features of L. rhinocerotis, an ethnobotanical mushroom of Southeast Asia.
Results and discussion
Features of L. rhinocerotis
Total length (bp)
Max length (bp)
Min length (bp)
Sequence GC content (%)
Genome assembly (Mb)
Number of protein-coding genes
Coding sequences/genome (%)
Average gene length (bp)
Average coding sequence length (bp)
Average exon length (nt)
Average intron length (nt)
Average number of exons per gene
Repeat elements of 74 diverse families make up about 4.01% or 1,374,638 bp of the assembled genome of L. rhinocerotis, where 1.97% of them are tandem repeat sequences and 2.03% are transposable elements (TEs). The tandem repeats (<4 kbp), not clearly associated with transposons, vary in copy number from 1.8 to 362.5. While among the retrotransposons, long terminal repeats (LTRs) and non-LTR retrotransposons (long and short interspersed nuclear elements) make up 1.26% and 0.55% of the genome, respectively. DNA transposons (Class II) comprised 0.24% of the genome. The DNA transposons elements were mainly categorized into three classes: Enhancer (En/spm), Tigger (TcMar), and Activator (hAT).
The total 10,742 predicted genes, 216 tRNAs, 17 snRNAs and a single rRNA together comprise 44.33% of the assembled genome. Gene density and the average size of protein coding genes are 5.42 genes/10 kb and 1,414.33 bp, respectively. Among the tRNAs, 13 are possible pseudogenes, four with undetermined anticodons and the remaining 199 anti-codon tRNAs correspond to the 20 common amino acid codons. About half of the tRNAs (109) are predicted to not contain an intron. The genome size of L. rhinocerotis, its average gene length, the proportion of repeat sequences, and the average number of exons and introns were comparable to the recently sequenced polyporaceous G. lucidum genome .
The L. rhinocerotis genome revealed a total of 1,686 predicted genes that encode for hypothetical proteins with no apparent homologs to currently available sequences. This is indicative of the uniqueness of L. rhinocerotis. On the other hand, up to 8986, 5883, 6669 and 8997 genes are homologous to known proteins in the NCBI nr, SwissProt, InterPro and TrEMBL databases, respectively. These homologous proteins represent 84.30% of the assembled genome.
KEGG-based comparative genomics analysis
Fungal genes distribution in P450 family and the third layer of KEGG pathways
00281: Geraniol degradation
00900: Terpenoid backbone biosynthesis
00903: Limonene and pinene degradation
01053: Biosynthesis of siderophore group nonribosomal peptides
00311: Penicillin and cephalosporin biosynthesis
00312: beta-Lactam resistance
00901: Indole alkaloid biosynthesis
00945: Stilbenoid, diarylheptanoid and gingerol biosynthesis
00960: Tropane, piperidine and pyridine alkaloid biosynthesis
00980: Metabolism of xenobiotics by cytochrome P450
00982: Drug metabolism - cytochrome P450
The Enzyme Commission (EC) number classification was used to link the respective enzyme genes to their repertoire of metabolic pathways . In the fourth layer of the reference KEGG pathway, L. rhinocerotis was found to have 26 putative enzymes that are two-fold greater than the other fungi compared (Additional file 2: Table S2, Additional file 2: Table S3). Among them, 15 were mapped to “Metabolism”, two for “Genetic information processing” and one for “Organismal systems” while two remain “Unclassified” according to KO terms. There were another six enzymes that mapped to multiple sections in the first layer of KEGG.
Interestingly, a total of 535 enzymes are exclusive to L. rhinocerotis and not present in any other Basidiomycota fungi compared (Additional file 2: Table S4). Some of the exclusive enzymes participate in multiple KO classes. Among them, 79.25% are predicted to involve in “Metabolism” where 20.56% and 18.69% play major roles in “Amino acid metabolism” and “Carbohydrate metabolism”, respectively. This is followed by “Genetic information processing” (8.79%) and “Cellular processes” (5.61%). About 14.21% remain “Unclassified” without mapping to any specific pathway.
Phylogeny of L. rhinocerotis
It should be noted that, although L. rhinocerotis falls into the same clade with G. lucidum, D. squalens, and T. versicolor, it is relatively distant from them and shows distinct morphological features. Unlike the other white-rot members from the core polyporoid clade that grow on wood, L. rhinocerotis has a terrestrial growth habit similar to the brown-rot W. cocos with the development of an underground sclerotium . The sclerotium of L. rhinocerotis is oblong to irregular shape and its fruiting body (basidiocarp) is centrally stipitate with an isodiametric cap. On the other hand, the cap of G. lucidum and T. versicolor is offset and sometimes indistinct with either a bare stipe for the former or lacking one for both fungi. On the contrary, D. squalens has a basidiocarp with poroid hymenophore and lacks a stipe. Although L. rhinocerotis shows similar growth habit to W. cocos with the presence of a sclerotium, the latter has resupinate fruiting body and spherical sclerotium. Therefore, L. rhinocerotis is relatively unique among the sequenced Basidiomycota mushrooms.
The CAZymes family
As L. rhinocerotis is known to thrive on cellulosic substrates, its genome was mapped to the CAZy database to identify the presence of carbohydrate-active enzymes (CAZymes) and auxiliary proteins . A total of 332 non-overlapping CAZyme-coding gene homologs were identified. This includes 178 glycoside hydrolases (GH), 77 glycosyl transferases (GT), three polysaccharide lyases (PL), 102 carbohydrate esterases (CE), 205 carbohydrate-binding module (CBM), and 37 with auxiliary activities (AA) distributed among 39, 26, 1, 13, 32, and 6 coinciding EC activities respectively (Additional file 3). The mapped EC activities may not be directly associated with the family but simply a result of similarity to adjacent modules due to the modular nature of CAZymes. The number of CAZyme candidates identified was almost similar to the average reported in several studies for Basidiomycota fungi [12, 13]. The high number of putative GH and GT genes suggests their plausible roles in the degradation of plant cell wall polysaccharides. These polysaccharides consist mainly of cellulose, hemicellulose (including xylan, xyloglucan, glucogalactomannan, galactan, and respective side chains), and pectin (composed of galacturonan, rhamnogalacturonan, and respective side chains).
The CYPs family
The cytochrome P450 (CYP) superfamily is a diverse group of enzymes involved in various physiological processes, including detoxification, degradation of xenobiotics and the biosynthesis of secondary metabolites . Although not substantial, when compared to most other fungi, it is noted that L. rhinocerotis has 33 genes engaged in “Metabolism of xenobiotics by cytochrome P450” and 36 in “Drug metabolism - cytochrome P450” KEGG sub-pathways (Table 2), respectively.
P450 genes and subfamilies in L. rhinocerotis
Corresponding gene number
Total gene number
A; C; D; F
6; 23; 1; 5
A; B; C
17; 1; 2
A; B; D
3; 2; 1
Secondary metabolite biosynthetic genes are often clustered . The L. rhinocerotis genome contains several secondary metabolite gene clusters that suggest the potential for production of certain biologically active compounds (Additional file 2: Table S6). There are ten gene clusters encoding key enzymes, such as terpene synthases (TS), non-ribosomal peptide synthetase (NRPS), and polyketide synthase (PKS), that are crucial for the biosynthesis of terpenes, peptides, and polyketides, respectively. It is noted that, like most basidiomycetes, L. rhinocerotis has very few PKS genes and multi-domain NRPS genes compared to ascomycetes. The only PKS gene that can be found in L. rhinocerotis is GME5066_g, which encodes a non-reducing PKS which are often associated with the biosynthesis of aromatic polyketides. This non-reducing PKS appears to be conserved among basidiomycetes and an ortholog of the gene can be found in most of the sequenced basidiomycetes genomes, including G. lucidum, T. versicolor, and A. bisporus. Interestingly, GME5066_g shared a head-to-tail homology (38% identity and 55% similarity) and domain architecture with the orsellinic acid synthase from Coprinopsis cinerea (CC1G_05377), the only basidiomycete PKS gene that has been characterized so far . Like CCIG_05377, GME5066_g contains a starter unit acyl-carrier protein transacylase (SAT), ketosynthase (KS), acyltransferase (AT), product template (PT), two acyl-carrier proteins (ACPs) and a thioesterase (TE) domain. GME5066_g is clustered with GME5065_g, which is a predicted flavin-dependent oxidoreductase. It remains to be determined if the GME5066_g gene cluster produces orsellinic acid derivatives or related polyketides. The L. rhinocerotis genome also harbours a single multidomain NRPS gene. The NRPS has a single adenylation domain along with three thiolation and condensation domains, and are conserved among several basidiomycetes, including D. squalens DICSQDRAFT_132068 (61% identity) and T. versicolor TRAVEDRAFT_27949 (59% identity), but none are characterized.
Putative genes involved in terpenoid backbone biosynthesis
Gene name and definition
E22.214.171.124; 3-hydroxy-3-methylglutaryl-CoA reductase
metC; cystathionine beta-lyase (homologous to mevalonate kinase at the C-terminal)
atoB; acetyl-CoA C-acetyltransferase
FDPS; farnesyl diphosphate synthase
GGPS1; geranylgeranyl diphosphate synthase, type III
126.96.36.199 188.8.131.52 184.108.40.206
mvaK2; phosphomevalonate kinase
MVD; diphosphomevalonate decarboxylase
E220.127.116.11; hydroxymethylglutaryl-CoA synthase
idi; isopentenyl-diphosphate delta-isomerase
hexPS; hexaprenyl diphosphate synthase
SPS; solanesyl diphosphate synthase
DHDDS; cis-prenyltransferase, dehydrodolichyl diphosphate synthase
We next searched the L. rhinocerotis genome for potential triterpenoid biosynthesis genes and found an open reading frame (GME631_g) that encodes a single copy gene for lanosterol synthase (LSS; K01852; EC18.104.22.168). LSS is a squalene/oxidosqualene cyclase family enzyme that catalyzes the cyclization of the triterpenes squalene or 2-3-oxidosqualene to lanosterol, the precursor of all steroids . This enzyme has been implicated in biosynthesis of ganoderic acids, which are the bioactive triterpenes in G. lucidum. Similarly, the LSS in L. rhinocerotis can be involved in biosynthesis of bioactive triterpenes. The CYP5144 and CYP512 families of P450 genes have been previously implicated in triterpenoid biosynthesis in G. lucidum due to their co-expression with LSS . As mentioned earlier, CYP5144 is the largest P450 family in L. rhinocerotis with 35 genes, while six CYP512 family genes are present in its genome as well. This suggests that L. rhinocerotis may be a potential triterpenoid source.
Mushrooms are known to be prolific producers of bioactive sesquiterpenes . The L. rhinocerotis genome is enriched with sesquiterpenoid biosynthesis genes compared to some of the other seven Basidiomycota genomes (Additional file 2: Table S1). The L. rhinocerotis genome encodes up to 12 sesquiterpene cyclase genes. This is comparable to the number of sesquiterpene cyclase genes found in the recently sequenced genome of the Jack O’Lantern mushroom Omphalotus olearius, which is the producer of anticancer illudins . Many of these terpene synthase genes are clustered together with various modifying enzymes (Additional file 2: Table S6). Comparatively, the common filamentous ascomycetes have fewer sesquiterpene cyclase genes, for example, both the Aspergillus nidulans and Aspergillus oryzae have only one sesquiterpene cyclase gene, while the Aspergillus fumigatus has none . This suggests that unlike the filamentous ascomycetes that are enriched with the polyketide and nonribosomal peptide biosynthesis genes, the sesquiterpenoids are major secondary metabolites produced by L. rhinocerotis.
Biosynthesis of potential bioactive proteins and polysaccharides
Polysaccharides are the most extensively investigated mushroom constituents due to their pharmaceutical potential. The water soluble 1,3-β- and 1,6-β-glucans are some of the most active immunomodulatory compounds reported . Additional file 2: Table S7 lists enzymes that may be involved in the biosynthesis of uridine diphosphate glucose (UDP-glucose, precursor of glucans) and 1,6-β-glucans in L. rhinocerotis. These enzymes include hexokinase, α-phosphoglucomutase, UTP-glucose-1-phosphate uridylyltransferase, 1,3-β-glucan synthases, and β-glucan biosynthesis-associated proteins.
Mushrooms have also been an important source of bioactive proteins, which include lectins, fungal immunomodulatory proteins (FIP), ribosome inactivating proteins (RIP), antimicrobial proteins, ribonucleases, and laccases . The genome of L. rhinocerotis codes for nine putative lectins, two putative fungal immunomodulatory proteins (FIP), and four putative laccases (Additional file 2: Table S7). It is interesting to note that both of the L. rhinocerotis FIPs (GME7566_g and GME10641_g) are homologous to LZ-8 (64% identities), a member of the FIP family from G. lucidum that has been shown to possess immunomodulation and anti-cancer activity [35, 36]. Both the putative FIP proteins carry an Fve domain (pfam09259) found in the major fruiting body protein isolated from Flammulina velutipes with immunomodulatory activity .
L. rhinocerotis genome sequencing has allowed us to perform comparative genomics and phylogenetic analysis. This has provided valuable insights into the biology of this medicinal mushroom from Southeast Asia. A survey of the secondary metabolite biosynthesis genes in the L. rhinocerotis genome shows that it is particularly enriched with sesquiterpenoid biosynthesis genes. Thus, future bioactive molecule discovery efforts should focus on this class of metabolites. Furthermore, L. rhinocerotis appears to encode the capabilities to produce 1,3-β- and 1,6-β-glucans as well as bioactive proteins, such as lectins and FIPs. Our genomic analysis of L. rhinocerotis will provide the foundation for future research and exploitation of L. rhinocerotis in pharmacological and functional food applications.
Fungal material, sequencing, and assembly
Sclerotium of L. rhinocerotis was collected from tropical forest at Lata Iskandar, Cameron Highland, Pahang, Malaysia (4.3245°N, 101.3324°E) in 2010. The fungus was deposited at Royal Botanic Gardens, Kew (Richmond, London, England) with the accession number K(M) 177812. Genomic DNA was extracted using a modified cetrimonium bromide (CTAB) procedure  from the sclerotium of L. rhinocerotis TM02 strain cultivated by Ligno Biotech Sdn. Bhd. (Balakong Jaya, Selangor, Malaysia). Paired-end reads were generated by sequencing of four cloned insert libraries of 200, 700, 2,000, and 5,000 bp using Hiseq2000 system (Illumina Inc., San Diego, CA, USA) at BGI-Shenzhen, China. Reads of low complexity and low quality with adapter and duplication contamination were removed from the raw data to strengthen the accuracy of follow-up analysis. To avoid issues associated with heterozygosity and/or low sequence quality, reads with significant poly-A structure and kmer frequency of 1 were removed. The clean short reads were then assembled using SOAPdenovo based on de Bruijn graph theory . The gaps were filled using the GapCloser module from SOAPdenovo. During scaffold construction, contigs with certain distance relationships but without genotypes were connected with wildcards. The GapCloser module then replaced these wildcards using the context and paired-end reads information. The GapCloser assembled sequences iteratively in the gaps to fill large gaps where at each iterative cycle, GapCloser considered only the reads that could be aligned in the current cycle.
Gene prediction and annotation
Protein coding genes were predicted using the ab initio gene predictors Augustus , GeneMark-ES , and SNAP . The resulting gene sets were integrated to get the most comprehensive and non-redundant reference gene. Transposon sequences were predicted by aligning the assembled gene sequences with the transposon Repbase database  using RepeatMasker software at http://www.repeatmasker.org and RepeatProteinMasker software (transposon protein library). Tandem repeat sequences were predicted using Tandem Repeat Finder (TRF) . rRNA sequences were identified by rRNA pool alignment and rRNAmmer de novo prediction software . tRNA genes were predicted by tRNAscan-SE software  while others non-coding RNAs (miRNA, sRNA, and snRNA) were predicted by Rfam.
Predicted genes were functionally annotated based on homology to annotated genes in various databases via BLAST. Protein models were aligned to SwissProt, TrEMBL, InterPro and NCBI nr (BLASTP cut-off e-value ≤ 1e-5); and further classified according to GO , KOG , and KEGG pathways . KEGG terms are assigned into four layers. The first layer consists of seven main sections, including “Metabolism”, “Genetic information processing”, “Environmental information processing”, “Cellular processes”, “Organismal systems”, “Human diseases”, and “Drug development”; and is further divided into several small entries, the second layers. The third and fourth layers are the specific pathway map and specific genes regulated in each pathway, respectively.
Together with L. rhinocerotis, 14 Basidiomycota of agaricomycetes (G. lucidum, T. versicolor, D. squalens, W. cocos, F. pinicola, Fomitiporia mediterranea, A. bisporus, Coprinus cinereus (synonym C. cinerea), Laccaria amethystina, P. ostreatus), basidiomycete (S. commune), tremellomycete (T. mesenterica), pucciniomycete (P. graminis), and ustilaginomycete (U. maydis) were selected for analysis. Three Ascomycota of eurotiomycetes (Aspergillus aculeatus, Penicillium chrysogenum) and saccharomycete (Saccharomyces cerevisiae) were added to root the phylogenetic trees. All the selected genomic gene models were downloaded from the US Department of Energy Joint Genome Institute website at http://genome.jgi.doe.gov/ (Additional file 2: Table S8).
Protein sequences of each shared KOG family from the different species were aligned using CLUSTAL X . The multiple sequence alignments were concatenated using DAMBE5  upon the removal of poorly aligned regions by GBlocks server . PROTTEST  was used to select the best fit empirical substitution model of protein evolution for the concatenated alignment.
Maximum Parsimony and Neighbor Joining analyses were executed with Phylip  using PROTPARS and PROTDIST (JTT model). TREE-PUZZLE  was used to construct maximum likelihood quartet puzzling trees using the VT model . Bayesian inference using Markov chain Monte Carlo phylogenetic analysis was performed with MrBayes 3.2.1  under Rtrev + G + F model. Trees were sampled every 10 generations over a random starting trees of 50,000 generations, resulting in a total of 5,000 sampling trees, of which the first 2,000 were discarded. The remaining 3,000 trees were used to build a single consensus tree with ≥ 70% majority-rule using MEGA .
CYP and CAZy family classifications
L. rhinocerotis gene models were aligned to fungi P450 sequences and the detected CYPs were named according to nomenclature in the P450 database (cut-off e-value ≤ 1e-10, identity > 30%) at Cytochrome P450 homepage (http://drnelson.uthsc.edu/CytochromeP450.html) . Annotation of carbohydrate-active enzymes in L. rhinocerotis genome was carried out by BLASTP analysis against CAZy database at http://www.cazy.org/.
Secondary metabolites gene clusters annotation
Secondary metabolite gene clusters were determined using Secondary Metabolite Unique Regions Finder (SMURF, http://jcvi.org/smurf/index.php)  based on PFAM and TIGRFAM resources along with the gene’s chromosomal position and antibiotics & Secondary Metabolite Analysis Shell (antiSMASH 2.0, http://antismash.secondarymetabolites.org/) ; a web-based analysis platform.
This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AXZM00000000. The version described in this paper is version AXZM01000000.
This research is supported by High Impact Research Grant UM.C/625/1/HIR/MoE/E20040-20001 from the University of Malaya/Ministry of Education, Malaysia. H-YYY is supported by the postgraduate research grant (PPP) PV024/2012A from University of Malaya, Malaysia. Y-HC is a recipient of Australian Research Council Discovery Early Career Researcher Award (ARC DECRA). We are grateful to the team at BGI-Shenzhen for their assistance in genomic sequencing and analysis. Oliver Mead is thanked for proofreading the manuscript.
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