Abstract
The widely cultivated Chinese Lingzhi is a famous fungus with significant medicinal and economic value, which has commonly been misidentified as Ganoderma lucidum for a long period of time. The scientific binomial of the fungus is always a hotly debated question that revolves around G. lingzhi and G. sichuanense. To interpret the species concept of the taxon, six specific primers for G. sichuanense and one universal primer were designed. Through directed and nested PCRs, we obtained nine ITS sequences from the holotype (HMAS 42798) of G. sichuanense. By genome sequencing, the ITS sequence of the first cultivated Lingzhi (HMAS 25103) was assembled. Based on a phylogenetic study of the genus Ganoderma, the correct name for widely cultivated Ganoderma species in China was confirmed as G. sichuanense, and G. lingzhi should be a later synonym.
Keywords: DNA sequence, Ganoderma sichuanense, Ganoderma lingzhi, Lingzhi, nomenclature, type material
1. Introduction
Ganoderma P. Karst. is a cosmopolitan genus established by Karsten [1], based on the generic type G. lucidum (Curtis) P. Karst from England [2]. The use of Ganoderma mushroom in China can be traced back to 6800 years ago [3], and species of Ganoderma have had a considerable impact on Chinese history [4]. According to Tai [5], Patouillard first identified G. lucidum in China in 1907 by the specimens collected from Guizhou Province.
However, based on the morphological characters, such as the thickness of context and diameter of the stipe, Pegler and Yao suggested that the widely cultivated “G. lucidum” (as “Lingzhi” or “Ruizhi” in Chinese) in China was not conspecific with the species described in Europe [6]. The result was also supported by phylogenetic evidence [7,8,9,10,11]. In 1959, the first successful cultivation of the fruit bodies of Lingzhi was developed by the Institute of Microbiology, Chinese Academy of Sciences. Approximately 10 years later, under the vigorous promotion of the Ganoderma research group at the Institute of Microbiology [12], the cultivation of Lingzhi became an important industry in China and other adjacent countries. At present, this fungus is famous as a traditional Chinese medicine possessing great economic value [13,14,15,16,17].
The scientific binomial for this economically and medicinally important fungus, Lingzhi, has long been controversial, which was considered to be G. lucidum for a long period in China. Using molecular phylogeny, Wang et al. highlighted that the Asian G. lucidum specimens were separated from the European G. lucidum by two individual clades, and the tropical collections from Asian areas represented G. multipileum D. Hou 1950, while the classification status of the other collections obtained from mainland China, Japan, and Korea was uncertain [11]. Wang et al. recognized the uncertain clade as G. sichuanense J.D. Zhao & X.Q. Zhang [18,19], which is the Ganoderma species widely cultivated in China. However, Cao et al. proposed it as a new species G. lingzhi Sheng H. Wu, Y. Cao & Y.C. Dai based on a single available internal transcribed spacer (ITS) sequence from the holotype (HMAS 42798) of G. sichuanense [20]. Yao et al. designated an epitype (HMAS 252081) to interpret the species concept of Lingzhi and secured the position of the holotype of G. sichuanense (HMAS 42798), both morphologically and molecularly [21]. However, based on the holotype sequence from Cao et al. [20], the epitype was not accepted by some researches [22,23,24]. Yao et al. re-clarified the typification of G. sichuanense and demonstrated that the epitype of G. sichuanense was appropriately designated to support the holotype of the name [25].
To clarify the confusion of this important fungus, we designed six specific primers for G. sichuanense and one universal primer to obtain the ITS sequence from the G. sichuanense holotype (HMAS 42798) (by directed PCR and nested PCR), which is the key point of the hot topic. For the fruit bodies of the first cultivated Lingzhi (HMAS 25103), its DNA had been largely degraded, so genome sequencing was chosen. Based on all these representative sequences, we performed a phylogenetic study of the genus Ganoderma, including the type materials of G. sichuanense (holotype, epitype, and topotype) and G. lingzhi (holotype). As a result, we can confirm that G. lucidum is a name mistakenly applied to the widely cultivated Ganoderma species in China, that the scientific binomial for Lingzhi is G. sichuanense, and that the designation of the epitype is necessary to support the holotype because of its poor DNA status. G. lingzhi is the later synonym of G. sichuanense.
2. Materials and Methods
2.1. Specimens
The fungal collections are deposited in the Fungarium of the Institute of Microbiology (HMAS) of the Chinese Academy of Sciences; including the holotype of G. sichuanense (HMAS 42798), the topotype (HMAS 244431) collected from Panzhihua City (previously “Dukou Shi”) in Sichuan Province, and the first cultivated Lingzhi (HMAS 25103), performed by Zhuang Deng, the daughter and assistant of Professor Shu-Chün Teng, in 1959.
2.2. DNA Samples
A total of 24 genomic DNA samples were extracted from the holotype (HMAS 42798) by Xin-Cun Wang and Li Yi in 2010 using various methods, including the CTAB method described in Jiang and Yao [26], the Wizard® Genomic DNA Purification Kit (Promega, U.S.A.), and Chelex 100 Resin (Solarbio, China). The DNA samples were kept in ultra-low temperature freezer (below −80 °C) until use. The additional sampling of the topotype (HMAS 244431) was performed by Zhuo Du separately to avoid any possible contamination, using a DNA Extracting Kit (Cat#: NEP023-1) distributed by Beijing Dingguochangsheng Biotechnology Co. Ltd. (Beijing, China), following the instructions of the manufacturer.
2.3. Specific Primer Design, Amplification, and Sequencing
The specific primers for G. sichuanense were designed based on the sequence alignment of ITS sequences obtained from G. lucidum, G. multipileum, G. resinaceum, G. sichuanense, G. tropicum, and G. weberianum. Primer 3 v. 0.4.0 (http://bioinfo.ut.ee/primer3-0.4.0/, accessed on 15 June 2018) software was employed in combination with manual adjustments. The primers were selected and tested using Primer 5 v. 5.00 and then utilized to perform amplifications (Table 1). The suggested annealing temperature of Primer 5 v. 5.00 was tested in PCR and compared to the conventional temperature of 55 °C, and the latter was adopted throughout the experiment.
Table 1.
Primers designed in this study.
| Name | Sequence 5′-3′ | Tm (°C) | GC% | Length | Location |
|---|---|---|---|---|---|
| ITSGs1-1 | TAC TGT GGG CTT CAG ATT GC | 56.0 | 55.0 | 20 | ITS1 |
| ITSGs1-2 | GTG CCT CGC AAT CTG AAG C | 58.9 | 57.9 | 19 | ITS1 |
| ITSGs2-1 | TTA TCG GTC GGC TCC TCT TA | 57.7 | 50.0 | 20 | ITS2 |
| ITSGs2-2 | AAG AGG AGC CGA CCG ATA AC | 58.4 | 55.0 | 20 | ITS2 |
| ITSGs2-4 | AGC TGT CTT ATA AGA CGG T | 51.6 | 36.4 | 22 | ITS2 |
| ITSGs4-2 | CAG GTC ATA AAG CTG TCT TAT | 48.4 | 38.1 | 21 | ITS2 & 28s |
| ITSGs4-4 | GTC CTA CCT GAT TTG AGG TCA | 54 | 47.6 | 21 | 28s |
The primers used in the amplifications included ITS5, ITS1, and ITS4 for both ends, ITS2 and ITS3 were utilized for the internal positions of the whole length of ITS1-5.8S-ITS2 [27]. ITSGs1-1, ITSGs1-2, ITSGs2-1, ITSGs2-2, ITSGs2-4, and ITSGs4-2, are specific to G. sichuanense and ITSGs4-4 is a universal primer, all of which were designed in the present study. The sequences and locations of the newly designed primers are presented in Table 1 and Figure 1.
Figure 1.
The locations of primers in the internal transcribed spacer (ITS) region; the arrowheads represent the 3’end of each primer (primers designed in this study are in blue).
Both directed and nested PCRs with various combinations of primer pairs were used to obtain better results. PCR thermal cycling was performed in 25 μL reaction mixtures containing 1 μL of DNA template, 12.5 μL of 2 × PCR Master Mix, 1 μL of each PCR primer (10 μM), and 9.5 μL of double-distilled H2O. For the nested PCR, the second round of reactions consisted of a template at a 1:10 dilution of the first round PCR product. The PCR protocol comprised denaturation at 95 °C for 4 min, followed by 30 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 1 min, and a final cycle at 72 °C for 10 min.
Directed PCR: the following 4 primer combinations were used: ITS1/ITSGs1-2, ITSGs1-1/ITS2, ITS3/ITSGs2-2, and ITSGs2-1/ITS4.
Nested PCR: ITS5/ITS4 was followed by 6 different primer pairs as internal primers (Table 2).
Table 2.
Nested PCR primer combinations.
| Primers for the First Round PCR | Primers for the Second Round PCR |
|---|---|
| ITS5/ITS4 | ITS1/ITS4 |
| ITS1/ITSGs2-4 | |
| ITS1/ITSGs4-2 | |
| ITS1/ITSGs4-4 | |
| ITSGs1-1/ITSGs2-4 | |
| ITSGs1-1/ITSGs4-4 |
Based on the aim of obtaining a full-length ITS sequence, all the PCR products of directed PCRs and two groups of nested PCRs (internal primer sets: ITS1/ITSGs4-2 and ITSGs1-1/ITSGs4-4) were selected to create a sequence. DNA sequencing was performed using an ABI PRISM® 3730XL DNA Analyzer with a BigDye® Terminator Kit v3.1 at the Tsingke Biological Technology Company (Beijing, China)
2.4. Genome Sequencing
The first artificially cultivated Lingzhi (HMAS 25103) was performed in 1959. Due to the long time preservation, the surface was contaminated with other fungi. The DNA condition of the specimen was very poor and heavily disintegrated. All the methods mentioned above used to amplify the DNA fragments from this specimen were unsuccessful; therefore, genome sequencing was performed to obtain the ITS region sequence.
Approximately 50 mg of ground tissue from HMAS 25103 was sent to the Shanghai Biozeron Biotechnology Company (Shanghai, China). DNA extraction was performed by the company using E.Z.N.A.® Stool DNA Kits (OMEGA Bio-tek, Norcross, GA, USA), and the quality was tested on 1% agarose by Covaris M220. Paird-end (PE) libraries were developed using the TruSeq™ DNA Sample Prep Kit. Then a cBot Truseq PE Cluster Kit v3-cBot-HS was utilized to accomplish bridge PCR. Additionally, Illumina sequencing was carried out by a Truseq SBS Kit (300 cycles).
2.5. Phylogenetic Analyses
A total of 185 DNA sequences generated by each forward and reverse primer were used to obtain consensus sequences using Seqman v.7.1.0 in the DNASTAR laser gene core suite software (DNASTAR, Madison, WI, USA). The single gene ITS sequences were initially aligned with Clustal W and implemented in MEGA 6 and improved by MAFFT v.7 [28,29]. Tomophagus colossus (Fr.) Murrill was selected as the outgroup taxon for all analyses [18,21]. The aligned matrices used for the phylogenetic analyses were maintained in TreeBASE (www.treebase.org; accession number: 30118).
RAxML-HPC BlackBox v.8.2.10 was performed to construct a maximum likelihood (ML) tree, employing a GTRGAMMA substitution model with 1000 bootstrap replicates [30]. The branch support of ML analyses was evaluated using bootstrapping (BS) method for 1000 replicates. Bayesian inference (BI) was performed using a Markov Chain Monte Carlo (MCMC) algorithm to construct the topology of the tree [31]. Two MCMC chains were run from random trees for 10,000,000 generations and stopped when the average standard deviation of the split frequencies fell below 0.01. From each 1000 generations, the trees were saved. The first 25 % of trees were discarded as the burn-in phase of each analysis, and the posterior probabilities (BPP) were calculated to assess the remaining trees [32]. Phylograms were presented using Figtree v. 1.3.1 and processed by Adobe Illustrator CS v.5. Reference sequences were selected based on the type materials available in GenBank and published papers. The sequence data of the present study were deposited in GenBank, and the GenBank accession numbers of all accessions included in the phylogenetic analyses are listed in Table 3.
Table 3.
Strains and GenBank accession numbers used in this study.
| Species | Voucher/Strain | Origin | Accession Number (ITS) |
|---|---|---|---|
| Ganoderma adspersum (Schulzer) Donk | SFC 20141001-16 | Korea | KY364251 |
| G. adspersum | SFC 20141001-22 | Korea | KY364252 |
| G. angustisporum J.H. Xing, B.K. Cui & Y.C. Dai | Cui 13817 (holotype) | China | MG279170 |
| G. angustisporum | Cui 14578 | China | MG279171 |
| G. applanatum (Pers.) Pat. | SFC 20150930-02 | Korea | KY364258 |
| G. applanatum | XC 14080601 | China | MK345426 |
| G. aridicola J.H. Xing & B.K. Cui | Dai 12588 (holotype) | South Africa | KU572491 |
| G. australe (Fr.) Pat. | GDGM 25344 | China | JX195198 |
| G. australe | GACP 14061914 | China | MK345428 |
| G. austroafricanum M.P.A. Coetzee, M.J. Wingf., Marinc. & Blanchette | CBS 138724 (ex-type) | South Africa | KM507324 |
| G. bambusicola Sheng H. Wu, C.L. Chern & T. Hatt. | Wu 1207-151 (holotype) | China | MN957781 |
| G. bambusicola | Wu 1207-153 (paratype) | China | MN957783 |
| G. boninense Pat. | WD 2028 | Japan | KJ143905 |
| G. boninense | WD 2085 | Japan | KJ143906 |
| G. calidophilum J.D. Zhao, L.W. Hsu & X.Q. Zhang | MFLU 19-2174 | China | MN398337 |
| G. calidophilum | H36 | China | MW750241 |
| G. carnosum Pat. | JV 8709/8 | Czech R | KU572493 |
| G. carnosum | MJ 21/08 | Czech R | KU572492 |
| G. carocalcareum Douanla-Meli | DMC 322 (holotype) | Cameroon | EU089969 |
| G. carocalcareum | DMC 513 | Cameroon | EU089970 |
| G. casuarinicola J.H. Xing, B.K. Cui & Y.C. Dai | Dai 16336 (holotype) | China | MG279173 |
| G. casuarinicola | HKAS 104639 | Thailand | MK817650 |
| G. curtisii (Berk.) Murrill | CBS 100131 | USA | JQ781848 |
| G. curtisii | CBS 100132 | USA | JQ781849 |
| G. destructans M.P.A. Coetzee, Marinc. & M.J.Wingf. | CMW 43670 (ex-type) | South Africa | KR183856 |
| G. destructans | CMW 43671 | South Africa | KR183857 |
| G. dianzhongense J. He, H.Y. Su & S.H. Li | L4331 (holotype) | China | MW750237 |
| G. dianzhongense | L4230 | China | MW750236 |
| G. dunense Tchotet, Rajchenb. & Jol. Roux | CMW 42157 (holotype) | South Africa | MG020255 |
| G. dunense | CMW 42150 | South Africa | MG020249 |
| G. ecuadoriense A. Salazar, C.W. Barnes & Ordoñez | ASL 799 (holotype) | Ecuador | KU128524 |
| G. ecuadoriense | PMC 126 | Ecuador | KU128525 |
| G. eickeri Tchotet, M.P.A. Coetzee, Rajchenb. & Jol. Roux | CMW 49692 (holotype) | South Africa | MH571690 |
| G. eickeri | CMW 50325 | South Africa | MH571689 |
| G. ellipsoideum Hapuar., T.C. Wen & K.D. Hyde | GACP 1408966 (holotype) | China | MH106867 |
| G. ellipsoideum | GACP 14081215 (paratype) | China | MH106886 |
| G. enigmaticum M.P.A. Coetzee, Marinc. & M.J.Wingf. | CMW 43669 (ex-type) | South Africa | KR183855 |
| G. enigmaticum | Dai 15970 | South Africa | KU572486 |
| G. esculentum J. He & S.H. Li | L4935 (holotype) | China | MW750242 |
| G. esculentum | L4946 | China | MW750243 |
| G. flexipes Pat. | VT 17102301 | Vietnam | MK345430 |
| G. flexipes | Wei 5200 | China | JN383978 |
| G. gibbosum (Cooke) Pat. | SFC 20150630-23 | Korea | KY364264 |
| G. gibbosum | GZ 14070501 | China | MK345432 |
| G. heohnelianum Bres. | Yuan 6337 | China | MG279160 |
| G. heohnelianum | Dai 11995 | China | KU219988 |
| G. hochiminhense Karunarathna, Mortimer, Huyen & Luangharn | MFLU 19-2224 (holotype) | Vietnam | MN398324 |
| G. hochiminhense | MFLU 19-2225 (paratype) | Vietnam | MN396662 |
| G. knysnamense Tchotet, M.P.A. Coetzee, Rajchenb. & Jol. Roux | CMW 47755 (ex-type) | South Africa | MH571681 |
| G. knysnamense | CMW 47756 | South Africa | MH571684 |
| G. leucocontextum T.H. Li, W.Q. Deng, Sheng H. Wu, Dong M. Wang & H.P. Hu | GDGM 40200 (holotype) | China | KF011548 |
| G. leucocontextum | GDGM 44303(paratype) | China | KJ027607 |
| G. lingzhi Sheng H. Wu, Y. Cao & Y.C. Dai | Wu 1006-38 (holotype) | China | JQ781858 |
| G. lingzhi | Cui 4018 | China | JQ781856 |
| G. lingzhi | Cui 10165 | China | JQ781857 |
| G. lingzhi | Cui 9164 | China | JQ781859 |
| G. lingzhi | Dai 10631 | China | JQ781860 |
| G. lingzhi | Dai 12438 | China | JQ781861 |
| G. lingzhi | Dai 12479 | China | JQ781864 |
| G. lingzhi | IFP 01021 | China | JQ781865 |
| G. lingzhi | Dai 12443 | China | JQ781866 |
| G. lingzhi | Dai 12374 | China | JQ781867 |
| G. lingzhi | Dai 3583 | China | JQ781868 |
| G. lingzhi | Dai 12441 | China | JQ781869 |
| G. lingzhi | Dai 12426 | China | JQ781870 |
| G. lingzhi | Dai 12425 | China | JQ781871 |
| G. lingzhi | Dai 12447 | China | JQ781872 |
| G. lingzhi | Dai 12449 | China | JQ781873 |
| G. lingzhi | Cui 6982 | China | JQ781862 |
| G. lingzhi | Dai 12573 | China | JQ781855 |
| G. lingzhi | Li245 | China | JQ781863 |
| G. lingzhi | LPDR 18011910 | Laos | MK345437 |
| G. lingzhi | LPDR 18011911 | Laos | MK345438 |
| G. lobatum (Cooke) G.F. Atk. | JV1212/10J | USA | KF605676 |
| G. lobatum | JV0409/13J | USA | KF605675 |
| G. lucidum (Curtis) P. Karst. | HMAS 86597 | UK | AY884176 |
| G. lucidum | G1T 099 | Italy | AM269773 |
| G. martinicense Welti & Courtec | LIP SW-Mart08-44 | France | KF963257 |
| G. martinicense | LIP SW-Mart08-55 | France | KF963256 |
| G. mbrekobenum E.C. Otto, Blanchette, Held, C.W. Barnes & Obodai | UMN7-3 GHA (holotype) | Ghana | KX000896 |
| G. mbrekobenum | UMN7-4 GHA (paratype) | Ghana | KX000898 |
| G. mexicanum Pat. | MUCL 49453 | Martinique | MK531811 |
| G. mexicanum | MUCL 55832 | Martinique | MK531815 |
| G. mizoramense Zothanz., Blanchette, Held & C.W. Barnes | UMN-MZ4 (holotype) | India | KY643750 |
| G. mizoramense | UMN-MZ5 | India | KY643751 |
| G. multipileum Ding Hou | CWN 04670 | China | KJ143913 |
| G. multipileum | Dai 9447 | China | KJ143914 |
| G. multiplicatum (Mont.) Pat. | Dai 13122 | China | KU572488 |
| G. multiplicatum | MN 14091108 | Myanmar | MK345440 |
| G. mutabile Y. Cao & H.S. Yuan | Yuan 2289 (holotype) | China | JN383977 |
| G. mutabile | CLZhao 982 | China | MG231527 |
| G. myanmarense Karunarathna, Mortimer & Luangharn | MFLU 19-2167 ((holotype) | Myanmar | MN396330 |
| G. myanmarense | MFLU 19-2211 (paratype) | Myanmar | MN396329 |
| G. nasalanense Hapuar., Pheng., & K.D. Hyde. | LPDR 17060211 (holotype) | Laos | MK345441 |
| G. nasalanense | LPDR 17060212 (paratype) | Laos | MK345442 |
| G. neojaponicum Imazeki | FFPRI WD-1285 | Japan | MN957784 |
| G. neojaponicum | FFPRI WD-1532 | Japan | MN957785 |
| G. orbiforme (Fr.) Ryvarden | JFL 14081202 | China | MK345445 |
| G. orbiforme | GACP 14061414 | Laos | MK345446 |
| G. oregonense Murrill | CBS 265.88 | USA | JQ781875 |
| G. oregonense | CBS 266.88 | USA | JQ781876 |
| G. parvulum Murrill | MUCL 47096 | Cuba | MK554783 |
| G. parvulum | MUCL 52655 | French Guiana | MK554770 |
| G. philippii (Bres. & Henn. ex Sacc.) Bres. | E7098 | Malaysia | AJ536662 |
| G. philippii | E7425 | Malaysia | AJ608713 |
| G. podocarpense J.A. Flores, C.W. Barnes & Ordoñez | QCAM 6422 (holotype) | Ecuador | MF796661 |
| G. resinaceum Boud. | BCRC 36147 | Netherlands | KJ143916 |
| G. resinaceum | BR 4150 | France | KJ143915 |
| G. ryvardenii Tonjock & Mih | HKAS 58053 (holotype) | Cameroon | HM138671 |
| G. ryvardenii | GanoTK32 | Cameroon | JN105698 |
| G. sandunense Hapuar., T.C. Wen & K.D. Hyde. | SA 18012501 (holotype) | China | MK345450 |
| G. sandunense | SA 18012502 | China | MK345451 |
| G. sessile Murrill | JV 1209/27 | USA | KF605630 |
| G. sessile | 165MO | USA | MG654312 |
| G. shandongense J.D. Zhao & L.W. Xu | Dai 15785 | China | MG279190 |
| G. shandongense | Dai 15787 | China | MG279191 |
| G. shanxiense L. Fan & H. Liu | BJTC FM423 (holotype) | China | MK764268 |
| G. shanxiense | HSA 539 (paratype) | China | MK764269 |
| G. sichuanense J.D. Zhao & X.Q. Zhang | HMAS 42798-2 (holotype) | China | OP805615 |
| G. sichuanense | HMAS 42798-3 (holotype) | China | OP805616 |
| G. sichuanense | HMAS 42798-4 (holotype) | China | OP805617 |
| G. sichuanense | HMAS 42798-5 (holotype) | China | OP805618 |
| G. sichuanense | HMAS 42798-6 (holotype) | China | OP805619 |
| G. sichuanense | HMAS 42798-8 (holotype) | China | OP805620 |
| G. sichuanense | HMAS 42798-19 (holotype) | China | OP805621 |
| G. sichuanense | HMAS 42798-23 (holotype) | China | OP805622 |
| G. sichuanense | HMAS 42798-d (holotype) | China | OP805623 |
| G. sichuanense | HMAS 244431-1 | China | OP805624 |
| G. sichuanense | HMAS 244431-2 | China | OP805625 |
| G. sichuanense | HMAS 244431-3 | China | OP805626 |
| G. sichuanense | HMAS 244431-4 | China | OP805627 |
| G. sichuanense | HMAS 25103 | China | OP805628 |
| G. sichuanense | HMAS 252081 (epitype) | China | KC662402 |
| G. sichuanense | HMAS 25066 | China | JN197275 |
| G. sichuanense | HMAS 25067 | China | JN197276 |
| G. sichuanense | HMAS 42605 | China | JN197277 |
| G. sichuanense | HMAS 42745 | China | JN197278 |
| G. sichuanense | HMAS 47337 | China | JN197279 |
| G. sichuanense | HMAS 59482 | China | JN197280 |
| G. sichuanense | HMAS 60537 | China | JN197281 |
| G. sichuanense | HMAS 62503 | China | JF915405 |
| G. sichuanense | HMAS 76566 | China | JF915406 |
| G. sichuanense | HMAS 99391 | China | JF915407 |
| G. sichuanense | HMAS 130131 | China | JF915408 |
| G. sichuanense | HMAS 240175 | China | JF915393 |
| G. sichuanense | HMAS 240176 | China | JF915394 |
| G. sichuanense | HMAS 240177 | China | JF915395 |
| G. sichuanense | HMAS 240178 | China | JF915396 |
| G. sichuanense | HMAS 240187 | China | JF915397 |
| G. sichuanense | HMAS 250672 | China | JF915398 |
| G. sichuanense | HMAS 250677 | China | JF915399 |
| G. sichuanense | HMAS 251145 | China | JF915400 |
| G. sichuanense | HMAS 251146 | China | JF915401 |
| G. sichuanense | HMAS 251147 | China | JF915402 |
| G. sichuanense | HMAS 251148 | China | JF915403 |
| G. sichuanense | HMAS130128 | China | JF915404 |
| G. sichuanense | CGMCC 5.75 | China | JN197282 |
| G. sichuanense | CGMCC 5.425 | China | JN197283 |
| G. sichuanense | CGMCC 5.533 | China | JN197284 |
| G. sichuanense | Cui 7691 | China | JQ781878 |
| G. sichuanense | HMAS 42798 (holotype) | China | JQ781877 |
| G. sinense J.D. Zhao, L.W. Hsu & X.Q. Zhang | SA 17092559 | China | MK345452 |
| G. sinense | SA 17092539 | China | MK345453 |
| G. steyaertanum B.J. Sm. & Sivasith. | MEL:2382783 | Australia | KP012964 |
| G. steyaertanum | 6-WN-20BL-B | Indonesia | KJ654462 |
| G. subresinosum (Murrill) C.J. Humphrey | 5-D-3-D-26 | Indonesia | KJ654467 |
| G. subresinosum | LPDR 18011907 | Laos | MK345455 |
| G. thailandicum Luangharn, P.E. Mortimer, Karun. & J.C. Xu | HKAS 104640 (holotype) | Thailand | MK848681 |
| G. thailandicum | HKAS 104641 (paratype) | Thailand | MK848682 |
| G. tropicum (Jungh.) Bres. | Dai 9724 | China | JQ781879 |
| G. tropicum | TH 15081610 | Thailand | MK345456 |
| G. tsugae Murrill | Dai 12760 | USA | KJ143920 |
| G. tsugae | AFTOL-ID 771 | -- | DQ206985 |
| G. tuberculosum Murrill | GVL-21 | Mexico | MT232639 |
| G. tuberculosum | GVL-40 | Mexico | MT232634 |
| G. weberianum (Bres. & Henn. ex Sacc.) Steyaert | CBS 219.36 | Philippines | JQ520219 |
| G. weberianum | CBS 128581 | Taiwan, China | MK603805 |
| G. wiiroense E.C. Otto, Blanchette, C.W. Barnes &Held | UMN-20-GHA (paratype) | Ghana | KT952361 |
| G. wiiroense | UMN-21-GHA | Ghana | KT952363 |
| G. williamsianum Murrill | Dai 16809 | China | MG279183 |
| G. williamsianum | Wei 5032 | China | KU219994 |
| G. zonatum Murrill | FL-02 | USA | KJ143921 |
| G. zonatum | FL-03 | USA | KJ143922 |
| Tomophagus colossus (Fr.) Murrill | CBS 216.36 | Philippines | Z37071&Z37091 |
| T.s colossus | CGMCC 5.763 | Philippines | JQ081068 |
Note: --, not applicable; sequences obtained in the present study are in black and bold.
3. Results
3.1. Results of PCR, Sequencing Using Different Primers
Both directed and nested PCRs were adopted for 24 DNA samples. The results of various combinations of primer pairs are presented in Table 4.
Table 4.
The results of PCR amplification.
| Method | Primer Pair | Results | Product Size (bp) |
|---|---|---|---|
| Directed PCR | ITS5/ITS4 | * | 654 |
| ITS1/ITS4 | * | 633 | |
| ITS1/ITS2 | * | 266 | |
| ITS3/ITS4 | * | 367 | |
| ITS1/ITSGs1-2 | + | 116 | |
| ITSGs1-1/ITS2 | + | 157 | |
| ITS3/ITSGs2-2 | + | 180 | |
| ITSGs2-1/ITS4 | + | 176 | |
| Nested PCR | First round PCR | ||
| ITS5/ITS4 | * | 654 | |
| Second round PCR | |||
| ITS1/ITS4 | * | 633 | |
| ITS1/ITSGs4-4 | * | 597 | |
| ITS1/ITSGs2-4 | + | 567 | |
| ITS1/ITSGs4-2 | + | 576 | |
| ITSGs1-1/ITSGs2-4 | + | 458 | |
| ITSGs1-1/ITSGs4-4 | + | 488 |
Note: + specific PCR product; * nonspecific PCR product.
Throughout the directed PCR procedure, using published primer pair ITS5/ITS4, only sample 1 was successfully sequenced, but it proved to be Aspergillus sp. For ITS1/ITS4, the sequencing result for sample 1 was the same as when using primer pair ITS5/ITS4, and sample 4 was Gymnopus sp. When using the ITS1/ITS2, samples 1 and 22 were all Aspergillus sp. The ITS3/ITS4 results were the same as using the primer pair ITS1/ITS4.
When using specific primer pairs designed in this study for G. sichuanense (ITS1/ITSGs1-2, ITSGs1-1/ITS2, ITS3/ITSGs2-2, and ITSGs2-1/ITS4) from 24 DNA samples, we obtained 2, 6, 3, and 1 sequences respectively, 13 short fragments in total, which can assemble into one complete G. sichuanense sequences (HMAS 42798-d, Gene Bank number OP805623).
In the nested PCR experiment, ITS5/ITS4 was selected as the external primer pair, when using ITS1/ITS4 as the internal primer pair, the PCR amplification resulted in the presence of polymorphic bands. Only eight samples produced sequencing results (Tsingke Biological Technology). The results of the taxonomic groups belong to Aspergillus, Astraeus, Cercospora, Cladosporium, Cryptococcus, and Pleosporales. When using the ITS1/ITSGs4-4 primer pair as the internal primers, the agarose electrophoresis results were the same.
As for ITS1/ITSGs2-4, ITS1/ITSGs4-2, ITSGs1-1/ITSGs2-4, and ITSGs1-1/ITSGs4-4, the four electrophoretograms appeared to be consistent, each primer combination appeared as eight clear single target bands from the eight same samples (Figure 2). We selected ITS1/ITSGs4-2 (product size: 576 bp) and ITSGs1-1/ITSGs4-4 (product: size 488 bp) to perform the sequencing (Tsing Ke Biological Technology). We obtained 8 complete G. sichuanense sequences from each primer combination, 16 sequences in total were successfully sequenced.
Figure 2.
Gel electrophoresis image.
3.2. Results of Genome Sequencing and Assembly
Genome sequencing produced 7,230,782 raw reads (1,084,617,300 bp) for HMAS 25103, resulting in 4,121,318 clean reads (612,283,701 bp) following filtration. Filtration refers to removing adapter sequences, low-quality reads, and reads higher than a certain proportion (10%) of N (ambiguous sites). Cleaned reads were assembled using MegaHit [33]. The assemblies contained 15,034 contigs (N50 = 6656 bp), the lengths of which were 31,314,762. The ITS sequence alignments included 61 species of Ganoderma were used as queries to search the possible target sequences obtained from the genome assemblies. A sole 556 bp nuclear ribosomal DNA (nrDNA) fragment was obtained, which contained a partial 5.8S ribosomal RNA gene, complete ITS2, and partial large subunit ribosomal RNA gene sequence. Additionally, the sequence was submitted to GenBank (Gene Bank number OP805628).
3.3. Results of Phylogenetic Analyses
The ITS dataset from 185 strains was analyzed to infer the interspecific relationships within Ganoderma. The sequences were clustered in 62 groups representing 61 known species of Ganoderma with 49 type isolates and 1 outgroup taxon Tomophagus colossus. The topologies resulting from the ML and BI analyses of the concatenated dataset were congruent. A total of 14 sequences obtained from the present study were formed in 1 individual clade (clade A) representing the species G. sichuanese (Figure 3).
Figure 3.
Phylogram of Ganoderma resulting from a maximum likelihood analysis based on the ITS gene. Numbers above the branches indicate ML bootstrap values (left, ML BS ≥ 75%) and Bayesian Posterior Probabilities (right, BPP ≥ 0.90). The tree is rooted with Tomophagus colossus. Sequences from the present study are marked in blue; type materials are bold.
3.4. Taxonomy
Ganoderma sichuanense J.D. Zhao & X.Q. Zhang, Acta Mycol Sin. 2(3): 159 (1983)
Syn. Ganoderma lingzhi S.H. Wu, Y. Cao & Y.C. Dai, Fungal Divers. 56 (1): 54 (2012)
Materials examined—CHINA. Sichuan Province, Dukou (Panzhihua) City, Panzhihua Steel Plant, on the rotten wood of a broad-leaved tree, 1976, C.M. Li, 116 (Holotype HMAS 42798); CHINA. Panzhihua City, Renhe District, Zhongba Township, Xuefang Village, 26°25′11.43″ N, 101°40′17.54″ E, alt. 1458 m, purchased from a villager who gathered the specimens from mountainous areas surrounding the village, 14 October 2012, Y.J. Yao, B. Wang & X.C. Wang, 019 (HMAS 244431); CHINA. Beijing City, cultivated by Zhuang Deng, June 1959 (HMAS 25103).
Notes: A total of 43 sequences of G. sichuanense were used in this study and diverged into two different evolutionary branches. Except for two sequences (JQ781877 and JQ781878) grouped with G. weberianum, other sequences, including nine sequences obtained from the holotype of G. sichuanense (HMMAS 42798) in this study, were all gathered in clade A. Additionally, all sequences of the name “G. lingzhi” were also mixed in clade A. It is worth noting that clade A included many sequences from the type or pivotal materials of the two species mentioned above, as follows: (1) the sequence of G. lingzhi (Wu 1006-38) holotype and all other G. lingzhi sequences used in the paper of Cao et al. [20]; (2) nine sequences of the G. sichuanense (HMAS 42798) holotype obtained using two different independent PCR methods; (3) the sequence obtained from G. sichuanense (HMAS 252081) epitype [21] and four sequences obtained from different fruit bodies of topotype (HMAS 244431); (4) the sequence of first cultivated Lingzhi fruit bodies (HMAS 25103) in China. Our research suggests that clade A should be the authentic G. sichuanense. The new species G. lingzhi was proposed on the premise that ITS sequence JQ781877 was unquestionably obtained from the holotype of G. sichuanense [20], but the sequence JQ781877 was obtained only once [20,34]. The reasons why we insisted that the sequences of the holotype presented in this research are reliable are (1) the DNA samples of the G. sichuanense holotype were extracted using different methods, the CTAB method, the Wizard® Genomic DNA Purification Kit (Promega, U.S.A.), and Chelex 100 Resin (Solarbio, China); (2) by directed and nested PCRs, the sequences obtained from different DNA samples from the G. sichuanense (HMAS 42798) holotype were clustered together in the phylogenetic analysis; (3) the first cultivated Lingzhi (HMAS 25103), which represents the widely cultivated Chinese Ganoderma species, was also clustered in the evolutionary branch of G. sichuanense.
Complying with the International Code of Nomenclature for algae, fungi, and plants (Art.11.3), the earliest legitimate name of a taxon should be given priority [35]. Ganoderma sichuanense [19] has more preference than G. lingzhi [20]. The current results treat G. lingzhi as a later synonym of G. sichuanense.
4. Discussion
Although gene conversion [36] and unequal cross-over [37] are two of the most commonly proposed concerted evolution events [38], numerous studies have revealed that ITS is a multicopy gene and does not subscribe to evolution perfectly. Intra-strain and intra-species variations exist in several fungal taxa, such as Fusarium [39], Laetiporus [40], Ophiocordyceps [41], Scutellospora [42], Xanthophyllomyces [43], and also Ganoderma [44]. The results of our phylogenetic analysis demonstrated the ITS sequence heterogeneity within the holotype of G. sichuanense (HMAS 42798). This is the first report of ITS heterogeneity for G. sichuanense; heterogeneity occurs in three parts (ITS1, ITS2, and 5.8S) of the ITS region. This might explain why small divisions exist in the whole, large clade of G. sichuanense (Clade A). For nested PCR, the results are identical when using different primer pairs as second-round primer sets (ITS1/ITSGs4-2 and ITSGs1-1/ITSGs4-4). Therefore, we speculate that this phenomenon might be the nature of the species G. sichuanense.
In the specimen box of the holotype, two fruit bodies existed (Figure 4). We can confirm that the sequence OP805618 (sample 5, HMAS 42798-5) was obtained from the big fruit body, and the sequence OP805619 (sample 6, HMAS 42798-6) was obtained from the small one. For the other DNA samples from the holotype, depending on the information on the lid of the DNA sample container and the lab notebook of the operator, we were unable to verify which fruit body was taken for (the DNA samples were extracted in 2010), but samples 5 and 6 ensured that all the fruit bodies of the holotype obtained ITS sequence successfully.
Figure 4.
The holotype of Ganoderma sichuanense (HMAS 42798).
We provided ITS sequences to perform a phylogenetic study based on the root of the long-standing discussion and the obtainable experimental results. The aim of the research was to resolve the problem of the scientific binomial for the widely cultivated Lingzhi in China, the discussion of which has centered around the controversial ITS sequence JQ781877 since 2012 [20]. We designed seven primers, using different PCR methods to successfully obtain repeatable and reliable ITS sequences from the holotype. Additionally, in our experiment, the attempts to amplify the other gene sequences from the holotype failed due to the largely disintegrated DNA. In some research papers concerning Ganoderma, even though other gene loci were applied, for the specimen HMAS 42798, only ITS sequence JQ781877 was available [20,22,45]. Therefore, based on the fact that the crux of the dispute was the key ITS sequence, and no other gene sequences of the holotype were available, the ITS phylogenic tree presented in this study can break the present deadlock. Though the ITS gene can perform species division in the genus Ganoderma [20,21] and is the most abundant gene region in Ganodermataceae [45], depending on a single gene does not address all the problems in the classification of Ganoderma. For the complex groups in Ganoderma or the higher rank classification of Ganodermataceae, multigene phylogenetic analyses are essential [22,45,46,47,48,49,50,51,52].
For the old specimens and DNA samples used in this research, any preserved DNA was present only in small amounts and in various states of degradation. Therefore, we explored various approaches for DNA amplification from the important, old samples, including designing new primers for directed and nested PCRs and genome sequencing. All the methods mentioned in this paper may also be applied to type material of other important species.
Author Contributions
Conceptualization, Y.-J.Y. and Z.D.; methodology, Y.-J.Y., Z.D., K.W. and Y.L.; software, Z.D.; validation, Z.D., Y.-J.Y., Y.L., X.-C.W. and K.W.; formal analysis, Z.D.; resources, Y.-J.Y., X.-C.W. and Y.L.; data curation, Z.D. and Y.L.; writing—original draft preparation, Z.D.; writing—review and editing, Z.D., Y.-J.Y. and X.-C.W.; visualization, Z.D.; supervision, Y.-J.Y.; project administration, Y.-J.Y.; funding acquisition, Y.-J.Y. and K.W. All authors have read and agreed to the published version of the manuscript.
Institutional Review Board Statement
Not applicable for studies involving humans or animals.
Informed Consent Statement
Not applicable for studies involving humans.
Data Availability Statement
The sequences in the present study were submitted to the NCBI website (https://www.ncbi.nlm.nih.gov/), and the accession numbers are listed in Table 3.
Conflicts of Interest
The authors declare no conflict of interest.
Funding Statement
This research was supported by the Research on the key technology of exploitation and efficient processing of edible mushroom resources of the Ministry of Science and Technology (2018YFD0400201) and Biological Resources Programme of the Chinese Academy of Sciences (KFJ-BRP-017-49).
Footnotes
Disclaimer/Publisher’s Note: The statements, opinions and data contained in all publications are solely those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). MDPI and/or the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, methods, instructions or products referred to in the content.
References
- 1.Karsten P.A. Enumeratio boletinearum et polyporearum fennicarum, systemate novo dispositarum. Rev. Mycol. 1881;3:16–19. [Google Scholar]
- 2.Curtis W. Flora Londinensis: Or Plates and Descriptions of Such Plants as Grow Wild in the Environs of London. Curtis, W.; London, UK: 1781. p. 530. [Google Scholar]
- 3.Yuan Y., Wang Y.J., Sun G.P., Wang Y.R., Cao L.J., Shen Y.M., Yuan B., Han D., Huang L.Q. Archaeological evidence suggests earlier use of Ganoderma in Neolithic China. Chin. Sci. Bull. 2018;63:1180–1188. (In Chinese) [Google Scholar]
- 4.Pegler D.N. Useful fungi of the world: The Lingzhi—The mushroom of immortality. Mycologist. 2002;16:100–101. doi: 10.1017/S0269915X0200304X. [DOI] [Google Scholar]
- 5.Tai F.L. Sylloge Fungorum Sinicorum. Science Press; Beijing, China: 1979. p. 1527. [Google Scholar]
- 6.Pegler D.N., Yao Y.J. Oriental species of Ganoderma section Ganoderma. In: Wasser S.P., editor. Botany and Mycology for the Next Millenium: Collection of Scientific Articles Devoted to the 70th Anniversary of Academician Sytnik, K.M. National Academy of Sciences of Ukraine; Kiev, Ukraine: 1996. pp. 336–347. [Google Scholar]
- 7.Moncalvo J.M., Wang H.F., Hseu R.S. Gene phylogeny of the Ganoderma lucidum complex based on ribosomal DNA sequences. Comparison with traditional taxonomic characters. Mycol. Res. 1995;99:1489–1499. doi: 10.1016/S0953-7562(09)80798-3. [DOI] [Google Scholar]
- 8.Moncalvo J.M., Wang H.F., Wang H.H., Hseu R.S. The use of ribosomal DNA sequence data for species identification and phylogeny in the Ganodermataceae; Proceedings of the Contributed Symposium 59A, B, 5th International Mycological Congress; Vancouver, BC, Canada. 14–21 August 1994. [Google Scholar]
- 9.Smith B.J., Sivasithamparam K. Internal transcribed spacer ribosomal DNA sequence of five species of Ganoderma from Australia. Mycol. Res. 2000;104:943–951. doi: 10.1017/S0953756200002458. [DOI] [Google Scholar]
- 10.Hong S.G., Jung H.S. Phylogenetic analysis of Ganoderma based on nearly complete mitochondrial small-subunit ribosomal DNA sequences. Mycologia. 2004;96:742–755. doi: 10.1080/15572536.2005.11832922. [DOI] [PubMed] [Google Scholar]
- 11.Wang D.M., Wu S.H., Su C.H., Peng J.T., Shih Y.H., Chen L.Z. Ganoderma multipileum, the correct name for ‘G. lucidum’ in tropical Asia. Bot. Stud. 2009;50:451–458. [Google Scholar]
- 12.Yu Y.N., Shen M.Z. The history of ling-zhi (Ganoderma spp.) cultivation; Proceedings of the 3rd National Congress of Mycological Society of China and the 6th National Symposium on Mycology; Beijing, China. 22–25 September 2003. [Google Scholar]
- 13.Jong S.C., Birmingham J.M. Medicinal benefits of the mushroom Ganoderma. Adv. Appl. Microbiol. 1992;37:101–134. doi: 10.1016/s0065-2164(08)70253-3. [DOI] [PubMed] [Google Scholar]
- 14.Wasser S.P., Weis A.L. Medicinal properties of substances occurring in higher basidiomycetes mushrooms: Current perspectives (Review) Int. J. Med. Mushrooms. 1999;1:31–62. doi: 10.1615/IntJMedMushrooms.v1.i1.30. [DOI] [PubMed] [Google Scholar]
- 15.Tan B.K.H., Vanitha J. Immunomodulatory and antimicrobial effects of some traditional Chinese medicinal herbs: A review. Curr. Med. Chem. 2004;11:1423–1430. doi: 10.2174/0929867043365161. [DOI] [PubMed] [Google Scholar]
- 16.Paterson R.R.M. Ganoderma—A therapeutic fungal biofactory. Phytochemistry. 2006;67:1985–2001. doi: 10.1016/j.phytochem.2006.07.004. [DOI] [PubMed] [Google Scholar]
- 17.Rathore H., Prasad S., Sharma S. Mushroom nutraceuticals for improved nutrition and better human health: A review. PharmaNutrition. 2017;5:35–46. doi: 10.1016/j.phanu.2017.02.001. [DOI] [Google Scholar]
- 18.Wang X.C., Xi R.J., Li Y., Wang D.M., Yao Y.J. The species identity of the widely cultivated Ganoderma, ‘G. lucidum’ (Ling-zhi), in China. PLoS ONE. 2012;7:e40857. doi: 10.1371/journal.pone.0040857. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 19.Zhao J.D., Xu L.W., Zhang X.Q. Taxonomic studies on the family Ganodermataceae of China II. Acta Mycol. Sin. 1983;2:159–167. (In Chinese) [Google Scholar]
- 20.Cao Y., Wu S.H., Dai Y.C. Species clarifcation of the prize medicinal Ganoderma mushroom “lingzhi”. Fungal. Divers. 2012;56:49–62. doi: 10.1007/s13225-012-0178-5. [DOI] [Google Scholar]
- 21.Yao Y.J., Wang X.C., Wang B. Epitypifcation of Ganoderma sichuanense J.D. Zhao & X.Q. Zhang (Ganodermataceae) Taxon. 2013;62:1025–1031. [Google Scholar]
- 22.Zhou L.W., Cao Y., Wu S.H., Vlasák J., Li D.E., Li M.J., Dai Y.C. Global diversity of the Ganoderma lucidum complex (Ganodermataceae, Polyporales) inferred from morphology and multilocus phylogeny. Phytochemistry. 2015;114:7–15. doi: 10.1016/j.phytochem.2014.09.023. [DOI] [PubMed] [Google Scholar]
- 23.Dai Y.C., Zhou L.W., Hattori T., Cao Y., Stalpers J.A., Ryvarden L., Buchanan P., Oberwinkler F., Hallenberg N., Liu P.G., et al. Ganoderma lingzhi (Polyporales, Basidiomycota): The scientifc binomial for the widely cultivated medicinal fungus lingzhi. Mycol. Prog. 2017;16:1051–1055. doi: 10.1007/s11557-017-1347-4. [DOI] [Google Scholar]
- 24.Cui B.K., Wu S.H. The scientific name of the widely cultivated Ganoderma species. Mycosystema. 2020;39:7–12. (In Chinese) [Google Scholar]
- 25.Yao Y.J., Li Y., Du Z., Wang K., Wang X.C., Spooner B.M. On the typification of Ganoderma sichuanense (Agaricomycetes)the widely cultivated lingzhi medicinal mushroom. Int. J. Med. Mushrooms. 2020;22:45–54. doi: 10.1615/IntJMedMushrooms.2019033189. [DOI] [PubMed] [Google Scholar]
- 26.Jiang Y., Yao Y.J. ITS sequence analysis and ascomatal development of Pseudogymnoascus roseus. Mycotaxon. 2005;94:55–73. [Google Scholar]
- 27.White T.J., Bruns T., Lee S., Taylor J. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. PCR Protoc. Guide. Methods. Appl. 1990;18:315–322. [Google Scholar]
- 28.Katoh K., Standley D.M. MAFFT multiple sequence alignment software version 7: Improvements in performance and usability. Mol. Biol. Evol. 2013;30:772–780. doi: 10.1093/molbev/mst010. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 29.Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol. Biol. Evol. 2013;30:2725–2729. doi: 10.1093/molbev/mst197. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 30.Stamatakis A. RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014;30:1312–1313. doi: 10.1093/bioinformatics/btu033. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 31.Ronquist F., Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003;19:1572–1574. doi: 10.1093/bioinformatics/btg180. [DOI] [PubMed] [Google Scholar]
- 32.Rannala B., Yang Z. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference. J. Mol. Evol. 1996;43:304–311. doi: 10.1007/BF02338839. [DOI] [PubMed] [Google Scholar]
- 33.Li D.H., Liu C.M., Luo R.B., Sadakane K., Lam T.W. MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–1676. doi: 10.1093/bioinformatics/btv033. [DOI] [PubMed] [Google Scholar]
- 34.Yang Z.L., Feng B. What is the Chinese “lingzhi”?—A taxonomic mini-review. Mycology. 2013;4:1–4. doi: 10.1080/21501203.2013.774299. [DOI] [Google Scholar]
- 35.Turland N.J., Wiersema J.H., Barrie F.R., Greuter W., Hawksworth D.L., Herendeen P.S., Knapp S., Kusber W.H., Li D.Z., Marhold K., et al. International Code of Nomenclature for Algae, Fungi, and Plants (Shenzhen Code); Proceedings of the 19th International Botanical Congress; Shenzhen, China. 23–29 July 2017. [Google Scholar]
- 36.Hillis D.M., Moritz C., Porter C.A., Baker R.J. Evidence for biased gene conversion in concerted evolution of ribosomal DNA. Science. 1991;251:308. doi: 10.1126/science.1987647. [DOI] [PubMed] [Google Scholar]
- 37.Coen E.S., Dover G.A. Unequal exchanges and the coevolution of X and Y rDNA arrays in Drosophila melanogaster. Cell. 1983;33:849–855. doi: 10.1016/0092-8674(83)90027-2. [DOI] [PubMed] [Google Scholar]
- 38.Chen J., Parra L.A., De K.A., Khalid A.N., Qasim T., Ashraf A., Bahkali A.H., Hyde K.D., Zhao R.L., Callac P. Inter-and intra-specific diversity in Agaricus endoxanthus and allied species reveals a new taxon, A. punjabensis. Phytotaxa. 2016;252:1–16. doi: 10.11646/phytotaxa.252.1.1. [DOI] [Google Scholar]
- 39.O’Donnell K., Cigelnik E. Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous. Mol. Phylogenet. Evol. 1997;7:103–116. doi: 10.1006/mpev.1996.0376. [DOI] [PubMed] [Google Scholar]
- 40.Lindner D.L., Banik M.T. Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycologia. 2011;103:731–740. doi: 10.3852/10-331. [DOI] [PubMed] [Google Scholar]
- 41.Li Y., Jiao L., Yao Y.J. Non-concerted ITS evolution in fungi, as revealed from the important medicinal fungus Ophiocordyceps sinensis. Mol. Phylogenet. Evol. 2013;68:373–379. doi: 10.1016/j.ympev.2013.04.010. [DOI] [PubMed] [Google Scholar]
- 42.Hijri M., Hosny M., van Tuinen D., Dulieu H. Intraspecific ITS polymorphism in Scutellospora castanea (Glomales, Zygomycota) is structured within multinucleate spores. Fungal. Genet. Biol. 1999;26:141–151. doi: 10.1006/fgbi.1998.1112. [DOI] [PubMed] [Google Scholar]
- 43.Fell J.W., Scorzetti G., Statzell T.A., Boundy M.K. Molecular diversity and intragenomic variability in the yeast genus Xanthophyllomyces: The origin of Phaffia rhodozyma? FEMS Yeast Res. 2007;7:1399–1408. doi: 10.1111/j.1567-1364.2007.00297.x. [DOI] [PubMed] [Google Scholar]
- 44.Wang D.M., Yao Y.J. Intrastrain internal transcribed spacer heterogeneity in Ganoderma species. Can. J. Microbiol. 2005;51:113–121. doi: 10.1139/w04-118. [DOI] [PubMed] [Google Scholar]
- 45.Sun Y.F., Xing J.H., He X.L., Wu D.M., Song C.G., Liu S., Vlasák J., Gates G., Gibertoni T.B., Cui B.K. Species diversity, systematic revision and molecular phylogeny of Ganodermataceae (Polyporales, Basidiomycota) with an emphasis on Chinese collections. Stud. Mycol. 2022;101:287–415. doi: 10.3114/sim.2022.101.05. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 46.Cabarroi-Hernández M., Villalobos-Arámbula A.R., Torres-Torres M.G., Decock C., GuzmánDávalos L. The Ganoderma weberianum-resinaceum lineage: Multilocus phylogenetic analysis and morphology confirm G. mexicanum and G. parvulum in the Neotropics. MycoKeys. 2019;59:95–131. doi: 10.3897/mycokeys.59.33182. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 47.Hapuarachchi K.K. Ganodermataceae (Polyporales): Diversity in Greater Mekong Subregion countries (China, Laos, Myanmar, Thailand and Vietnam) Mycosphere. 2019;10:221–309. doi: 10.5943/mycosphere/10/1/6. [DOI] [Google Scholar]
- 48.Xing J.H., Sun Y.F., Han Y.L., Cui B.K., Dai Y.C. Morphological and molecular identification of two new Ganoderma species on Casuarina equisetifolia from China. MycoKeys. 2018;34:93–108. doi: 10.3897/mycokeys.34.22593. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 49.Xing J.H., Song J., Decock C., Cui B.K. Morphological characters and phylogenetic analysis reveal a new species within the Ganoderma lucidum complex from South Africa. Phytotaxa. 2016;266:115–124. doi: 10.11646/phytotaxa.266.2.5. [DOI] [Google Scholar]
- 50.Luangharn T., Karunarathna S.C., Mortimer P.E., Hyde K.D., Xu J.C. Morphology, phylogeny and culture characteristics of Ganoderma gibbosum collected from Kunming, Yunnan Province, China. Phyton Int. J. Exp. Bot. 2020;89:743–764. doi: 10.32604/phyton.2020.09690. [DOI] [Google Scholar]
- 51.Luangharn T., Karunarathna S.C., Dutta A.K., Paloi S., Mortimer P.E. Ganoderma (Ganodermataceae, Basidiomycota) species from the Greater Mekong Subregion. J. Fungi. 2021;7:819. doi: 10.3390/jof7100819. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 52.He J., Han X., Luo Z.L., Li E.X., Tang S.M., Luo H.M., Niu K.Y., Sun X.J., Li S.H. Species diversity of Ganoderma (Ganodermataceae, Polyporales) with three new species and a key to Ganoderma in Yunnan Province, China. Front. Microbiol. 2022;13:1–18. doi: 10.3389/fmicb.2022.1035434. [DOI] [PMC free article] [PubMed] [Google Scholar]
Associated Data
This section collects any data citations, data availability statements, or supplementary materials included in this article.
Data Availability Statement
The sequences in the present study were submitted to the NCBI website (https://www.ncbi.nlm.nih.gov/), and the accession numbers are listed in Table 3.