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Molecular and morphological evidence reveal a new genus and species in Auriculariales from tropical China
expand article infoHai-Sheng Yuan, Xu Lu§, Cony Decock|
‡ Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
§ University of the Chinese Academy of Sciences, Beijing, China
| Université Catholique de Louvain, Louvain-la-Neuve, Belgium
Open Access

Abstract

Grammatus labyrinthinus gen. et sp. nov. is proposed based on DNA sequences data and morphological characteristics. It is known so far from southern, tropical China. The new species is characterised by an annual, resupinate basidiocarp with a shallow, subporoid hymenophore, a hymenium restricted to the bottom of the tubes, a dimitic hyphal system, presence of encrusted skeletocystidia and dendrohyphidia, longitudinally septate basidia and smooth, oblong-ellipsoid to cylindrical, acyanophilous basidiospores. Phylogenetic analyses based on ITS + nLSU DNA sequences data indicate that G. labyrinthinus belongs to Auriculariaceae in which it has an isolated position. Phylogenetic inferences show G. labyrinthinus to be related to Heteroradulum. However, the ITS sequences similarity between G. labyrinthinus and H. kmetii, the type species of Heteroradulum, were 89.84% and support the establishment of the new genus. Inversely, Heteroradulum semis clustered with G. labyrinthinus with strong support and it is transferred to Grammatus.

Keywords

Grammatus labyrinthinus, ITS and nLSU, lignicolous fungi, phylogeny, taxonomy

Introduction

Auriculariales was established by Schroeter (1889) and originally accommodated species which, with transversely septate basidia, is also known as auricularioid basidia. Based on the micromorphology and ultra-structure of the septal pore and the spindle pole body, Bandoni (1984) redefined Auriculariales, in order to accommodate all heterobasidiomycetes with continuous parenthesomes, transversely or longitudinally septate basidia and hyphal haploid stages. Currently, one family, Auriculariaceae is accepted and 198 species are distributed into 32 genera of Auriculariales (Kirk et al. 2008).

Auriculariaceae are diverse as long as their basidiocarp consistency (flesh gelatinous, wax-like and corky) and hymenophore structures (smooth, plicate, hydnoid and poroid) are concerned. According to the Dictionary of the fungi (10th edition), the family includes 7 genera: Auricularia Bull., Eichleriella Bres., Elmerina Bres., Exidia Fr., Exidiopsis (Bref.) Möller, Fibulosebacea K. Wells & Raitv., Heterochaete Pat. and 112 species (Kirk et al. 2008). Two other genera related to Elmerina, viz. Aporpium Bondartsev & Singer and Protodaedalea Imazeki, were also described. However, the phylogenetic position of the type species of Elmerina is still unclear (Sotome et al. 2014). The latest study of Auriculariales using ITS + nLSU DNA sequences data introduced or revalidated several new genera, viz. Amphistereum Spirin & V. Malysheva, Sclerotrema Spirin & V. Malysheva, Heteroradulum Lloyd and allowed the inclusion of Exidia glandulosa (Bull.) Fr., Hirneolina hirneoloides (Pat.) Pat., Tremellochaete japonica (Lloyd) Raitviir in Auriculariaceae (Malysheva and Spirin 2017).

Molecular phylogeny had been widely used to investigate phylogenetic relationships amongst the genera and species in Auriculariales (Swann and Taylor 1993, Berres et al. 1995, Weiß and Oberwinkler 2001, Kirschner and Chen 2004, Wells et al. 2004, Kirschner et al. 2010, 2012, Zhou and Dai 2013, Sotome et al. 2014, Malysheva and Spirin 2017). These phylogenetic contributions provided a general overview of Auriculariales and show strong support at the species level, but so far, not all the deeper nodes received high support from molecular evidence.

China is very rich in wood-decaying fungi and extensive studies on species diversity, taxonomy, ecology and phylogeny of wood-decaying fungi have been carried out recently (Yuan and Dai 2008; Dai 2010, 2011, 2012; Yuan et al. 2015). During a continuous survey of wood-decaying Basidiomycetes in the Yunnan Province, tropical China, a species of Auriculariaceae was collected but could not be confidently identified to any known species. The morphology characteristics suggested they represent an undescribed genus in Auriculariaceae. The aim of this paper is to clarify the taxonomic status of the genus and to describe new taxa.

Materials and methods

Morphological studies. Specimens are deposited at the herbarium of Institute of Applied Ecology, Chinese Academy of Sciences (IFP). Microscopic procedures follow Yuan and Qin (2018). The microscopic studies were made from sections mounted in Cotton Blue (CB): 0.1 mg aniline blue dissolved in 60 g pure lactic acid; CB+/– = cyanophilous / acyanophilous. Amyloid and dextrinoid reactions were tested in Melzer’s reagent (IKI): 1.5 g KI (potassium iodide), 0.5 g I (crystalline iodine), 22 g chloral hydrate, aq. dest. 20 ml; IKI– = neither amyloid nor dextrinoid reaction. KOH (5%) was used as a mounting reagent. Sections were studied at magnifications up to 1000× using a Nikon Eclipse E600 microscope and phase contrast illumination and dimensions were estimated subjectively with an accuracy of 0.1 µm. For spore measurements, the apiculus was excluded. In presenting the variation of spore size, 5% of the measurements at each end of the range are given in parentheses. The following abbreviations are used in the text: L = mean spore length, W = mean spore width, Q = range of length/width ratios for studied specimens and n = total number of spores measured from a given number of specimens. Special colour terms are from Petersen (1996).

Molecular procedures and phylogenetic analyses. The fungal taxa and strains used in this study are listed in Table 1. Phire Plant Direct PCR Kit (Finnzymes, Finland) procedure was used to extract total genomic DNA from the fruiting body and for the polymerase chain reaction (PCR). PCR amplification was confirmed on 1% agarose electrophoresis gels stained with ethidium bromide (Stöger et al. 2006). DNA sequencing was performed at Beijing Genomics Institute (BGI). All newly generated sequences have been submitted to GenBank and are listed in Table 1.

DNA sequences used in the present study.

Species Collector/herbarium
number
ITS
GenBank#
LSU
GenBank#
Source
Amphistereum leveilleanum Lentz FP-106715 (CFMR) KX262119 KX262168 Malysheva and Spirin 2017
A. schrenkii Burdsall 8476 (CFMR) KX262130 KX262178 Malysheva and Spirin 2017
Aporpium hexagonoides ML297 (TFM) AB871754 AB871735 Sotome et al. 2014
Auricularia cornea AU110 KF297960 KF297995 unpublished
A. fuscosuccinea MW530 AB615231 AF291291 Weiß and Oberwinkler 2001
A. mesenterica FO 25132 AF291271 AF291292 Weiß and Oberwinkler 2001
A. mesenterica TUFC12805 AB915192 AB915191 Sotome et al. 2014
A. polytricha TUFC12920 AB871752 AB871733 Sotome et al. 2014
Basidiodendron caesiocinereum MW 320 AF291293 Weiß and Oberwinkler 2001
B. eyrei MW 529 AF291296 Weiß and Oberwinkler 2001
B. eyrei TUFC14484 AB871753 AB871734 Sotome et al. 2014
Bourdotia galzinii FO 2278 AF291301 Weiß and Oberwinkler 2001
Ductifera pululahuana KW 1733 AF291315 Weiß and Oberwinkler 2001
Eichleriella alliciens Burdsall 7194 (CFMR) KX262120 KX262169 Malysheva and Spirin 2017
E. bactriana I. Parmasto (TAAM 96698) KX262123 KX262172 Malysheva and Spirin 2017
E. bactriana E. Parmasto (TAAM 104431) KX262138 KX262186 Malysheva and Spirin 2017
E. crocata E. Parmasto (TAAM 101077) KX262100 KX262147 Malysheva and Spirin 2017
E. crocata E. Parmasto (TAAM 125909) KX262118 KX262167 Malysheva and Spirin 2017
E. desertorum Ryvarden 49350 (O) KX262142 KX262190 Malysheva and Spirin 2017
E. flavida Ryvarden 49412 (H) KX262137 KX262185 Malysheva and Spirin 2017
E. leucophaea Barsukova (LE 303261) KX262111 KX262161 Malysheva and Spirin 2017
E. leucophaea Larsson 15299 (O) KX262136 KX262184 Malysheva and Spirin 2017
E. shearii USJ 54609 AF291284 AF291335 Weiß and Oberwinkler 2001
E. sicca Miettinen 17349 (H) KX262143 KX262191 Malysheva and Spirin 2017
E. tenuicula Ryvarden 17599 (O) KX262141 KX262189 Malysheva and Spirin 2017
Elmerina caryae WD2207 AB871751 AB871730 Sotome et al. 2014
E. caryae Dai 4549 JQ764652 JQ764631 Zhou and Dai 2013
E. cladophora Wei 5621 JQ764659 JQ764634 Zhou and Dai 2013
E. dimidiata O18238 JQ764663 JQ764640 Zhou and Dai 2013
E. dimidiata O18261 JQ764664 JQ764641 Zhou and Dai 2013
E. efibulata Dai 9322 JQ764669 JQ764647 Zhou and Dai 2013
E. foliacea Yuan 5691 JQ764666 JQ764644 Zhou and Dai 2013
E. hispida WD548 (TFM) AB871768 AB871749 Sotome et al. 2014
E. hispida E701 AB871767 AB871748 Sotome et al. 2014
E. hispida Wei 5584 JQ764667 JQ764645 Zhou and Dai 2013
Exidia glandulosa TUFC 34008 AB871761 AB871742 Sotome et al. 2014
E. glandulosa MW 355 AF291273 AF291319 Weiß and Oberwinkler 2001
E. pithya MW 313 AF291275 AF291321 Weiß and Oberwinkler 2001
E. uvapsassa AFTOL-ID 461 DQ241776 AY645056 unpublished
Exidiopsis calcea MW 331 AF291280 AF291326 Weiß and Oberwinkler 2001
E. effusa Miettinen 19136 (H) KX262145 KX262193 Malysheva and Spirin 2017
E. grisea RK 162 AF291281 AF291328 Weiß and Oberwinkler 2001
E. grisea TUFC100049 AB871765 AB871746 Sotome et al. 2014
E. sp. TUFC34333 AB871764 AB871745 Sotome et al. 2014
E. sp. FO 46291 AF291282 AF291329 Weiß and Oberwinkler 2001
Grammatus labyrinthinus Yuan 1759 KM379137 KM379138 This study
G. labyrinthinus Yuan 1600 KM379139 KM379140 This study
Heterochaete andina Lagerheim (FH, lectotype) KX262187 Malysheva and Spirin 2017
H. delicata TUFC33717 AB871766 AB871747 Sotome et al. 2014
Heterochaetella brachyspora RK 96 AF291337 Weiß and Oberwinkler 2001
Heteroradulum adnatum Ryvarden 23453 (O) KX262116 KX262165 Malysheva and Spirin 2017
H. deglubens LE 38182 KX262112 KX262162 Malysheva and Spirin 2017
H. deglubens TAAM 064782 KX262101 KX262148 Malysheva and Spirin 2017
H. kmetii Kmet (H, lectotype) KX262124 KX262173 Malysheva and Spirin 2017
H. kmetii Spirin 6466 (H) KX262104 KX262152 Malysheva and Spirin 2017
H. semis Miettinen 10618.1 (H) KX262146 KX262194 Malysheva and Spirin 2017
Myxarium grilletii RK 218 AF291349 Weiß and Oberwinkler 2001
M. nucleatum ZP TRE2M AF291351 Weiß and Oberwinkler 2001
Protodontia subgelatinosa USJ 54661 AF291357 Weiß and Oberwinkler 2001
Protomerulius africanus Ryvarden 9800 (O) AF291358 Weiß and Oberwinkler 2001
Pseudohydnum gelatinosum MW 298 AF291360 Weiß and Oberwinkler 2001
Sclerotrema griseobrunneum Niemelä 2722 (H) KX262144 KX262192 Malysheva and Spirin 2017
Sistotrema brinkmannii Isolate 236 JX535169 JX535170 GenBank
Tremellochaete japonica LE 303446 KX262110 KX262160 Malysheva and Spirin 2017
Tremellodendropsis sp. USJ 54427 AF291375 Weiß and Oberwinkler 2001
Tremiscus helvelloides MW 337 AF291377 Weiß and Oberwinkler 2001

Nuclear ribosomal RNA genes were used to determine the phylogenetic position of the new species. The internal transcribed spacer (ITS) regions were amplified with the primers ITS4 and ITS5 and the partial nLSU regions were amplified with primers LR7 and LR0R (White et al. 1990). The most similar sequences were searched for in GenBank NCBI (http://www.ncbi.nlm.gov) using the BLAST option and downloaded (Table 1). Sequences were aligned using ClustalX (Thompson et al. 1997) and the alignment was deposited in TreeBASE (http://treebase.org/treebase-web/) (submission ID: 22496). Identity/similarity between two sequences was calculated using the BioEdit v. 7.2.6 (Hall 2005). Maximum parsimony (MP), Maximum likelihood (ML) and Bayesian inference were applied to the ITS + LSU dataset. All characters were weighted and gaps were treated as missing data. Maximum parsimony analysis (PAUP* version 4.0b10) was used (Swofford 2002). Trees were inferred using the heuristic search option with TBR branch swapping and 1000 random sequence additions. Max-trees were set to 5000 and no-increase, branches of zero length were collapsed and all parsimonious trees were saved. Clade stability was assessed using a bootstrap (BT) analysis with 1,000 replicates (Felsenstein 1985). Maximum likelihood (ML) analysis was performed in RAxML v8.2.4 with GTR + I + G model (Stamatakis 2014). The best tree was obtained by executing 100 rapid bootstrap inferences and, thereafter, a thorough search for the most likely tree using one distinct model/data partition with joint branch length optimisation (Stamatakis et al. 2008). Bayesian analysis with the latest version of MrBayes 3.2.6 (Ronquist and Huelsenbeck 2003) implementing the Markov Chain Monte Carlo (MCMC) technique. The best-fit models (GTR + I + G) were selected by hLRT in MrModeltest 2.3 (Nylander 2004). Four simultaneous Markov chains were run starting from random trees and keeping one tree every 100th generation until the average standard deviation of split frequencies was below 0.01. The value of burn-in was set to discard 25% of trees when calculating the posterior probabilities. Bayesian posterior probabilities were obtained from the 50% majority rule consensus of the trees kept.

Results

Phylogenetic analyses

The combined ITS + nLSU sequence dataset includes the new species and other related species in Auriculariales. Sistotrema brinkmannii was used as outgroup (Malysheva and Spirin 2017). The data matrix comprised 1413 base pairs with 818 constant characters, 206 parsimony-uninformative variable characters and 389 parsimony informative positions. Maximum parsimony analysis was performed and a strict consensus tree was obtained from the 2 equally most parsimonious trees. The same dataset and alignment was analysed using RAxML v8.2.4 and MrBayes 3.2.6 with the best-fit model (GTR + I + G) selected by MrModeltest 2.3 and a similar topology was generated and the maximum likelihood tree is shown in Fig. 1. Bayesian analysis ran 4 million generations and resulted in average standard deviation of split frequencies = 0.008219. In the phylogenetic tree, two sampled specimens of Grammatus labyrinthinus group together with full support and form a monophyletic lineage with Heteroradulum semis with strong support (97 % in ML, 100 % in MP and 1.00 BPP). The new taxon belongs to Auriculariales in which it has an isolated position.

Figure 1. 

Maximum likelihood tree illustrating the phylogeny of Grammatus labyrinthinus and related taxa in Auriculariales, based on the combined ITS + nLSU sequence dataset. Branches are labelled with maximum likelihood bootstrap higher than 50%, parsimony bootstrap proportions higher than 50% and Bayesian posterior probabilities more than 0.95.

Taxonomy

Grammatus H.S. Yuan & C. Decock, gen. nov.

MycoBank No: MB825392

Notes

Basidiocarps annual, resupinate; hymenophoral surface hydnoid, irregularly poroid to labyrinthine, hymenium restricted to the area surround the spines or the bottom of the tubes; Hyphal system dimitic; skeletocystidia heavily encrusted in trama; dendrohyphidia thin- to slightly thick-walled; basidia longitudinally septate; basidiospores thin-walled, smooth, oblong-ellipsoid to cylindrical.

Type species

Grammatus labyrinthinus H.S. Yuan & C. Decock.

Etymology

grammatus: referring to the hymenophore striped with raised lines.

Basidiocarps annual, resupinate, coriaceous; hymenophoral surface cream to pale buff, covered by evenly distributed blunt-pointed spines or irregularly irpicoid to subporoid, then developing into labyrinthiform to sinuous pores; hymenium restricted to the area surrounding the spines or the bottom of the tubes. Subiculum very thin. Spine or tubes corky, concolorous with hymenophoral surface, shallow. Hyphal system dimitic; generative hyphae bearing clamp connections; skeletal hyphae IKI–, CB+; tissue unchanged in KOH. Skeletocystidia clavate, upper part heavily encrusted. Dendrohyphidia present. Basidia subglobose, longitudinally septate. Basidiospores oblong-ellipsoid to cylindrical, hyaline, thin-walled, smooth, IKI–, CB–.

Grammatus labyrinthinus H.S. Yuan & C. Decock, sp. nov.

MycoBank No: MB825393
Figures 3, 4

Diagnoses

Basidiocarps annual, resupinate; hymenium restricted to the base of the tubes. Hymenophoral surface irregularly irpicoid to subporoid, then labyrinthine to sinuous. Subiculum very thin. Tubes shallow. Hyphal system dimitic; generative hyphae bearing clamp connections; skeletal hyphae IKI–, CB+. Skeletocystidia clavate, the upper part heavily encrusted. Dendrohyphidia present, thin- to slightly thick-walled. Basidia subglobose, longitudinally septate. Basidiospores oblong-ellipsoid to cylindrical, hyaline, thin-walled, smooth, IKI–, CB–.

Type

China. Yunnan Province, Xishuangbanna, Jinghong County, Nabanhe Nat. Res., fallen angiosperm branch, 17.VIII.2005 Yuan 1759 (holotype: IFP 019121).

Etymology

labyrinthinus (Lat.): refers to labyrinthine hymenophore.

Basidiocarps annual, resupinate, coriaceous, without special odour or taste when fresh, corky when dry, up to 15 cm long, 3 cm wide and 0.2 mm thick. Hymenophoral surface cream to pale buff when fresh, cinnamon-buff to yellowish-brown upon drying, firstly irregularly irpicoid to subporoid, the separate plates grow laterally and then develop into labyrinthine to sinuous pores, mostly 4–5 per mm, dissepiments thin; sterile margin up to 0.2 mm wide, pale yellow. Subiculum very thin (ca. 0.1 mm thick), cream to pale buff. Tubes corky, concolorous with pore surface, shallow, up to 130 µm deep, tube walls 120–200 µm thick. Hymenium restricted to the base of the tubes.

Hyphal structure. Hyphal system dimitic; generative hyphae bearing clamp connections, skeletal hyphae IKI–, CB+; tissue unchanged in KOH.

Subiculum. Dominated by skeletal hyphae; generative hyphae hyaline, thin-walled, rarely branched, 1.5–2.8 µm diam; skeletal hyphae hyaline, thick-walled to subsolid, straight to flexuous, covered by fine crystals, occasionally branched, interwoven, 1.8–3 µm diam.

Tubes. Generative hyphae infrequent, hyaline, thin-walled, rarely branched, 1.5–2.5 μm diam; skeletal hyphae dominant, hyaline, thick-walled to subsolid, moderately branched, interwoven, 1.8–2.8 μm diam. Skeletocystidia numerous, clavate, thick-walled, originating from and tightly embedded in trama, upper part heavily encrusted, 10–30 × 4–8 µm (with encrustation). Dendrohyphidia present, especially along the dissepiments, arising from generative hyphae, thin- to slightly thick-walled, apically moderately to strongly branched. Basidia subglobose, longitudinally septate, already septate as probasidia, 18–25 × 10–13 μm, epibasidia divided into four parts up to 20 μm long, bearing four sterigmata and without clamp connection at the base, sterigmata up to 20 μm long.

Basidiospores. Oblong-ellipsoid to cylindrical, hyaline, thin-walled, smooth, IKI–, CB–, (13–)13.3–15.7(–16) × (6–)6.4–7.4(–7.7) μm, L = 14.4 μm, W = 6.94 μm, Q = 2.07–2.1 (n = 60/2).

Type of rot

White rot.

Additional specimens examined – China. Yunnan Province, Xishuangbanna, Jinghong County, Elephant Valley Forest Park, fallen angiosperm branch, 14.VIII.2005 Yuan 1600 (IFP 019118); Nabanhe Nat. Res., fallen angiosperm branch, 15.VIII.2005 Yuan 1683 (IFP 019119); fallen angiosperm branch, 17.VIII.2005 Yuan 1734 (IFP 019120).

Grammatus semis (Spirin & Malysheva) H.S. Yuan & C. Decock, comb. nov.

MycoBank No: MB825394

Basionym

Heteroradulum semis Spirin & Malysheva, in Malysheva & Spirin, Fungal Biology 121: 712. 2017.

Figure 2. 

Basidiocarps of Grammatus labyrinthinus (Yuan 1734).

Figure 3. 

Hymenophoral surface of Grammatus labyrinthinus under ×8 lens (holotype).

Figure 4. 

Microscopic structures of Grammatus labyrinthinus (drawn from the holotype). a Basidiospores b Probasidia c Probasidia transection d Epibasidia e Dendrohyphidia f Hyphae from subiculum g Hyphae from trama h Basidiocarp transection.

Discussion

Anatomically, the longitudinally septate basidia of Grammatus labyrinthinus point toward affinities with Auriculariales, which is confirmed by molecular data. The new taxa are phylogenetically closely related to Heteroradulum. Heteroradulum kmetii, type of the genus, has perennial, effused-reflexed and pinkish or reddish basidiocarps with hymenial surface first smooth then with irregularly arranged, sharpened outgrowths (Malysheva and Spirin 2017), in which feature, it differs from G. labyrinthinus. The similarity between the ITS sequences of G. labyrinthinus and H. kmetii are of 89.84%. The unique morphological characteristics and molecular sequence analyses both support the establishment of the new genus.

Heteroradulum semis was originally found and described from high elevation temperate north-eastern China. It is characterised by resupinate, leathery basidiocarps covered by blunt-pointed spines, a dimitic hyphal structure with clamped generative hyphae, encrusted tramal skeletocystidia, simple or sparsely branched dendrohyphidia, longitudinally septate basidia and broadly cylindrical to narrowly obovate basidiospores (Malysheva and Spirin 2017). The sterile and blunt-pointed outgrowths on the hymenial surface of H. semis identify the irregularly irpicoid and separate plates of G. labyrinthinus when young, but the irregularly irpicoid and separate plates of G. labyrinthinus would form the labyrinthine or subporoid structure when old and can be distinguished from the former species. Phylogenetic analyses confirm that H. semis clustered with G. labyrinthinus with strong support. So it is transferred to Grammatus and a new combination, G. semis is proposed.

Aporpium, Elmerina and Protomerulius Möller all have a poroid hymenophore (Ryvarden and Johansen 1980, Núñez and Ryvarden 2001, Sotome et al. 2014). However, they are all distant from Grammatus labyrinthinus in phylogenetic inferences (Fig. 1).

There are 216 genera and more than 1800 species of wood-inhabiting fungi in Polyporales (Kirk et al 2008) with high diversity of hymenophore structure from smooth, hydnoid, lamellate and poroid. Amongst the poroid taxa, Grammothele Berk. & M.A. Curtis, Hymenogramme Mont. & Berk., Porogramme (Pat.) Pat. and Theleporus Fr. are characterised by a hymenium restricted to the bottom of the pores, which differentiate them from the other typical polypores. These genera are characterised by non-septate basidia and are members of Polyporales. In comparison, Auriculariales are relatively poor in genera and species, but still, their hymenophore structures are diverse. Grammatus labyrinthinus is the representative of poroid species with a hymenium restricted to the bottom in Auriculariales. It is another instance of morphological convergent evolution across the order.

Acknowledgements

We thank Dr. Hancheng Wang (Chongqing Normal University, China) for accompanying us during the field trips. This research was financed by the National Natural Science Foundation of China (Project Nos. 31470148 & 31770028).

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