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Research Article
Diversity of Trametes (Polyporales, Basidiomycota) in tropical Benin and description of new species Trametes parvispora
expand article infoBoris Armel Olou§|, Franz-Sebastian Krah, Meike Piepenbring#, Nourou Soulemane Yorou|, Ewald Langer§
‡ University of Abomey-Calavi, Abomey-Calavi, Benin
§ Universität Kassel, Kassel, Germany
| University of Parakou, Parakou, Benin
¶ Philipps-Universität Marburg, Marburg, Germany
# Goethe Universität, Frankfurt am Main, Germany
Open Access

Abstract

Trametes is a globally distributed genus of white-rot polypores and well sampled in temperate and boreal areas. However, the diversity, taxonomy, and phylogenetic positions of Trametes spp. are poorly known in tropical Africa. This study aims at documenting the diversity of Trametes species in Benin (tropical Africa) and their phylogenetic positions with a focus on the T. elegans species complex. Therefore, we collected specimens of Trametes from different forest types across Benin. To infer phylogenetic relationships between Trametes species, we investigated sequences of five gene regions and added available sequences from GenBank. Using Maximum likelihood and Bayesian phylogeny inference methods, we found eight supported species clades. For the T. elegans species complex, we re-establish the name Trametes palisotii for species previously known as T. elegans in tropical Africa. Furthermore, we propose Trametes parvispora as a species new to science and provide the description of this species. Our molecular phylogeny of Trametes with a focus on tropical Benin contributes to taxonomic clarity of an important wood-decay fungal genus, which is the basis for biodiversity assessments of Trametes in the tropics.

Keywords

Africa, morphology, new taxa, phylogeny, Polyporales, taxonomy, tropics, white rot

Introduction

The genus Trametes Fr. (Polyporales, Basidiomycota) consists of wood-decay fungi with a distribution covering all continents and all major climatic zones (Gilbertson and Ryvarden 1987; Ryvarden 1991). Species of Trametes are characterized by a combination of a pileate basidioma, a poroid hymenophore, a trimitic hyphal system, and non-amyloid, thin-walled basidiospores (Gilbertson and Ryvarden 1987). They are saprotrophs causing white rot during the decay of woody substrates (Wong and Wilkes 1988). Species of the genus Trametes have a long ethnomycological history as medicinal fungi in many cultures (Cui et al. 2011; Ss and Pandey 2012; Ueitele et al. 2017) and some species are studied in the context of cancer research (Zmitrovich et al. 2012; Cruz et al. 2016; Blagodatski et al. 2018). Despite the global-scale distribution, importance for wood decomposition, and medicinal properties, the taxonomic and phylogenetic knowledge of Trametes spp. worldwide is still incomplete (Carlson et al. 2014).

Since the first formal description of the genus Trametes by Fries (1835), based on the type species Trametes suaveolens (L.) Fr., the concept of this genus was interpreted in different ways, resulting in different numbers of species attributed to the genus (Karsten 1881; Murrill 1905; Kavina and Pilát 1936; Kotlaba and Pouzar 1957; Gilbertson and Ryvarden 1987; Corner 1989). Recently, based on phylogenetic analyses, the concept of Trametes was re-delimited and circumscribed (Justo and Hibbett 2011). Here, we apply the broad concept of Trametes as proposed by Justo and Hibbett (2011). This concept includes in addition to species of Trametes sensu stricto, species of Artolenzites Falck, Coriolopsis Murrill, Lenzites Fr., and Pycnoporus P. Karst.

Previous studies on Trametes spp. mainly concentrated on specimens from temperate and boreal regions (David 1967; Gilbertson and Ryvarden 1987; Hattori 2005; Tomšovský et al. 2006; Pieri and Rivoire 2007; Ryvarden et al. 2009; Gomes-Silva et al. 2010; Hattori and Sotome 2013), and thus most Trametes spp. have been described from these regions. By contrast, little is known on Trametes spp. in tropical Africa (Fig. 1A), and most known specimens of Trametes spp. from this area are missing in most phylogenetic analyses.

For Benin, seven species of Trametes, namely T. cingulata Berk., T. elegans (Spreng.) Fr., T. flavida (Lév.) Zmitr., Wasser & Ezhov (cited as Leiotrametes flavida), T. polyzona (Pers.) Justo, T. sanguinea (L.) Lloyd (cited as Pycnoporus sanguineus), and T. socotrana Cooke were reported by Olou et al. (2019). Taking a closer look at these species, we noticed that sequence data are lacking for specimens from tropical Africa and that the knowledge on taxonomical and phylogenetic placements is incomplete.

Figure 1. 

a Observations of Trametes spp. retrieved from MyCoPortal and GBIF, based on herbarium specimens and citizen science observations b The study area (Benin) in the western part of Africa (highlighted in black) c Locations of the sampling sites within macroclimatic zones, which are delimited by black lines. The circles in orange indicate respectively from bottom to top the sampling sites: dry dense forest of Pahou, dense semi-deciduous forest of Lama, woodlands of Kilibo, woodlands of Ouémé Superieur, Trois Rivières woodland, and savanna ecosystems of the national park W.

Additional to these known species in Benin, we recently found a putatively new species of Trametes (Olou et al. 2019), but morphological and phylogenetic analyses were outstanding. In the same study, we reported the occurrence of T. elegans in Benin.

Trametes elegans was found to be a species complex and has therefore recently been split into three distinct species, namely T. aesculi (Fr.) Justo, T. elegans s.str., and T. repanda (Pers.) Justo (Carlson et al. 2014). However, this study did not include tropical African specimens although T. elegans exists in this area.

Our study thus aims to report the diversity of Trametes species in Benin and their phylogenetic positions, with a focus on a new species of Trametes and the T. elegans species complex.

Material and methods

Specimens sampling and preservation

A total of 37 specimens of Trametes were collected in three different macroclimatic zones and different forests of Benin (Fig. 1A, C) from July to September in 2017 (Olou et al. 2019) and in 2018 (another series of surveys). Small pieces of fresh fruit bodies were placed in plastic bags half-filled with silica gel for DNA extraction. The rest of fruit bodies were air- or oven-dried at 45–50 °C for 1–2 days depending on the consistency of the fruit body. The dried fruit bodies were then preserved in plastic bags for morphological investigation. Specimens are deposited at the mycological herbaria of the University of Parakou (UNIPAR; Thiers 2019) and the University of Kassel (KAS).

DNA extraction, amplification, sequencing and alignment

DNA extraction. Genomic DNA of all specimens classified into nine morphotypes was extracted using the microwave DNA extraction method (Dörnte and Kües 2013) or the NucleoSpin Plant II DNA extraction kit (Macherey, Nagel, Germany).

Amplifications and sequencing. The extracted genomic DNA was amplified targeting two nuclear ribosomal DNA (nrDNA) regions, internal transcribed spacer (ITS) and ribosomal large subunit-coding DNA (28S rRNA) for all specimens. Additionally, three protein-coding genes, RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2), and translation elongation factor 1-alpha (TEF1) were amplified for specimens forming part of the T. elegans species complex and specimens of Trametes sp. The amplification of the 5.8S rRNA gene region, including ITS were performed in Mastercycler nexus gradient (Eppendorf, Germany), using the primer pair ITS-1F/ITS4 (White et al. 1990; Gardes and Bruns 1993). The Polymerase Chain Reaction (PCR) procedure for the ITS region, was as follows: initial denaturation at 95 °C for 3 min, followed by 35 cycles at 95 °C for 30 s, 52 °C for 30 s and 68 °C for 1 min, and a final extension at 68 °C for 3 min. Amplifications of LSU and three protein-coding genes were performed in 96-well TGradient Thermocycler (Biometra, Göttingen, Germany). PCR procedure for amplifying partial LSU rDNA using the primer pair LR0R/LR5 (Vilgalys and Hester 1990) approximately 964 bp differed to the ITS only by the annealing temperature (55 °C instead of 52 °C) and increased cycle extension time (90 s per cycle). The primer pairs EF1-983F/EF1-1567R (Rehner and Buckley 2005), RPB1-Af/RPB1-Cr (Stiller and Hall 1997; Matheny et al. 2002), and RPB2-b6F/RPB2-b7.1R (Liu et al. 1999; Matheny 2005) were used to amplify approximately 500 bp of TEF1, 1000 bp of RPB1, and 800 bp of RPB2. To amplify the protein-coding genes RPB1 and RPB2, the touchdown PCR protocol following Justo and Hibbett (2011) was used. PCR products were checked on 1% agarose gel stained with GelRed fluorescence dye (Biotium, Hayward, California, USA) in the Transilluminator Biometra Ti5 equipped with BioDocAnalyze software (Biometra GmbH, Göttingen, Germany). They were further cleaned up with QIAquick PCR Purification Kit according to manufacturer’s instructions (QIAGEN GmbH, Hilden, Germany). Thereafter, Sanger sequenced at GATC Biotech in Germany.

At least one sequence per specimen was generated for each morphotype except for the morphotype named Trametes aff. versicolor (Fig. 2N; Suppl. material 1). All newly generated sequences composed of 25 ITS, 20 LSU, two RPB1, four RPB2, and three TEF1 were deposited in GenBank (for accession numbers, see Table 1).

Table 1.

Taxa names with collection details and GenBank accession numbers of all sequences of Trametes spp.

Species name Voucher or strain Origin GenBank N° Reference
ITS LSU RPB1 RPB2 TEF1
Dentocorticium sulphurellum FP11801 JN165018 JN164815 JN164841 JN164876 Justo and Hibbett 2011
Lopharia cinerascens FP105043sp USA: Mississippi JN165019 JN164813 JN164840 JN164874 Justo and Hibbett 2011
T. aesculi (T. elegans species complex) HHB4626sp USA JN164950 KF573173 KF573134 KF573083 Justo and Hibbett 2011, Carlson et al. 2014
FP105679sp USA/Georgia JN164944 JN164799 JN164833 JN164861 JN164899
HHB6551 USA/Florida JN164938 KF573172 KF573136 KF573082
FP105038sp USA: Mississippi JN164951 KF573174 KF573135 KF573081
T. betulina (Lenzites betulinus) HHB9942sp USA JN164983 JN164794 JN164860 Justo and Hibbett 2011
Dai6847 KC848305 KC848390 unpublished
T. cingulata MUCL:40167 Malawi JN645075 Welti et al. 2012
Dollinger 629 USA/Florida KY264043 unpublished
DMC814 Cameroon KC589133 KC589159 unpublished
OAB0135 Benin MK736973 this study
OAB0117 Benin MK736972
OAB0093 Benin MK736970
OAB0114 Benin MK736971 MK736950
OAB0161 Benin MK736975 MK736951
OAB0155 Benin MK736974
OAB0171 Benin MK736976 MK736952
OAB0173 Benin MK736977 MK736953
OAB0178 Benin MK736978 MK736954
OAB0231 Benin MK736979 MK736955
T. cinnabarina (cited as Pycnoporus cinnabarinus) Dai 14386 China KX880629 KX880667 KX880818 KX880854 unpublished
T. coccinea (cited as Pycnoporus coccineus) Cui-7096 KC848330 KC848414 unpublished
T. conchifer FP106793sp USA/Mississippi JN164924 JN164797 JN164823 JN164849 Justo and Hibbett 2011
T. cubensis TJV93_213sp USA/Mississippi JN164923 JN164798 JN164834 JN164865 Justo and Hibbett 2011
AJ177 USA: Florida JN164905
UZ526_17 Malaysia MF363158 unpublished
T. ectypa FP103976sp USA: FLorida JN164961 Justo and Hibbett 2011
FP106037T USA JN164929 JN164803 JN164824 JN164848
T. elegans (T. elegans species complex) PR1133 Puerto Rico JN164937 KF573178 KF573139 KF573075 Justo and Hibbett 2011, Carlson et al. 2014
FPRI10 Philippines JN164973 KF573138 KF573074
FP150762 Belize JN164928 KF573137 KF573076
T. flavida OAB0047 Benin MK736966 MK736946 this study
OAB0090 Benin MK736967
OAB0196 Benin MK736968 MK736947
T. flavida (cited as Leiotrametes flavida) DMC811 Cameroon KC589130 KC589156 unpublished
CBS 158.35 MH855616 MH867126 Vu et al. 2019
T. gibbosa DMC815 Cameroon KC589144 KC589164 unpublished
L11664sp England JN164943 JN164800 JN164831 JN164859 Justo and Hibbett 2011
T. hirsuta DMC341 Cameroon KC589146 KC589166 unpublished
RLG5133T USA: New York JN164941 JN164801 JN164829 JN164854 Justo and Hibbett 2011
T. junipericola 145295(O) KC017758 KC017763 unpublished
T. lactinea DMC346 Cameroon KC589126 KC589152 unpublished
T. lactinea (cited as Leiotrametes lactinea) CBS 109427 Taiwan MH862825 Vu et al. 2019
T. lactinea LIP:GUY09-110 French Guiana JN645069 Welti et al. 2012
Dai6865 KC848327 KC848411 unpublished
OAB0232 Benin MK736983 MK736948 this study
BCC 33266 Thailand GQ982888 GQ982881 unpublished
Yuan5493 KC848320 KC848404
T. ljubarskyi Wei1653 KC848332 KC848416 unpublished
Li286 KC848331 KC848415
T. maxima OH189sp Venezuela JN164957 JN164804 JN164816 JN164864 Justo and Hibbett 2011
T. membranacea PRSC82 Puerto Rico JN164945 JN164805 JN164832 JN164857 Justo and Hibbett 2011
T. menziesii BRFM<FRA>:1368 Martinique JN645103 Welti et al. 2012
Dai6782 KC848289 KC848374 unpublished
T. meyenii Philippines JN164933 KF573179 KF573145 Justo and Hibbett 2011
T. meyenii CBS:453.76 India MH860991 MH872762 Vu et al. 2019
T. ochracea HHB13445sp USA/Michigan JN164954 JN164812 JN164826 JN164852 Justo and Hibbett 2011
Dai2005 China KC848272 KC848357 unpublished
T. palisotii (T. elegans species complex) OAB0118 Benin MK736980 MK736956 MK802884 MK802882 MK802886 this study
OAB0153 Benin MK736981 MK736957 MK802885 MK802883 MK802887
OAB0198 Benin MK736982 MK736958 MK802888
T. palisotii DMC360 Cameroon KC589139 KC589160 unpublished
DMC817 Cameroon KC589142 KC589163
DMC816 Cameroon KC589141 KC589162
T. parvispora OAB0022 Benin MK736989 MK736964 MN127965 this study
OAB0023 Benin MK736990 MK736965 MN127964
T. pavonia FP103050sp USA/Florida JN164958 JN164806 JN164835 JN164862 Justo and Hibbett 2011
T. polyzona DMC370 Cameroon KC589125 KC589151 unpublished
Cui 11040 China KX880647 KX880689 KX880836 KR610849
BKW004 Ghana JN164978 JN164790 Justo and Hibbett 2011
OAB0092 Benin MK736984 MK736959 this study
OAB0128 Benin MK736985 MK736960
OAB0195 Benin MK736986 MK736961
T. pubescens FP101414sp USA/Wisconsin JN164963 JN164811 JN164827 JN164851 Justo and Hibbett 2011
T. pucinea (cited as Pycnoporus puniceus) BCC26408 Thailand FJ372685 FJ372707 unpublished
T. punicea BCC27595 FJ372686 FJ372708 unpublished
T. rependa (T. elegans species complex) FRI437T JN164985 KF573177 KF573142 KF573080 Justo and Hibbett 2011, Carlson et al. 2014
FPRI390 Philippines JN164921 KF573175 KF573141 KF573077
OH271sp Venezuela JN164936 KF573176 KF573143 KF573079
M0138339 Papua New Guinea KF573029 KF573140 KF573078
T. sanguinea OAB0088 Benin MK736969 MK736949 this study
T. sanguinea (cited as Pycnoporus sanguineus) PRSC95 Puerto Rico JN164982 JN164795 JN164842 JN164858 Justo and Hibbett 2011
BCC 36861 Thailand GQ982885 GQ982878 unpublished
8R_1_2 Thailand FJ372672 FJ372694
CBS:614.73 Sri Lanka MH860781 MH872513
T. socotrana BJFC12724 China KC848313 KC848397 unpublished
OAB0131 Benin MK736987 MK736962 this study
OAB0162 Benin MK736988 MK736963
Trametes sp. (cited as Leiotrametes sp.) LIP:GUY08-156 French Guiana JN645062 Welti et al. 2012
Trametes sp. BC1 Finland KT896651 Linnakoski et al. 2016
Trametes sp. (cited as Leiotrametes sp.) LIP:GUY08-167 French Guiana JN645063 Welti et al. 2012
T. suaveolens FP102529sp USA/Wisconsin JN164966 JN164807 JN164828 JN164853 Justo and Hibbett 2011
Dai 10729 China JN048770 JN048789 unpublished
T. versicolor FP135156sp USA/New York JN164919 JN164809 JN164825 JN164850 Justo and Hibbett 2011
T. villosa FP71974R USA/Tennessee JN164969 JN164810 JN164830 JN164855 Justo and Hibbett 2011
Figure 2. 

Macromorphology of Trametes species in Benin and specimen numbers in parentheses. A Trametes cingulata B hymenophore of Trametes cingulata (10) C Trametes flavida D hymenophore of Trametes flavida (05) E Trametes lactinea F hymenophore of Trametes lactinea (01) G Trametes palisotii H hymenophore of Trametes palisotii (04) I Trametes parvispora J hymenophore of Trametes parvispora (04) K Trametes polyzona L hymenophore of Trametes polyzona (06) M Trametes sanguinea (04) N Trametes aff. versicolor (01) O Trametes socotrana P hymenophore of Trametes socotrana (02). Scale bar corresponds to 1cm except in E, F where it corresponds to 2 cm.

Sequence alignment and phylogenetic analyses. To place all the 25 generated ITS sequences of specimens of Trametes spp. in a phylogenetic context, we aligned them in addition to 66 ITS sequences retrieved from GenBank (Benson et al. 2011). Further, 48 LSU sequences were aligned with 20 LSU sequences generated here. For the T. elegans species complex, seven newly generated sequences of protein-coding genes were aligned in addition to sequences used by Carlson et al. (2014). Each marker was aligned separately using MAFFT version 7, with the algorithm L-INS-i (Katoh et al. 2017) and standard settings as default. The resulting multiple species alignments were slightly adjusted and trimmed at both ends a bit from incomplete sequences in Geneious 5.6.7 (Kearse et al. 2012). Eight different datasets were assembled for the phylogenetic analyses: (i) ITS dataset with 91 sequences of Trametes spp., (ii) combined ITS-LSU dataset with 91 sequences Trametes spp., (iii) combined RPB1-RPB2 dataset with 23 sequences of Trametes spp., (iv) ITS dataset with 17 sequences of T. elegans species complex, (v) RPB1 dataset with ten sequences of the T. elegans species complex, (vi) RPB2 dataset with 12 sequences of T. elegans species complex, (vii) TEF1 dataset with 14 sequences of T. elegans species complex, and (viii) combined dataset of four genes (ITS, RPB1, RPB2, TEF1) of T. elegans species complex. The combined datasets were concatenated using Geneious 5.6.7 (Kearse et al. 2012). For the phylogenetic analyses, the partitioning of the combined datasets of Trametes spp. was considered. Lopharia cinerascens (Schwein.) G. Cunn., and Dentocorticium sulphurellum (Peck) M.J. Larsen & Gilb., were chosen as the outgroup in all datasets (Justo and Hibbett 2011). Two phylogenetic tree inference methods, Maximum likelihood (ML) and Bayesian (BY) were performed in each dataset. The ML of all datasets were performed using RAxML 8.2.10 (Stamatakis 2014) and the BY of all individual genes and combined dataset of T. elegans species complex were performed using MrBayes 3.2.6 (Ronquist et al. 2012) at the Cipres Science Gateway V.3.3. (Miller et al. 2010). The BY of the partitioned datasets of Trametes spp. were run independently using MrBayes 3.2.7 (Ronquist et al. 2012). The parameters in BY inference were set as follows: lset applyto = (all), nst = 6, rates = invgamma, ngammacat = 4, sampling frequency = 1000, and the command “unlink” was used to unlink parameters across characters on partitioned datasets. Two independent Markov Chain Monte Carlo (MCMC) processes were run, each in 4 chains, for 5 million generations, and 0.2 fraction were discarded as burn-in. The Phylogenetic Tree Summarization (SumTrees) program within DendroPy 4.3.0. (Sukumaran and Holder 2010) was used to build the consensus tree with branch supports (posterior probabilities). Further, by using IQ-Tree (Trifinopoulos et al. 2016), we assigned the bootstrap values (BS) of ML to the consensus tree of BY. The resulting phylogenetic trees were inspected in FigTree v. 1.4.2 (Rambaut 2014). All sequence alignments and phylogenetic trees generated in the study were deposited in TreeBASE: http://purl.org/phylo/treebase/phylows/study/TB2:S24354. The topologies of the consensus trees obtained from BY are presented in all figures throughout the document. Posterior probabilities (PP) and bootstrap values (BS) on or below branches as followed (PP/BS).

Microscopic analyses of specimens of the new species of Trametes

Macro-morphological descriptions were based on fresh and dried herbarium specimens. Microstructures are described using dried herbarium specimens. Fine sections through the basidiomata were prepared for observation using a razor blade under a stereomicroscope Leica EZ4 and mounted in 5% aqueous solution of potassium hydroxide (KOH) mixed with 1% aqueous solution of Phloxine. Melzer’s reagent (to test for dextrinoid or amyloid reactions), Cotton Blue (to test for cyanophilic reaction) were used and then examined at a magnification of 1000× using a Leica DM500 light microscope. Measurements were done with the software “Makroaufmaßprogramm” from Jens Rüdigs (https://ruedig.de/tmp/messprogramm.htm) and analysed with the software “Smaff” version 3.2 (Wilk 2012). In total, 135 basidiospores were measured from the sequenced specimen OAB0022 and additional examined specimen OAB0268. The basidiospore size is given as length and width of the spore. As measurements we present the mean with standard deviation and minimum and maximum values in parentheses (see below). The length (L), arithmetic average of all spore lengths, and the width (W), arithmetic average of all spore widths, were calculated. In addition, the ratio of length/width (Q) was calculated.

Availability of data and materials

All alignments and phylogenetic trees generated in this study are available in TreeBASE under this link: http://purl.org/phylo/treebase/phylows/study/TB2:S24354. Newly generated sequences are available in GenBank, and the accession numbers are given in Table 1. Alignments, phylogenetic trees, and accession numbers of newly generated sequences will be public after the paper is published. Collected specimens are available at the mycological herbarium of the University of Parakou (UNIPAR). The new species was registered in mycoBank, and the registration number is given in the taxonomy section of this paper.

Abbreviations

a.s.l. above sea level

BS Bootstrap values

BY Bayesian

ITS Internal Transcribed Spacer

KAS Mycological herbarium of the University of Kassel

L Length

LSU Large Subunit

MCMC Markov chain Monte Carlo

ML Maximum likelihood

nrDNA nuclear ribosomal DNA

PP Posterior probabilities

Q Length to width ratio

RPB1 RNA polymerase II largest subunit

RPB2 RNA polymerase II second largest subunit

TEF1 Translation elongation factor 1-alpha

UNIPAR Mycological herbarium of the University of Parakou

Results

Phylogenetic analyses of sequences of Trametes species from Benin

ITS dataset. The 25 ITS sequences obtained from Trametes spp. from Benin clustered in eight distinct clades (Suppl. material 2). All sequences of Trametes spp. from Benin fell into the monophyletic corresponding clades except the clade of Trametes lactinea (Berk.) Sacc., which, besides sequences of T. lactinea, accommodated also sequences of Trametes cubensis (Mont.) Sacc. with a very high support (BP = 1.00/BS = 100). Sequences of specimens of Trametes sp. (OAB0022 and OAB0023) from Benin formed a separated and well-supported clade within the Trametes clade (BP = 0.73/BS = 66).

ITS-LSU dataset. Results of ML and of BY show higher congruency, higher support values, and a higher number of resolved nodes than the results obtained with ITS data only. As evident by the ITS dataset, the sequence of T. lactinea from Benin clustered in addition to other sequences of T. lactinea retrieved from GenBank with sequences of T. cubensis with high support (BP = 1.00/BS = 92). Like in the analysis of the ITS dataset, sequences of Trametes sp. from Benin formed a distinct clade (Fig. 3). The two sequences of the new species of Trametes from Benin clustered in a distinct lineage within the Trametes clade (Figs 2I, J; 4). The clade of the T. elegans species complex is presented in the section below.

Figure 3. 

ML phylogeny of Trametes spp. based on combined ITS-LSU dataset. Branch support values given as PP/BS. All clades where newly generated sequences clustered are highlighted in grey and bars with names are given beside for more readability. Taxon names are followed by voucher or stain number and country of origin.

Phylogenetic placement of Trametes elegans from tropical Africa within the Trametes elegans species complex

The phylogenetic trees generated from individual gene regions ITS, RPB1, RPB2, and TEF1 (Suppl. material 3) and the combined datasets (Fig. 5) show similar results for phylogenetic relationships within the T. elegans species complex. Four distinct and well-supported clades were evident in all datasets. The clade highlighted in grey (Fig. 5; Suppl. material 3) is distinct from all other clades within T. elegans species complex and highly supported in all individual gene and combined dataset. This clade contains only sequences of T. elegans from Benin and Cameroon.

Figure 4. 

Crossection of the hymenium at the base of a pore of Trametes parvispora. Basidiospores, hyphae, basidia, basidioles, and a hyphal peg are showing. The box (lower left corner) shows the location (small rectangle) of the line drawing in the cross-section of the hymenophore. Scale bar = 10 μm

Figure 5. 

ML phylogeny of Trametes elegans species complex based on combined dataset of four-gene regions (ITS, RPB1, RPB2, TEF1). Branch support values given as PP/BS. Sequences of T. elegans from tropical Africa investigated in this study are highlighted in grey.

Taxonomy

Trametes parvispora Olou, Yorou & Langer, sp. nov.

MycoBank No: 830395
Figures 2I, J, 4

Diagnosis

Trametes parvispora differs from known species of Trametes in the combination of the following characteristics: daedaleoid hymenophore, context whitish, thin 1–1.5 mm, homogeneous, without black lines, small spores 3.2–4.6 × 2.1–2.8 μm, regular hyphal pegs 25–30 μm long, cystidia absent, abundance of basidioles, and basidia 12–15 × 3–5 μm.

Type

BENIN. Atlantic province, dry dense forest of Pahou in Ouidah, 6°23'2.97"N, 2°9'15.90"E, altitude: 33.1 m, on dead part of living tree of Dialium guineense Willd., leg. Boris A. Olou, sampling date: 21.07.2017, OAB0022 (dried specimen, holotype in UNIPAR and isotype in KAS). Holotype Sequences: ITS MK736989, LSU MK736964, and RPB2 MN127965

Etymology

parvispora (Lat.): referring to the small size of the spores.

Description

Basidiomata probably perennial, sessile, pileate, applanate, semicircular, up to 13 cm long and 8 cm wide, up to 2.5 cm thick at the base, coriaceous to woody and hard when dry, without odour or taste when fresh. Pileus surface dull, glabrous, and whitish, zonate, margin thick, obtuse. Pore surface whitish, daedaleoid. Context whitish, thin (1–1.5 mm), homogeneous, without black lines.

Hyphal system trimitic, generative hyphae hyaline branched with clamp connections, thin-walled, 1.5–2.0 μm in diameter, acyanophilous; skeletal hyphae solid to thick-walled, hyaline, non-septate, 3–4 μm in diameter, totally dominating in the context, acyanophilous, tissues unchanged in KOH, unbranched; binding hyphae very common in both the context and trama, hyaline, thick-walled, acyanophilous, and much branched.

Cystidia absent, but the branches of the binding hyphae may easily be mistaken for thick-walled cystidia in the hymenium unless a careful examination is undertaken. Hyphal pegs present, especially at the base of pores, and regular, 25–30 μm long.

Basidia 12–15 × 3–5 μm, clavate, tetrasterigmatic, sterigmata 3 μm long; Basidioles numerous, similar in shape to basidia but slightly smaller than basidia, up to 4 μm in diameter.

Basidiospores broadly ellipsoid, hyaline, thin-walled, smooth, usually with one guttule each, negative in Melzer’s reagent, acyanophilous, (2.9)3.2–4.6(4.9) × 2.1–2.8(2.9) μm, L = 3.88 μm, W = 2.48 μm; Q = (1.17)1.24–1.91(2.05), Q = 1.57.

Ecology and distribution

Saprotrophic, on dead part of living tree Dialium guineense and only known from dry dense forest of Pahou in southern Benin.

Additional materials examined

BENIN. Atlantic province, dry dense forest of Pahou/ Ouidah, leg. Boris A. Olou, on dead wood of D. guineense, 21.07.2017, 6°23'3.07"N, 2°9'16.32"E, altitude 18.4 m a.s.l., OAB0023 (UNIPAR); on dead part of living tree of D. guineense, 6°23'2.49"N, 2°9'16.27"E, altitude 33.1 m a.s.l., 20.07.2018, OAB0267 (UNIPAR); at the same locality, 26.09.2018, OAB0268 (UNIPAR).

Discussion

Trametes spp. diversity in Benin

In Benin, seven species of Trametes were previously reported (Olou et al. 2019). By the present, study two additional species, namely T. lactinea and Trametes aff. versicolor (Fig. 2E, F, N), were recorded in addition to previous species. Thus, to our knowledge, nine species of Trametes are currently known for Benin. Of these nine species, only two species, T. elegans and T. sanguinea, were reported in Benin until 2002 (Yorou and De Kesel 2002). The remaining seven species, namely T. cingulata, T. flavida, T. lactinea, T. parvispora, T. polyzona, T. socotrana, and Trametes aff. versicolor, were recorded between 2017 and 2018. Given this history, it is most likely that more species will be found. Nonetheless, this number is significant when compared to the total diversity of 9–14 species of Trametes reported for Europe (Ryvarden and Gilbertson 1994; Ryvarden and Melo 2014). Further studies are needed to document the overall diversity of species of Trametes in Benin.

Phylogenetic positions of Trametes species of Benin

To place specimens of Trametes spp. from Benin in a larger phylogenetic context, we generated sequences of several genes. Generated sequences were placed into the phylogeny of the genus Trametes as established by Justo and Hibbett (2011). Eight distinct clades corresponding to eight different species were obtained from these sequences.

Our phylogenetic analyses from ITS and combined ITS-LSU datasets reveal sequence similarities and taxonomic misplacement within the clades of T. flavida and T. lactinea (Fig. 3; Suppl. material 2). The clade of T. flavida accommodated, in addition to sequences of T. flavida, sequences of Trametes sp. from French Guiana which is known as Leiotrametes sp. (Welti et al. 2012). This species was proposed as a new species by Welti et al. (2012). Here, Trametes sp. clustered together with T. flavida with high support in the ITS dataset (PP = 0.84/BS = 89) and the combined ITS-LSU datasets (PP = 0.98/BS = 99). Both species share also high morphological similarity (Welti et al. 2012; Fig. 2C, D) and a tropical distribution. We therefore suggest that Trametes sp. from French Guiana should not be considered as a new species but should be referred to as T. flavida. In addition to the T. flavida clade, our phylogenetic analyses showed that the T. lactinea clade contains not only sequences of T. lactinea, but also sequences of T. cubensis with high support in the ITS and ITS-LSU datasets (Fig. 3; Suppl. material 2). This result is similar to previous phylogenetic analyses on Trametes using the ITS marker (Justo and Hibbett 2011; Carlson et al. 2014). Trametes lactinea and T. cubensis are still valid names and both species share quite similar morphological characters. They are characterized by an applanate, broadly attached to dimidiate, white to cream basidiomata and a white to cream pore surface (Ryvarden and Johansen 1980; Gilbertson and Ryvarden 1987). Nevertheless, although both species are sharing quite similar morphological characters, they also differ in some characters. Trametes. cubensis is characterized by an annual basidioma, small pores, almost invisible to the naked eye, 5–7 per mm, and cylindrical basidiospores 7–9 × 3–3.5 μm (Gilbertson and Ryvarden 1987), while T. lactinea has an annual to perennial basidioma and large pores, which are visible to the naked eye, mostly 1.5–2 per mm, but can reach up to 3–4 (5) per mm in some specimens with cylindrical-ellipsoid basidiospores 4–7.5 × 2.2–3 μm (Ryvarden and Johansen 1980). Our specimen of T. lactinea (Fig. 2E, F) matches the morphological description of T. lactinea with 3–4 pores per mm, but we did not observe any spore despite numerous attempts. Thus, considering the result of our phylogenetic analyses, absence of spores in our T. lactinea specimen, and the high morphological similarity between species within Trametes (Gilbertson and Ryvarden 1987), we cannot reasonably distinguish T. lactinea from T. cubensis. Further morphological, chemotaxonomic, and molecular studies integrating proteins coding genes (e.g. RPB1, RPB2, and TEF1) are therefore needed to confirm whether T. lactinea and T. cubensis refer to the same species.

Previously the phylogenetic resolution of T. cingulata was problematic due to low sequence availability. Here we generated a total of 17 de novo sequences and show that T. cingulata appears as a monophyletic group within Trametes with high support in ITS and combined ITS-LSU datasets respectively (PP = 1.00/BS = 97) and (PP = 1.00/BS = 100) (Fig. 3; Suppl. material 2). Thus, contrary to the uncertain position of T. cingulata within the genus Trametes (Welti et al. 2012), our results revealed that the latter does not belong to Trametes sensu stricto in the sense of Justo and Hibbett (2011) and Welti et al. (2012) (Fig. 3; Suppl. material 2) but rather to Trametes sensu lato.

Species diversity in the Trametes elegans species complex

The specimens from Benin identified as members of the T. elegans species complex correspond to the morphological descriptions of T. elegans by Gilbertson and Ryvarden (1987) and Ryvarden and Johansen (1980). The clades evident in all datasets within the T. elegans complex (Figs 3, 5; Suppl. material 2, 3) represent three clades previously attributed to three different species by Carlson et al. (2014), and a new clade highlighted in grey (Fig. 5; Suppl. material 3) represents specimens of T. elegans from Benin and Cameroon (Tropical Africa). This new clade contains only sequences of T. elegans from Benin and Cameroon due to the non-publication of most T. elegans sequences from tropical Africa (Olusegun 2015; Awala and Oyetayo 2016; Ueitele et al. 2018). Thus, prior to this study, only sequences of T. elegans from Cameroon and Gabon are available in GenBank for Africa. However, the sequences of T. elegans from Gabon (GenBank accession number: KY449397, KY449398) were not considered because they fell outside the T. elegans species complex and were instead closely related to T. lactinea. We, therefore, excluded these sequences from our analyses. All in all, since the sequences of T. elegans from tropical Africa investigated in this study are demarcated from sequences of T. elegans s. str., the adoption of another correct name for specimens of T. elegans from this area is necessary.

Specimens belonging to the T. elegans species complex have been reported in the past for tropical African countries (Ryvarden and Johansen 1980), with the first name applied to such specimens being Daedalea amanitoides P. Beauv., which was based on a specimen from Nigeria (cited as kingdom of Oware) (Palisot-Beauvois 1804). The morphological characteristics evident in the very short description and illustration of a fruiting body of D. amanitoides match the characteristics of the specimens examined in this study. However, for reasons that we ignore, Fries (1821) replaced this name (D. amanitoides) by the name Daedalea palisotii Fr., which is sanctioned and therefore must be used. The combination Trametes palisotii (Fr.) Imazeki (Imazeki 1952) is available and must be used for African specimens known previously as T. elegans (Fig. 5).

Phylogenetic position and taxonomy of the new species Trametes parvispora

The sequences belonging to the new species named T. parvispora form a distinct and well-supported clade in the ITS and the combined ITS-LSU datasets (Fig. 3; Suppl. material 2). This species forms a sister clade with the still formally undescribed Trametes sp. (KT896651) from Finland. However, unlike T. parvispora where fruiting bodies were available for morphological characterization (Fig. 2I, J), the Finnish specimen was isolated as mycelium from the bark beetle Ips typographus L. (Linnakoski et al. 2016). Thus, anatomical and morphological comparisons are currently not possible. Furthermore, both sequences of T. parvispora share a clade with Trametes meyenii (Klotzsch) Lloyd. This clade was confirmed by phylogenetic analyses including two additional markers RPB1 and RPB2 (Suppl. material 4). Trametes meyenii has hispid and cream-yellow pilei, irpicoid and white to ochraceous hymenophore, pores 1–3 per mm, 4.5–6 × 2–2.5 μm basidiospores (Zmitrovich et al. 2012), whereas T. parvispora has glabrous and whitish pilei, a daedaleoid and white hymenophore, 3.2–4.6 × 2.1–2.8 μm basidiospores, and the presence of regular hyphal pegs (Figs 2I, J, 4). These morphological differences confirm that T. parvispora and T. meyenii are distinct species as shown by the phylogenetic analyses (Fig. 3; Suppl. material 2, 4). However, some species lacking DNA sequences, namely Trametes barbulata Corner, Trametes daedaleoides Corner, and Trametes rugosituba Corner (Corner 1989; Hattori 2005; Hattori and Sotome 2013), share with T. parvispora a quite similar spore size range. But the latter species differs from each other species by the combination of macro- and microscopic characteristics outlined above. Thus, the rare anatomic features of the regular hyphal pegs and the small size of the basidiospores together with the phylogenetic placement within the Trametes clade, provide enough evidence for T. parvispora as a distinct new species.

Acknowledgements

The research grant “Bi-nationally Supervised Doctoral Degrees” from the German Academic Exchange Services (DAAD) allowed for the stay of Boris Armel Olou in Germany while carrying out this study.

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Supplementary materials

Supplementary material 1 

Names, voucher numbers, and substrates of specimens of Trametes spp. collected in Benin

Boris Armel Olou, Franz-Sebastian Krah, Meike Piepenbring, Nourou Soulemane Yorou, Ewald Langer

Data type: species data

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (184.91 kb)
Supplementary material 2 

ML phylogeny of Trametes spp. based on a single gene region ITS

Boris Armel Olou, Franz-Sebastian Krah, Meike Piepenbring, Nourou Soulemane Yorou, Ewald Langer

Data type: phylogeny data

Explanation note: Support values are given as PP/BS. Newly generated sequences are highlighted in bold italic. Taxon names are followed by the voucher or stain numbers and the country of origin.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (253.09 kb)
Supplementary material 3 

ML phylogeny of Trametes elegans species complex as recovered from four individual gene regions

Boris Armel Olou, Franz-Sebastian Krah, Meike Piepenbring, Nourou Soulemane Yorou, Ewald Langer

Data type: phylogeny data

Explanation note: Support values are given as PP/BS. Taxon names are followed by the voucher or stain numbers and the country of origin. The clade formed by the sequences of T. elegans from tropical Africa are highlighted in grey.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (3.36 MB)
Supplementary material 4 

ML phylogeny of Trametes parvispora, based on two-gene dataset (RPB1, RPB2)

Boris Armel Olou, Franz-Sebastian Krah, Meike Piepenbring, Nourou Soulemane Yorou, Ewald Langer

Data type: phylogeny data

Explanation note: Support values given as PP/BS. Taxon names are followed by the voucher or stain numbers and the country of origin.

This dataset is made available under the Open Database License (http://opendatacommons.org/licenses/odbl/1.0/). The Open Database License (ODbL) is a license agreement intended to allow users to freely share, modify, and use this Dataset while maintaining this same freedom for others, provided that the original source and author(s) are credited.
Download file (165.84 kb)