Research Article
Research Article
Phaeotubakia lithocarpicola gen. et sp. nov. (Tubakiaceae, Diaporthales) from leaf spots in China
expand article infoNing Jiang, Ya-Quan Zhu, Han Xue, Chun-Gen Piao, Yong Li
‡ Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, China
Open Access


Tubakiaceae represents a distinct lineage of Diaporthales, including its type genus Tubakia and nine additional known genera. Tubakiaceous species are commonly known as endophytes in leaves and twigs of many tree species, but can also be plant pathogens causing conspicuous leaf symptoms. In the present study, isolates were obtained from diseased leaves of Lithocarpus glaber collected in Guangdong Province, China. The identification was conducted based on morphology and phylogeny of combined loci of 28S nrRNA gene (LSU), internal transcribed spacer regions and intervening 5.8S nrRNA gene (ITS) of the nrDNA operon, translation elongation factor 1-alpha (tef1) and beta tubulin (tub2). As a result, a distinct clade in Tubakiaceae was revealed named Phaeotubakia lithocarpicola gen. et sp. nov., which was distinguished from the other tubakiaceous taxa by its dark brown conidiogenous cells and conidia.


Ascomycota, morphology, new genus, phylogeny, plant disease, taxonomy, Tubakiaceae


The fungal order Diaporthales contains members usually inhabiting plant tissues as pathogens, endophytes and saprophytes (Rossman et al. 2007; Senanayake et al. 2017, 2018; Fan et al. 2018; Jiang et al. 2021a; Udayanga et al. 2021). Tubakiaceae was proposed as a diaporthalean family based on its type genus Tubakia, and the other seven genera, namely Apiognomonioides, Involutiscutellula, Oblongisporothyrium, Paratubakia, Racheliella, Saprothyrium and Sphaerosporithyrium (Braun et al. 2018). Subsequently, Ellipsoidisporodochium and Obovoideisporodochium were added to this family based on morphological and phylogenetical evidence (Zhang et al. 2021; Liu et al. 2022). Hence, ten genera have been accepted in Tubakiaceae before the present study.

Species of Tubakiaceae are usually characterized by forming pycnothyria composed of convex scutella with radiating threads of cells fixed to the substratum by a central columella, mostly surrounded by a sheath of small fertile cells that give rise to one-celled, phialidic conidiogenous cells (Harrington et al. 2012; Braun et al. 2018). However, some species also form crustose or pustulate pycnidioid conidiomata, for example, Tubakia californica is known to only have crustose pycnidioid conidiomata during its lifecycle (Braun et al. 2018). Moreover, conidia of tubakiaceous species are globose, subglobose, ellipsoid, broad ellipsoid-obovoid to subcylindrical or somewhat irregular in shape, aseptate, hyaline, subhyaline to pigmented (Braun et al. 2018; Zhang et al. 2021). Conidia of Apiognomonioides, Ellipsoidisporodochium, Oblongisporothyrium, Obovoideisporodochium and Saprothyrium species are known to be hyaline (Braun et al. 2018; Zhang et al. 2021; Liu et al. 2022). Conidia of Involutiscutellula, Paratubakia and Sphaerosporithyrium species are hyaline to slightly pigmented (Braun et al. 2018), while conidia of Racheliella and Tubakia species are hyaline to pigmented (Braun et al. 2014, 2018; Zhu et al. 2022).

Tubakiaceae species are known to be endophytes in leaves and twigs of many tree species, but can also cause conspicuous symptoms on host leaves as plant pathogens (Harrington et al. 2012; Braun et al. 2018; Zhu et al. 2022). Nearly all tubakiaceous species are reported from Fagaceae, such as species of Castanea, Castanopsis, Fagus, Lithocarpus and Quercus (Braun et al. 2018; Morales-Rodríguez et al. 2021). In addition, these fungi are also discovered from the other plant families, i.e., Altingiaceae, Anacardiaceae, Nyssaceae, Oleaceae, Rosaceae, Sapindaceae and Ulmaceae (Braun et al. 2018; Liu et al. 2022).

The aim of the present study is to identify two isolates obtained from diseased leaves of Lithocarpus glaber from Guangdong Province by morphological characters and phylogeny based on combined loci of 28S nrRNA gene (LSU), internal transcribed spacer regions and intervening 5.8S nrRNA gene (ITS) of the nrDNA operon, translation elongation factor 1-alpha (tef1) and beta tubulin (tub2).

Materials and methods

Sample collection, fungal isolation and morphology

Diseased leaves of Lithocarpus glaber were collected from Guangdong Province, China. The leaf samples were packed in paper bags and transferred to the laboratory for isolation. The leaves were firstly surface-sterilized for 2 min in 75% ethanol, 4 min in 1.25% sodium hypochlorite, and 1 min in 75% ethanol, then rinsed for 2 min in distilled water and blotted on dry sterile filter paper. Then diseased tissues were cut into 0.5 cm × 0.5 cm pieces using a double-edge blade, and transferred onto the surface of potato dextrose agar (PDA, 200 g potatoes, 20 g dextrose, 20 g agar per L), and incubated at 25 °C to obtain cultures. The hyphal tips were then transferred to clean plates of PDA, malt extract agar (MEA, 30 g malt extract, 5 g mycological peptone, 15 g agar per L) and synthetic low nutrient agar (SNA, 1 g KN2PO4, 1 g KNO3, 0.5 g MgSO4-7H2O, 0.5 g KCl, 0.2 g glucose, 0.5 g gucrose per L) under a dissecting stereomicroscope with sterile needles. The cultures were deposited in China Forestry Culture Collection Center (CFCC,; accessed on 6 December 2022), and the specimens in the herbarium of the Chinese Academy of Forestry (CAF,; accessed on 6 December 2022).

Morphology of the new taxa was studied based on conidiomata formed on PDA plates under a dissecting microscope (M205 C, Leica, Wetzlar, Germany). The conidiogenous cells and conidia were immersed in tap water, then the microscopic photographs were captured with an Axio Imager 2 microscope (Zeiss, Oberkochen, Germany) equipped with an Axiocam 506 color camera, using differential interference contrast (DIC) illumination. More than 50 conidia were randomly selected for measurement. Culture characters were recorded from PDA, MEA and SNA after 10 days at 25 °C in the dark.

DNA extraction, PCR amplification and phylogenetic analyses

The fungal genomic DNA was extracted from mycelia grown on PDA palates after 10 days following the method in Doyle and Doyle (1990). Four partial loci, ITS and LSU regions, tef1 and tub2 genes were amplified by the following primer pairs: ITS1 and ITS4 for ITS (White et al. 1990), LR0R and LR5 for LSU (Vilgalys and Hester 1990), EF1-688F and EF2 for tef1 (Carbone and Kohn 1999), and Bt2a and Bt2b for tub2 (Glass and Donaldson 1995).

The polymerase chain reaction (PCR) conditions were set as follows: an initial denaturation step of 5 min at 94 °C, followed by 35 cycles of 30 s at 94 °C, 50 s at 48 °C (ITS and LSU) or 54 °C (tef1 and tub2), and 1 min at 72 °C, and a final elongation step of 10 min at 72 °C. PCR products were assayed via electrophoresis in 2% agarose gels. DNA sequencing was performed using an ABI PRISM 3730XL DNA Analyser with a BigDye Terminator Kit v.3.1 (Invitrogen, Waltham, MA, USA) at the Shanghai Invitrogen Biological Technology Company Limited (Beijing, China).

The sequences obtained in the current study were assembled using SeqMan v. 7.1.0, and reference sequences were retrieved from the website of the National Center for Biotechnology Information (NCBI,; accessed on 15 October 2022), based on sequences from Braun et al. (2018) and Zhang et al. (2021). The sequences were aligned using MAFFT v. 7 and corrected manually using MEGA v. 7.0.21 (Katoh et al. 2019).

The phylogenetic analyses of combined matrixes of ITS-LSU-tef1-rpb2 were performed using maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. MP analysis was run using a heuristic search option of 1000 search replicates with random-additions of sequences with a tree bisection and reconnection (TBR) algorithm in PAUP v. 4.0b10 (Swofford 2003). Maxtrees were set to 5 000, branches of zero length were collapsed and all equally parsimonious trees were saved. Other calculated parsimony scores were tree length (TL), consistency index (CI), retention index (RI) and rescaled consistency (RC). ML was implemented on the CIPRES Science Gateway portal ( using RAxML-HPC BlackBox 8.2.10 (Miller et al. 2010; Stamatakis 2014), employing a GTR-GAMMA substitution model with 1000 bootstrap replicates. Bayesian inference was performed using a Markov Chain Monte Carlo (MCMC) algorithm in MrBayes v. 3.0 (Ronquist and Huelsenbeck 2003). Two MCMC chains, starting from random trees for 1000000 generations and trees, were sampled every 100th generation, resulting in a total of 10000 trees. The first 25% of trees were discarded as burn-in of each analysis. Branches with significant Bayesian Posterior Probabilities (BPP > 0.9) were estimated in the remaining 7500 trees. Phylogenetic trees were viewed with FigTree v. 1.4.2 and processed by Adobe Illustrator CS5. The nucleotide sequence data of the new taxa were deposited in GenBank, and the GenBank accession numbers of all accessions included in the phylogenetic analyses are listed in Table 1.

Table 1.

Isolates and GenBank accession numbers used in the phylogenetic analyses.

Species Isolatea Host Location GenBank accession number
ITS LSU tef1 tub2
Apiognomonioides supraseptata CBS 632.92* Quercus glauca Japan MG976447 MG976448 NA NA
Ellipsoidisporodochium photiniae SAUCC 210421* Photinia serratifolia China OK175559 OK189532 OK206440 OK206442
Ellipsoidisporodochium photiniae SAUCC 210423 Photinia serratifolia China OK175560 OK189533 OK206441 OK206443
Involutiscutellula rubra CBS 192.71* Quercus phillyraeoides Japan MG591899 MG591993 MG592086 MG592180
Involutiscutellula rubra MUCC2303 Quercus phillyraeoides Japan MG591900 MG591994 MG592087 MG592181
Involutiscutellula rubra MUCC2305 Quercus phillyraeoides Japan MG591902 MG591996 MG592089 MG592182
Melanconis groenlandica CBS 116540* Betula nana Greenland KU878552 KU878553 KU878554 KU878555
Oblongisporothyrium castanopsidis CBS 124732 Castanopsis cuspidata Japan MG591849 MG591942 MG592037 MG592131
Oblongisporothyrium castanopsidis CBS 189.71* Castanopsis cuspidata Japan MG591850 MG591943 MG592038 MG592132
Obovoideisporodochium lithocarpi SAUCC 0748* Lithocarpus fohaiensis China MW820279 MW821346 MZ996876 MZ962157
Paratubakia subglobosa CBS 124733 Quercus glauca Japan MG591913 MG592008 MG592102 MG592194
Paratubakia subglobosa CBS 193.71* Quercus glauca Japan MG591914 MG592009 MG592103 MG592195
Paratubakia subglobosoides MUCC2293* Quercus glauca Japan MG591915 MG592010 MG592104 MG592196
Phaeotubakia lithocarpicola CFCC 54422* Lithocarpus glaber China OP951017 OP951015 OQ127584 OQ127586
Phaeotubakia lithocarpicola RK7CX Lithocarpus glaber China OP951018 OP951016 OQ127585 OQ127587
Racheliella wingfieldiana CBS 143669* Syzigium guineense South Africa MG591911 MG592006 MG592100 MG592192
Saprothyrium thailandense MFLUCC 12-0303* Decaying leaf Thailand MF190163 MF190110 NA NA
Sphaerosporithyrium mexicanum CPC 31361 Quercus eduardi Mexico MG591894 MG591988 MG592081 MG592175
Sphaerosporithyrium mexicanum CPC 32258 Quercus eduardi Mexico MG591895 MG591989 MG592082 MG592176
Sphaerosporithyrium mexicanum CPC 33021* Quercus eduardi Mexico MG591896 MG591990 MG592083 MG592177
Tubakia americana CBS 129014 Quercus macrocarpa USA MG591873 MG591966 MG592058 MG592152
Tubakia californica CPC 31496 Quercus agrifolia USA MG591829 MG591922 MG592017 MG592111
Tubakia californica CPC 31499 Quercus wislizeni USA MG591832 MG591925 MG592020 MG592114
Tubakia dryina CBS 112097* Quercus robur Italy MG591851 MG591944 MG592039 MG592133
Tubakia dryina CBS 114912 Quercus sp. Netherlands MG591853 MG591946 MG592041 MG592135
Tubakia dryina CBS 129016 Quercus alba USA MG591870 MG591963 MG592056 MG592150
Tubakia dryinoides CBS 329.75 Quercus sp. France MG591874 MG591967 MG592059 MG592153
Tubakia dryinoides CBS 190.71 Castanea crenata Japan MG591876 MG591968 MG592061 MG592155
Tubakia hallii CBS 129013* Quercus stellata USA MG591880 MG591972 MG592065 MG592159
Tubakia hallii CBS 129015 Quercus stellata USA MG591881 MG591973 MG592066 MG592160
Tubakia japonica CBS 191.71 Castanea crenata Japan MG591885 MG591977 MG592070 MG592164
Tubakia liquidambaris CBS 139744 Liquidambar styraciflua USA MG605068 MG605077 MG603578 NA
Tubakia melnikiana CPC 32249 Quercus canbyi Mexico MG591889 MG591983 MG592076 MG592170
Tubakia oblongispora MUCC2295* Quercus serrata Japan MG591897 MG591991 MG592084 MG592178
Tubakia paradryinoides MUCC2294* Quercus acutissima Japan MG591898 MG591992 MG592085 MG592179


Phylogenetic analyses

The alignment based on the sequence dataset (ITS, LSU, tef1 and tub2) included 35 ingroup taxa, comprising 2736 characters in the aligned matrix. Of these, 1721 characters were constant, 206 variable characters were parsimony-uninformative and 809 characters were parsimony informative. The MP analysis resulted in two equally most parsimonious trees (TL = 2708, CI = 0.615, RI = 0.804, RC = 0.385) and the first tree is shown in Fig. 1. The topologies resulting from MP, ML and BI analyses of the concatenated dataset were congruent. Isolates from the present study formed an individual clade in Tubakiaceae representing a new genus and species named Phaeotubakia lithocarpicola.

Figure 1. 

Phylogram of Tubakiaceae based on combined ITS, LSU, tef1 and tub2 loci. Numbers above the branches indicate maximum parsimony bootstrap (MP BP ≥ 50%), ML bootstrap values (ML-BS ≥ 50%) and Bayesian Posterior Probabilities (BPP ≥ 0.9). The tree is rooted with Melanconis groenlandica (CBS 116540). Ex-type strains are marked with *, and strains from the present study are marked in bold blue.


Phaeotubakia Ning Jiang, gen. nov.

MycoBank No: MB846813


Named derived from phaeo (= pigmented) and its morphological similarity to Tubakia.

Type species

Phaeotubakia lithocarpicola Y.Q. Zhu & Ning Jiang.


Sexual morph: Unknown. Asexual morph in vitro: Conidiomata sporodochial, slimy, black, semi-submerged. Conidiophores reduced to conidiogenous cells. Conidiogenous cells brown, smooth, guttulate, cylindrical to ampulliform, attenuate towards apex, phialidic. Conidia blastic, subglobose, broad ellipsoid to ellipsoid, seldom irregular, brown to dark brown, walls smooth, becoming thicker with age, base rounded or with truncate basal hilum.


Phaeotubakia is proposed as the eleventh genus of Tubakiaceae based on morphological features and phylogeny of combined ITS, LSU, tef1 and tub2 loci (Fig. 1). Phaeotubakia is distinguished from Apiognomonioides, Ellipsoidisporodochium, Involutiscutellula, Oblongisporothyrium, Obovoideisporodochium, Paratubakia, Racheliella, Saprothyrium and Sphaerosporithyrium by having brown to dark brown conidia (Braun et al. 2018; Zhang et al. 2021). Several species of Tubakia are known to have brown conidia, which is similar to Phaeotubakia lithocarpicola (Braun et al. 2018; Zhu et al. 2022). However, they are phylogenetically distinct (Fig. 1).

Phaeotubakia lithocarpicola Y.Q. Zhu & Ning Jiang, sp. nov.

MycoBank No: MB846814
Fig. 2


Named after the host genus, Lithocarpus.


From leaf spots, circular to subcircular, margin distinct, brown to fuscous. Sexual morph: Unknown. Asexual morph in vitro: Conidiomata sporodochial, appeared after 10 days on PDA surface, slimy, black, semi-submerged, 50–350 μm diam. Conidiophores reduced to conidiogenous cells. Conidiogenous cells brown, smooth, guttulate, cylindrical to ampulliform, attenuate towards apex, phialidic, 6–15.5 × 3.5–5 μm. Conidia blastic, subglobose, broad ellipsoid to ellipsoid, seldom irregular, brown to dark brown, walls smooth, becoming thicker with age, base rounded or with truncate basal hilum, (13.5–)14–16.5(–18) × (5.5–)7–8.5(–9) μm (n = 50), L/W = 1.7–3.2.

Figure 2. 

Morphology of Phaeotubakia lithocarpicola (CFCC 54452) A colonies on PDA, MEA and SNA after 10 days at 25 °C B conidiomata formed on PDA C conidiogenous cells giving rise to conidia D–G conidia. Scale bars: 200 μm (B); 10 μm (C–G).

Culture characters

Colonies on PDA flat, spreading, with flocculent aerial mycelium, white to pale luteous, with age forming concentric zones, reaching a 90 mm diameter and forming abundant black conidiomata after 10 days at 25 °C; on MEA flat, spreading, with flocculent aerial mycelium and crenate edge, pale luteous to pale grey, reaching a 45 mm diameter after 10 days at 25 °C; on SNA flat, spreading, with flocculent aerial mycelium forming concentric rings and entire edge, pale luteous, reaching a 60 mm diameter after 10 days at 25 °C.

Specimens examined

China, Guangdong Province, Qingyuan City, Yangshan County, Guangdong Nanling Nature Reserve, on diseased leaves of Lithocarpus glaber, 4 December 2019, Yong Li (holotype CAF 800071; ex-holotype culture CFCC 54422). Guangdong Province, Qingyuan City, Yangshan County, Guangdong Nanling Nature Reserve, on diseased leaves of Lithocarpus glaber, 3 December 2019, Dan-ran Bian (culture RK7CX).


Phaeotubakia lithocarpicola is the sole species within the newly proposed genus, which is associated with leaf spot disease of Lithocarpus glaber. Two tubakiaceous species were reported from the host genus Lithocarpus before the present study, viz. Obovoideisporodochium lithocarpi from Lithocarpus fohaiensis in China and Tubakia californica from Lithocarpus densiflorus in the USA (Braun et al. 2018; Zhang et al. 2021). Phaeotubakia lithocarpicola represents the third tubakiaceous species discovered from the host genus Lithocarpus. However, P. lithocarpicola differs from O. lithocarpi and T. californica by brown conidiogenous cells and brown to dark brown conidia (Braun et al. 2018; Zhang et al. 2021).


Diaporthales is a well-resolved fungal order based on evidence of both morphology and phylogeny (Senanayake et al. 2017, 2018; Fan et al. 2018; Jiang et al. 2020). Tubakia was placed in Melanconiellaceae of Diaporthales (Senanayake et al. 2017), and subsequently transferred to the newly established family of its own Tubakiaceae (Braun et al. 2018). Meanwhile, some species were removed from Tubakia, and seven new genera were proposed based on these species (Braun et al. 2018). Soon after, Ellipsoidisporodochium and Obovoideisporodochium were added to Tubakiaceae (Zhang et al. 2021; Liu et al. 2022). In the present study, the eleventh genus Phaeotubakia is proposed to be included in this family.

Members of Tubakiaceae are quite similar in morphology, but phylogenetically distinct (Braun et al. 2018; Senanayake et al. 2018; Zhang et al. 2021). The sexual morph of Tubakiaceae is not prominent, hence genera and species are distinguished mainly based on their asexual morphology and molecular data.

The newly proposed genus and species Phaeotubakia lithocarpicola in the present study produce brown to dark brown conidia on the PDA plates, which is morphologically different from the other tubakiaceous taxa, but similar to Melanconis-like taxa of Diaporthales (Voglmayr et al. 2012, 2017; Jiang et al. 2021b). Four families of Diaporthales are known to contain Melanconis-like genera and species, namely Juglanconidaceae, Melanconidaceae, Melanconiellaceae and Pseudomelanconidaceae (Jiang et al. 2018; Fan et al. 2018; Senanayake et al. 2018). Hence, traditional morphological identification of diaporthalean fungi is insufficient.

The center of genetic diversity of Tubakia appears to be in East Asia, e.g. China and Japan, where Fagaceae hosts are the most common hosts (Harrington and McNew 2018). Obovoideisporodochium lithocarpi and several new Tubakia species (T. cyclobalanopsidis and T. quercicola) recently discovered from trees of Fagaceae (Zhang et al. 2021; Zhu et al. 2022), and Phaeotubakia lithocarpicola proposed in the present study support this phenomenon well. More taxa of Tubakiaceae may be revealed by more investigations of fungal diversity on Fagaceae in the future.


This research was funded by the National Microbial Resource Center of the Ministry of Science and Technology of the People’s Republic of China (NMRC-2021-7).


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