Research Article |
Corresponding author: Yong Li ( aisuntaifu@163.com ) Academic editor: Jennifer Luangsa-ard
© 2023 Ning Jiang, Ya-Quan Zhu, Han Xue, Chun-Gen Piao, Yong Li.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Jiang N, Zhu Y-Q, Xue H, Piao C-G, Li Y (2023) Phaeotubakia lithocarpicola gen. et sp. nov. (Tubakiaceae, Diaporthales) from leaf spots in China. MycoKeys 95: 15-25. https://doi.org/10.3897/mycokeys.95.98384
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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 (
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 (
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 (
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).
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,
http://cfcc.caf.ac.cn/; accessed on 6 December 2022), and the specimens in the herbarium of the
Chinese Academy of Forestry (
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.
The fungal genomic DNA was extracted from mycelia grown on PDA palates after 10 days following the method in
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, https://www.ncbi.nlm.nih.gov; accessed on 15 October 2022), based on sequences from
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 (https://www.phylo.org) using RAxML-HPC BlackBox 8.2.10 (
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 |
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.
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.
Named derived from phaeo (= pigmented) and its morphological similarity to Tubakia.
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.
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.
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.
China, Guangdong Province, Qingyuan City, Yangshan County, Guangdong Nanling Nature Reserve, on diseased leaves of Lithocarpus glaber, 4 December 2019, Yong Li (holotype
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 (
Diaporthales is a well-resolved fungal order based on evidence of both morphology and phylogeny (
Members of Tubakiaceae are quite similar in morphology, but phylogenetically distinct (
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 (
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 (
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).