MycoKeys 98: 273-297 (2023) DOI: 10.3897/mycokeys.98.107093 (93 MycoKeys Pleomorphic Dematiomelanomma yunnanense gen. et sp. nov. (Ascomycota, Melanommataceae) from grassland vegetation in Yunnan, China Ying Gao'?8®©, Tingfang Zhong*>®, Jayarama D. Bhat®’®, Antonio Roberto Gomes de Farias*®, Turki M. Dawoud®, Kevin D. Hyde?8®, Weiqiang Xiong®®, Yunju Li®'°®, Heng Gui'*®, Xuefei Yang*®, Shixi Wu®®, Dhanushka N. Wanasinghe'*© Center for Mountain Futures, Kunming Institute of Botany, Honghe 654400, Yunnan, China 1 2 School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand 3 Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand 4 Key Laboratory of Economic Plants and Biotechnology and the Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China University of Chinese Academy of Sciences, Beijing 100049, China Department of Botany and Microbiology, College of Science, King Saud University, PO. Box 2455, Riyadh-11451, Saudi Arabia Science and Technology on Aerospace Chemical Power Laboratory, Hubei Institute of Aerospace Chemotechnology, Xiangyang, 441003, Hubei, China 5 6 7 Biology Division, Vishnugupta Vishwavidyapeetam, Ashoke, Gokarna 581326, India 8 9 The State Phosphorus Resource Development and Utilization Engineering Technology Research Centre, Yunnan Phosphate Chemical Group Co. Ltd, Kunming, China 10 YTH Modern Agriculture Development Co. Ltd, Kunming, China Corresponding authors: Shixi Wu (shixi_wu@outlook.com); Dhanushka N. Wanasinghe (dnadeeshan@gmail.com) OPEN Qaceess Academic editor: N. Wijayawardene Received: 27 May 2023 Accepted: 3 July 2023 Published: 25 July 2023 Citation: Gao Y, Zhong T, Bhat JD, Gomes de Farias AR, Dawoud TM, Hyde KD, Xiong W, Li Y, Gui H, Yang X, Wu S, Wanasinghe DN (2023) Pleomorphic Dematiomelanomma yunnanense gen. et sp. nov. (Ascomycota, Melanommataceae) from grassland vegetation in Yunnan, China. MycoKeys 98: 273-297. https://doi.org/10.3897/ mycokeys.98.107093 Copyright: © Ying Gao et al. This is an open access article distributed under terms of the Creative Commons Attribution License (Attribution 4.0 International - CC BY 4.0). Abstract During a survey of microfungi associated with grasslands and related vegetation types from Yunnan Province in China, various ascomycetous and coelomycetous fungi were isolated. This study reports the discovery of four strains of ascomycetous and coe- lomycetous fungi from dead stalks of Hypericum monogynum L. (Hypericaceae) and Rubus parvifolius L. (Rosaceae) in the Zhaotong region of Yunnan Province, China. The isolates were characterized using multi-locus phylogenetic analyses and were found to represent a new monophyletic lineage in Melanommataceae (Pleosporales, Dothideo- mycetes). This new clade was named as Dematiomelanomma yunnanense gen. et sp. nov. which consists of both sexual and asexual morphs. The sexual morph is charac- terized by globose to subglobose ascomata with a central ostiole, cylindrical asci with a pedicel and ocular chamber, and muriform, ellipsoidal to fusiform ascospores. The asexual morph has synanamorphs including both brown, muriform macroconidia and hyaline, round to oblong or ellipsoidal microconidia. These findings contribute to the understanding of fungal diversity in grasslands and related vegetation types in Yunnan Province, China. Key words: Asexual morph, Greater Mekong Subregion, molecular phylogeny, muriform, Pleosporales, sexual morph, taxonomy Introduction Melanommataceae is a species-rich family in the order Pleosporales and currently encompassing 351 species (Banki et al. 2023) which have diverse 273 Ying Gao et al.: Dematiomelanomma yunnanense gen. et sp. nov. lifestyles viz., fungicolous, hyperparasitic, parasitic or saprobic (Tian et al. 2015; Hashimoto et al. 2017; Wijayawardene et al. 2017; Beenken et al. 2020; Hongsanan et al. 2020). The majority of species in this family have a wide distribution in temperate and subtropical regions and are commonly found on twigs or barks of various woody plants in terrestrial, marine, or freshwater habitats (Hyde et al. 2013; Tian et al. 2015). The latest treatment of the family by Wijayawardene et al. (2022a) accepted 35 genera in Melanommataceae. Except for Asymmetricospora, Bicrouania, Calyptronectria, Exosporiella, Mamillisphaeria, Melanocamarosporium, Navicella and Nigrolentilocus, all other genera have available sequence data for molecular comparisons. Melanommataceae is a family of fungi that has been studied extensively, but few reports exist on its species found in China. Among the earliest reports are Aposphaeria fugax (Saccardo 1921; Wei and Huang 1939), Aposphaeria pu- nicina (Teng 1936), and Melanomma glumarum (Tai 1979). Subsequent stud- ies have identified additional species, including Camposporium hyderabadense (Matsushima 1980), Byssosphaeria jamaicana (Sivanesan and Hsieh 1989), Melanomma cucurbitarioideum (Yuan and Barr 1994), and Navicella xinjiangen- sis (Yuan and Barr 1994). More recent studies have introduced Seifertia shan- grilaensis (Li et al. 2016), Fusiconidium aquaticum (Li et al. 2017), Alpinaria rho- dodendri (Thiyagaraja et al. 2020), and Byssosphaeria phoenicis (Kularathnage et al. 2022). Despite these findings, there is still much to learn about the fungal diversity of Melanommataceae in China. Grassland ecosystems are a vital component of the Earth’s land surface, covering an area of 52.5 million km2 and providing numerous ecosystem services (Bai and Cotrufo 2022). The plant species in this biome host var- ious microorganisms, including fungi, with a broad spectrum of nutritional modes (Karunarathna et al. 2022). Grassland ecosystems support a high di- versity of fungi and are likely to harbor numerous undescribed taxa (Hyde et al. 2020). However, human disturbance and climate change have been caus- ing the rapid destruction and degradation of grasslands, leading to slow or non-existent recovery of biodiversity and essential functions (White et al. 2000; Chen et al. 2018; Bardgett et al. 2021; Lugato et al. 2021; Buisson et al. 2022; Zhu et al. 2022). Fungi are sensitive to environmental changes and global warming, which may be triggering the extinction of many species that cannot adapt fast enough to the rate of ecological change (Wanasinghe et al. 2022). In order to mitigate species loss and understand their ecological significance, extensive fungal sampling across various grasslands in dif- ferent geographic regions is urgently required. Therefore, we are continu- ously surveying the grassland-associated microfungi in Yunnan, China. As a result, several strains of unknown species were isolated from different plant hosts. This paper describes a fungus associated with Hypericum monogynum and Rubus parvifolius in the Zhaotong region as a new species in a new genus (Dematiomelanomma) within Melanommataceae, with its phylogenetic posi- tion being confirmed based on multi-locus phylogenetic analyses of ITS, LSU, SSU, tef1-a and rpb2. Furthermore, we compared it with the known genera in the family. This study provides insight into the grassland fungi in China and empha- sizes that Zhaotong grasslands may have many undiscovered fungal resources waiting to be described. Mycokeys 98: 273-297 (2023), DOI: 10.3897/mycokeys.98.107093 274 Ying Gao et al.: Dematiomelanomma yunnanense gen. et sp. nov. Materials and methods Sample collection and isolation Specimens were collected from the dead wood of Hypericum monogynum L. (Hypericaceae) and Rubus parvifolius L. (Rosaceae) in Zhaotong, Yunnan, Chi- na, during autumn. The local environment in Zhaotong features Poaceae as the most abundant tree species and a typical plateau vegetation with a three-dimen- sional monsoon climate at a maximum elevation of ~4000 m (Pei 2022). Sam- ples were taken to the laboratory in plastic Ziplock bags for observation and examination. Fungal specimens were rehydrated with tap water and examined using an Olympus SZ-61 dissecting microscope. Single spore isolation of both ascospores and conidia was conducted, and germinated spores were processed by following the methods described in Senanayake et al. (2020). Pure cultures were incubated at 26 °C for two weeks. The living cultures were deposited in the Kunming Institute of Botany Culture Collection (KUNCC), and duplicates were maintained in the China General Microbiological Culture Collection Center (CGMCC). Dried herbarium specimens (at room temperature) were deposited in the herbarium of the Kunming Institute of Botany Academia Sinica (HKAS). The Index Fungorum and Faces of fungi (FoF) numbers were obtained for the new taxa (Jayasiri et al. 2015; Index Fungorum 2023). Data from the Greater Mekong Subregion are deposited to the GMS database (Chaiwan et al. 2021). Morphological observations Ascomata and conidiomata were hand-sectioned using a sterilized razor blade. Internal structures such as asci, ascospores, hamathecium tissues, conidio- phores, and conidia were mounted on a slide in a drop of tap water using a sterilized needle to observe the micromorphological characteristics. These fea- tures were examined under a Nikon ECLIPSE Ni-U complex microscope with differential interference contrast (DIC) and phase contrast (PC) illumination. Images of microscopic structures were captured using a Nikon DS-Ri2 camera. Photo plates and measurements were processed using Adobe Photoshop CS6 Extended version 13.0.1 (Adobe Systems, CA, USA). Wherever possible, at least 30 measurements were taken. For morphological structures, mean, minimum, maximum and standard deviation were calculated. Structural dimensions are reported as mean + standard deviation. DNA extraction, PCR amplification and DNA sequencing Fungal mycelia grown on PDA for 2-3 weeks were scraped using a sterilized scal- pel and transferred to 1.5 mL centrifuge tubes. The extraction of genomic DNA was performed using these fresh mycelia following the methods of Wanasinghe et al. (2016), using the Biospin Fungus Genomic DNA Extraction Kit (BioFlux, Hangzhou, PR. China) following manufacturer guidelines. Also, genomic DNA from the fresh fruiting bodies was extracted using an E.Z.N.A. Forensic DNA Kit-D3591 (Ome- ga Biotek, Inc) following the manufacturer’s protocol for further confirmation of our single spore isolations. The reference DNA for the polymerase chain reaction (PCR) were stored at 4 °C for regular use and at -20 °C for long-term usage. MycoKkeys 98: 273-297 (2023), DOI: 10.3897/mycokeys.98.107093 275 Ying Gao et al.: Dematiomelanomma yunnanense gen. et sp. nov. The genomic DNA was used to amplify gene regions 18S small subunit rDNA (SSU), 28S large subunit rDNA (LSU), internal transcribed spacers (ITS), transla- tion elongation factor 1-alpha (tef1-a) and RNA polymerase second largest sub- unit (rpb2) as described in Wanasinghe and Mortimer (2022). The total volume of PCR mixtures for amplification was 25 pL containing 8.5 uL ddH,0, 12.5 pL 2xF8FastLong PCR MasterMix (Beijing Aidlab Biotechnologies Co.Ltd), 2 uL of DNA template, 1 tL of each forward and reverse primers (stock of 10 pM). The PCR thermal cycle profiles for ITS, LSU, SSU and tef1-a: the thermal conditions included initial denaturation at 94 °C for 3 min, followed by 35 cycles of denatur- ation at 94 °C for 10 s; annealing temperatures at 55 °C for 15s, elongation at 72 °C for 20 s, and final extension at 72 °C for 10 min. The PCR amplification con- dition of rpb2 was set as denaturation at 95 °C for 3 min, followed by 35 cycles of denaturation at 95 °C for 45 s, annealing temperatures at 57 °C for 50 s, elon- gation at 72 °C for 90 s, and final extension at 72 °C for 10 min. The amplified PCR fragments were then sent to a private company for sequencing (Shanghai Sangon Biological Engineering Technology and Service Co., Ltd., China). Alignment and phylogenetic analyses Sequence contigs of SSU, LSU, ITS, tef7-a and rpb2 gene regions were assem- bled, trimmed, and manually checked using BioEdit v. 7.0.5.3 (Hall 1999). The consensus sequences generated in this study were supplemented by additional sequences obtained from GenBank (Table 1) based on BLAST searchers and the past literature (Wanasinghe et al. 2018; Pem et al. 2019; Hongsanan et al. 2020; Hyde et al. 2021; Tennakoon et al. 2021). Multiple sequence alignments with individual gene datasets were generated with MAFFT v.7. online platform (Katoh et al. 2019) and trimmed with TrimAl v. 1.3 (Capella-Gutiérrez et al. 2009) via the web server Phylemonz2 (http://phylemon.bioinfo.cipf.es/utilities.html; accessed on 1 January 2023). Individual datasets were concatenated into a combined dataset using BioEdit v. 7.0.5.3. The individual and combined datasets were sub- jected to maximum likelihood (ML) and Bayesian (BI) phylogenetic inference. The FASTA format of the combined datasets was converted to PHYLIP for- mat via the Alignment Transformation Environment (ALTER) online program (http://www.sing-group.org/ALTER/; accessed on 1 January 2023) and used for maximum likelihood analysis (ML). Maximum likelihood trees were inferred us- ing RAXML-HPC2 on the XSEDE (8.2.12) (Stamatakis 2014) in CIPRES Science Gateway v.3.3 (Miller et al. 2010) online platform using the GTR+GAMMA model of nucleotide evolution with 1000 bootstrap replicates. The alignments contain- ing SSU, LSU, ITS, tef1-a and rpb2 were converted to NEXUS format (.nxs) using CLUSTAL X (2.0) and PAUP v. 4.0610 (Thompson etal. 1997; Swofford 2002). The evolutionary models for BI analysis were selected independently for each locus using MrModeltest v. 2.3 (Nylander et al. 2008) under the Akaike Information Cri- terion (AIC). GTR+I+G was selected as the best-fit model for all five analyses and processed for Bayesian inference analysis (Bl). BI analysis was conducted using MrBayes on XSEDE (3.2.7a) (Ronquist et al. 2012) in CIPRES Science Gateway v.3.3 setting GTR+I+G, six simultaneous Markov chains were run for 50,000,000 generations, and the trees were sampled for every 100" generation. The first 25% of trees were considered burn-in and discarded. The two runs were considered converged when the standard deviation of split frequencies dropped below 0.01. Mycokeys 98: 273-297 (2023), DOI: 10.3897/mycokeys.98.107093 276 Ying Gao et al.: Dematiomelanomma yunnanense gen. et sp. nov. Table 1. GenBank accession numbers of the strains used for phylogenetic analysis in this study. “*” Denotes ex-type, ex-isotype, ex-paratype or ex-epitype strains. “t’ Denotes type species. Newly generated sequences are shown in bold. NA: sequence data is not available. GenBank accession no. Species Aposphaeria corallinolutea MFLU 16-2412 MT177916 MT177943 MT177971 MT432199 MFLUCC 17-2015 MG543922 MG543913 MG547226 MG547224 NCYU 19-0073# MW063224 MWw079352 MW183787 NA NA Bertiella ellipsoidea Bertiella fici Beverwykella pulmonaria* KY189974 KY189974 — Ky190005 | = NAC KY189990 Cyclothyriella rubronotata* KX650571 Cyclothyriella rubronotatat KX650574 Dematiomelanomma yunnanense* 00413234 Dematiomelanomma yunnanense* - KUNCC 23-12730 | 0225529 | 00360648 | 00360652 | 00413239 00413236 Dematiomelanomma yunnanense* / CGMCC 3.23744 | 00225530 | 00360649 | 00360653 | 00413240 | 00413237 Dematiomelanomma yunnanense* - KUNCC 22-1267 | 09225531 | 09360650 | 09360654 | 00413241 — 0Q413235 Fusiconidium mackenziei* KX611116 Melanocamarosporium galiicolat NA Melanocamarosporioides ugamicat NA Melanocucurbitaria uzbekistanica* NA Melanodiplodia tianschanicat MG829256 Melanodiplodia tianschanica*t MG829257 Phragmotrichum chailletii* MN313840 MycoKeys 98: 273-297 (2023), DOI: 10.3897/mycokeys.98.107093 277 Ying Gao et al.: Dematiomelanomma yunnanense gen. et sp. nov. GenBank accession no. ae seh ITS LSU SSU tef1-a rpb2 Phragmotrichum chailletii* CPC 33341 MN313813 MN317294 NA MN313859 MN313841 Phragmocephala garethjonesii MFLUCC 15-0018* KP698722 KP698726 KP698730 NA NA Pleotrichocladium opacum* AU-BD04 JN995638 JN941370 JN938733 NA NA Pleotrichocladium opacum* FMR 12416# KY853462 KY853523 NA NA NA Praetumpfia obducenst WU 36895 KY189982 KY189982 NA KY190017 KY189998 Praetumpfia obducetis* CBS 141474# KY189984 KY189984 KY190008 KY190019 KY190000 Pseudobyssosphaeria bambusaet MFLU 18-0151* MG737556 MG737555 NA MG737557 NA Pseudostrickeria ononidis MFLUCC 14-0949# NA KT934255 KT934259 KT934263 KT934264 Pseudostrickeria rosae MFLUCC 17-0643* MG828954 MG829065 MG829169 MG829234 NA Pseudotrichia mutabilis SMH 1541 NA GU385209 NA NA NA Pseudotrichia mutabilis WU 36923 KY189988 KY189988 NA KY190022 KY190003 Sarimanas pseudofluviatile KT760# LC001717 LC001714 LC001711 NA NA Sarimanas shirakamiense* HHUF 30454* NR_138017 NG_059803 NG_061263 NA NA Seifertia alpina ZT Myc 59953* MK502003 MK502026 MK502037 MK502083 MK502059 Seifertia azaleaet ZT Myc 59954 MK502004 MK502028 MK502038 MK502085 MK502061 Tumularia aquatica CBS 212.46# MH856165 MH867689 NA NA NA Tumularia tuberculata* CBS 256.84 NA GU301851 NA GU349006 NA Uzbekistanica rosae-hissaricae* MFLUCC 17-081 9# MG828975 MG829087 MG829187 MG829242 MG829262 Uzbekistanica yakutkhanika MFLUCC 17-0842* MG828978 MG829090 MG829190 MG829245 MG829265 AU-BD: Personal collection of Gareth Griffith; CBS: Culture Collection of the Westerdijk Fungal Biodiversity Institute, Netherlands; CPC: Personal collection of PW. Crous, Netherlands; FMR: culture collection of the Faculty of Medicine at the Rovira i Virgili University, Spain; GKM: Personal collection of George K. Mugambi; HHUF: Herbarium of Hirosaki University, Fungi, Japan; KT: Personal collection of Kazuaki Tanaka; KUNCC: Kunming Institute of Botany Culture Collection, China; MAFF: Genebank Project of NARO, Japan; MFLUCC/MFLU: Mae Fah Luang University Culture Collection, Chiang Rai, Thailand; NCYU: National Chiayi University Herbarium, Taiwan, China; NFCCI: National Fungal Culture Collection of India; SMH: Personal collection of Sabine M. Huhndorf; TASM: Tashkent Mycological Herbarium of the Institute of Botany, Uzbekistan; ZT Myc: Fungal collection of the ETH (Eidgendssische Technische Hoch- schule) Zurich, Switzerland. The Fig Tree v 1.4.0 program (Rambaut 2012) was used to visualize the phy- logenetic trees and reorganized in Microsoft PowerPoint before being saved in PDF format and finally converted to TIFF format using Adobe Photoshop CS6 Extended version 13.0.1 (Adobe Systems, CA, USA). In this paper, we follow the guidelines of Aime et al. (2021), Chethana et al. (2021) and Pem et al. (2021) when introducing new species. Results Phylogenetic analysis The combined sequence data of SSU, LSU, ITS, tefl-a and rpb2 comprised 62 strains of Melanommataceae and Cyclothiyriella rubronotata (CBS 121892 and CBS 141486) as outgroup taxa (Fig. 1). Atotal of 4,678 characters, including gaps, were obtained in the phylogenetic analysis, viz. SSU = 1-1,020 bp, LSU = 1,021- 1,867 bp, ITS = 1,868-2,398 bp, tef1-a = 2,399-3,828 bp, rpb2 = 3,829-4,678 bp. The RAXML analysis of the combined dataset yielded a best scoring tree with a final ML optimization likelihood value of -25464.925021. The matrix had 1513 distinct alignment patterns, with 30.36% undetermined characters or gaps. MycoKeys 98: 273-297 (2023), DOI: 10.3897/mycokeys.98.107093 978 Ying Gao et al.: Dematiomelanomma yunnanense gen. et sp. nov. j ia tianschanica TASM 6112 eoy oe Melanodiplodia tianschanica TASM 6 Melanodiplodia tianschanica TASM 6111 Melanodiplodia Melanodiplodia tianschanica MFLUCC 17-0805 99/1 .00 Melanocamarosporioides ugamica MFLU 17-0064 Melanocamarosporioides N Muriformistrickeria rubi MFLUCC 17-2550 Muriformistrickeria rubi MFLUCC 15-0681 Muriformistrickeria mony 7 | Muriformistrickeria rosae MFLU 16-0227 * | Alpinaria rhododendri KT 2520 Alpinaria rhododendri CBS 141994 Herpotrichia juniperi CBS 200.31 Herpotrichia Melanocamarosporium galiicola MFLUCC 13-0545 Melanocamarosporium *T Seifertia azaleae ZT Myc 59954 Alpinaria 66/0.97 pian 2 Seiferti 98/-- Seifertia alpina ZT Myc 59953 Sige 98/1.00 4 Phragmotrichum chailletii CPC 33263 Phragmotrichum chailletii CPC 33341 yearclesiaeunle TEs : Petrakia echinata WU 36922 Ronee Petrakia echinata CBS 133070 Melanocucurbitaria uzbekistanica MFLUCC 17-0829 Melanocucurbitaria Marjia uzbekistanica TASM 6122 erie 68/- Marjia tianshanica TASM 6120 : Pseudotrichia mutabilis SMH 1541 BSSUCONTe idl Pseudotrichia mutabilis WU 36923 w Herpotrichia xiaokongense KUMCC 21-0004 Herpotrichia Herpotrichia macrotricha GKM 196N f Tumularia tuberculata CBS 256.84 ig ! Tumularia aquatica CBS 212.46 a aos 98/1.00 86/1.00 Pleotrichocladium opacum FMR 12416 ePyarrancrahc tiie 791.091" Pleotrichocladium opacum AU-BD04 ?1/1.90— $arimanas pseudofluviatile KT760 é : Sarimanas Sarimanas shirakamiense HHUF 30454 Monoseptella rosae MFLUCC 17-0815 Monoseptella 96/0.98 -~ Byssosphaeria macarangae MFLUCC 17-2655 Econ enciene a Byssosphaeria taiwanense MFLUCC 17-2643 3 ;