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Species concepts of Dothideomycetes:classification,phylogenetic inconsistencies and taxonomic standardization

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Fungal Diversity 2021年第4期109卷 283-319页

作者： Dhandevi Pem Rajesh Jeewon Kandawatte Wedaralalage Thilini Chethana Sinang Hongsanan Mingkwan Doilom Nakarin Suwannarach kevin david hyde Innovative Institute of Plant Health Zhongkai University of Agriculture and EngineeringHaizhu DistrictGuangzhou 510225People’s Republic of China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Health Sciences Faculty of Medicine and Health SciencesUniversity of MauritiusReduitMauritius Faculty of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Guangdong Provincial Key Laboratory for Plant Epigenetics Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Science and OceanographyShenzhen UniversityShenzhen 518060People’s Republic of China Research Center of Microbial Diversity and Sustainable Utilization Chiang Mai UniversityChiang Mai 50200Thailand

The species is one of the basic units of biological *** species concepts and recognition are essential topics in taxonomic studies and other biological *** the first part of this review,we briefly discuss the taxonomic history of the class *** the second part of the paper,we review four commonly used species concepts,focusing on morphological,ecological,biological and phylogenetic criteria and their applicability in the taxonomy of *** application and utility of the four criteria is discussed with examples in the genera Ascochyta,Cercospora and *** problems and challenges of studying Dothideomycetes are analyzed and basic guidelines for classifying species under the above criteria are provided.

关键词： Challenges DNA Fungi Morph Phylogeny Species Taxonomy

Live-cell imaging:new avenues to investigate retinal regeneration

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Neural Regeneration Research 2017年第8期12卷 1210-1219页

作者： Manuela Lahne david R.hyde Department of Biological Sciences University of Notre Dame Notre Dame IN USA

Sensing and responding to our environment requires functional neurons that act in concert. Neuronal cell loss resulting from degenerative diseases cannot be replaced in humans, causing a functional impairment to integrate and/or respond to sensory cues. In contrast, zebrafish（Danio rerio） possess an endogenous capacity to regenerate lost neurons. Here, we will focus on the processes that lead to neuronal regeneration in the zebrafish retina. Dying retinal neurons release a damage signal, tumor necrosis factor α, which induces the resident radial glia, the Müller glia, to reprogram and re-enter the cell cycle. The Müller glia divide asymmetrically to produce a Müller glia that exits the cell cycle and a neuronal progenitor cell. The arising neuronal progenitor cells undergo several rounds of cell divisions before they migrate to the site of damage to differentiate into the neuronal cell types that were lost. Molecular and immunohistochemical studies have predominantly provided insight into the mechanisms that regulate retinal regeneration. However, many processes during retinal regeneration are dynamic and require live-cell imaging to fully discern the underlying mechanisms. Recently, a multiphoton imaging approach of adult zebrafish retinal cultures was developed. We will discuss the use of live-cell imaging, the currently available tools and those that need to be developed to advance our knowledge on major open questions in the field of retinal regeneration.

关键词： multiphoton microscopy live-cell imaging zebrafish interkinetic nuclear migration tissue culture retinal regeneration Miiller glia neuronal progenitor cell differentiation phagocytosis

Retinal regeneration requires dynamic Notch signaling

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Neural Regeneration Research 2022年第6期17卷 1199-1209页

作者： Leah J.Campbell Jaclyn L.Levendusky Shannon A.Steines david R.hyde Department of Biological Sciences Center for Zebrafish ResearchCenter for Stem Cells and Regenerative MedicineUniversity of Notre DameNotre DameINUSA

Retinal damage in the adult zebrafish induces Müller glia reprogramming to produce neuronal progenitor cells that proliferate and differentiate into retinal *** signaling,which is a fundamental mechanism known to drive cell-cell communication,is required to maintain Müller glia in a quiescent state in the undamaged retina,and repression of Notch signaling is necessary for Müller glia to reenter the cell *** dynamic regulation of Notch signaling following retinal damage also directs proliferation and neurogenesis of the Müller glia-derived progenitor cells in a robust regeneration *** contrast,mammalian Müller glia respond to retinal damage by entering a prolonged gliotic state that leads to additional neuronal death and permanent vision *** the dynamic regulation of Notch signaling in the zebrafish retina may aid efforts to stimulate Müller glia reprogramming for regeneration of the diseased human *** findings identified DeltaB and Notch3 as the ligand-receptor pair that serves as the principal regulators of zebrafish Müller glia *** addition,multi-omics datasets and functional studies indicate that additional Notch receptors,ligands,and target genes regulate cell proliferation and neurogenesis during the regeneration time ***,our understanding of Notch signaling during retinal regeneration is *** fully appreciate the complex regulation of Notch signaling that is required for successful retinal regeneration,investigation of additional aspects of the pathway,such as post-translational modification of the receptors,ligand endocytosis,and interactions with other fundamental pathways is *** we review various modes of Notch signaling regulation in the context of the vertebrate retina to put recent research in perspective and to identify open areas of inquiry.

关键词： differentiation gliosis Müller glia neuronal progenitor cell Notch signaling proliferation quiescence retinal development retinal regeneration zebrafish

Evolution of non‑lichenized,saprotrophic species of Arthonia(Ascomycota,Arthoniales)and resurrection of Naevia,with notes on Mycoporum

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Fungal Diversity 2020年第3期102卷 205-224页

作者： Vinodhini Thiyagaraja Robert Lücking Damien Ertz Dhanushka N.Wanasinghe Samantha C.Karunarathna Erio Camporesi kevin D.hyde CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Entomology and Plant Pathology Faculty of AgricultureChiang Mai UniversityChiang Mai 50002Thailand World Agro Forestry Centre East and Central Asia Kunming 650201YunnanPeople’s Republic of China Botanischer Garten und Botanisches Museum Freie Universitat BerlinKonigin‑Luise‑Str.6-814195 BerlinGermany Research Department Meise Botanic GardenNieuwelaan 381860 MeiseBelgium Service Général de l’Enseignement Supérieur et de la Recherche Scientifique Fédération Wallonie-BruxellesRue A.Lavallée 11080 BrusselsBelgium A.M.B.G.Gruppo Micologico Forlivese“Antonio Cicognani” Via Roma 18ForliItaly A.M.B Circolo Micologico“Giovanni carini”C.P.314BresciaItaly Societa per gli Studi Naturalistici della Romagna C.P.144BagnacavalloRAItaly

Fungi that are barely lichenized or non-lichenized and closely related to lichenized taxa,the so-called borderline fungi,are an important element in reconstructing the evolutionary history of lichenized *** is a prime example including non-lichenized,saprotrophic lineages which potentially were precursors to lichenized *** this study,we focused on saprotrophic species of Arthonia sensu lato,including new sequence data for Arthonia *** obtained fresh material of this taxon from a living branch of Fraxinus ornus in Italy to assess its taxonomic status and to elucidate its phylogenetic relationships within *** sections of the thallus and ascomata of *** confirmed the absence of a *** likelihood and Bayesian analyses of combined mtSSU,nuLSU and RPB2 sequence data placed the species close to ***(barely lichenized or non-lichenized)and ***(non-lichenized)in a clade closely related to Arthonia sensu stricto,and the *** clade is here resurrected under the name *** character state analysis within a broader context of Arthoniales does not support the saprotrophic lifestyle to be a plesiomorphic feature,but suggests loss of lichenization in Naevia,as well as loss and possible regain in a second clade containing saprotrophic species and including taxa resembling Mycoporum,underlining the evolutionary plasticity of *** two clades constitute model taxa to further investigate the evolution of alternative biological lifestyles within the context of chiefly lichenized taxa.

关键词： Arthonia susa Arthothelium Evolution Lichenization Mycarthonia Pseudoarthonia Saprobes

SAR of tricyclic sulfones as γ-secretase inhibitors

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Science China Chemistry 2011年第11期54卷 1688-1701页

作者： COLE david ASBEROM Ted BARA Tom BENNETT Chad BURNETT Duane A. CLADER John DOMALSKI Martin GREENLEE William J. hyde Lynn JOSIEN Hubert McBRIAR Mark McKITTRICK Brian PISSARNITSKI Dmitri RAJAGOPALAN Murali SASIKUMAR Thavalakulamgara Merck Research Laboratories 2015 Galloping Hill RoadKenilworth New Jersey 07033 USA

Novel tricyclic sulfones as γ-secretase inhibitors have been reported by this laboratory for the treatment of Alzheimer's disease. Compounds in this series have comparable or better in vitro activities and in vivo efficacies than sulfonamide analogues re- ported previously by this laboratory. Based on the previously reported tricyclic sulfone scaffold, additional SAR studies of C ring were carried out. Various C-ring structures including cyclohexane, pyran, and piperidine were tolerated. Additionally, the 7- and 8- positions of the C-ring were identified as the best sites to introduce substituent for modulating the pharmacokinetic properties of compounds from this series.

关键词： tricyclic sulfones T-secretase Alzheimer's disease inhibitors

FungalTraits:a user-friendly traits database of fungi and fungus-like stramenopiles

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Fungal Diversity 2020年第2期105卷 I0001-I0016页

作者： Sergei Põlme Kessy Abarenkov RHenrik Nilsson Björn D.Lindahl Karina Engelbrecht Clemmensen Havard Kauserud Nhu Nguyen Rasmus Kjøller Scott T.Bates Petr Baldrian Tobias Guldberg Frøslev Kristjan Adojaan Alfredo Vizzini Ave Suija Donald Pfister Hans-Otto Baral Helle Järv Hugo Madrid Jenni Nordén Jian-Kui Liu Julia Pawlowska Kadri Põldmaa Kadri Pärtel Kadri Runnel Karen Hansen Karl-Henrik Larsson kevin david hyde Marcelo Sandoval-Denis Matthew E.Smith Merje Toome-Heller Nalin N.Wijayawardene Nelson Menolli Jr Nicole K.Reynolds Rein Drenkhan Sajeewa S.N.Maharachchikumbura Tatiana B.Gibertoni Thomas Læssøe William Davis Yuri Tokarev Adriana Corrales Adriene Mayra Soares Ahto Agan Alexandre Reis Machado Andrés Argüelles-Moyao Andrew Detheridge Angelina de Meiras-Ottoni Annemieke Verbeken Arun Kumar Dutta Bao-Kai Cui C.K.Pradeep César Marín Daniel Stanton Daniyal Gohar Dhanushka N.Wanasinghe Eveli Otsing Farzad Aslani Gareth W.Griffith Thorsten H.Lumbsch Hans-Peter Grossart Hossein Masigol Ina Timling Inga Hiiesalu Jane Oja John Y.Kupagme József Geml Julieta Alvarez-Manjarrez Kai Ilves Kaire Loit Kalev Adamson Kazuhide Nara Kati Küngas Keilor Rojas-Jimenez Krišs Bitenieks Laszlo Irinyi LászlóGNagy Liina Soonvald Li-Wei Zhou Lysett Wagner M.Catherine Aime MaarjaÖpik María Isabel Mujica Martin Metsoja Martin Ryberg Martti Vasar Masao Murata Matthew PNelsen Michelle Cleary Milan C.Samarakoon Mingkwan Doilom Mohammad Bahram Niloufar Hagh-Doust Olesya Dulya Peter Johnston Petr Kohout Qian Chen Qing Tian Rajasree Nandi Rasekh Amiri Rekhani Hansika Perera Renata dos Santos Chikowski Renato L.Mendes-Alvarenga Roberto Garibay-Orijel Robin Gielen Rungtiwa Phookamsak Ruvishika S.Jayawardena Saleh Rahimlou Samantha C.Karunarathna Saowaluck Tibpromma Shawn P.Brown Siim-Kaarel Sepp Sunil Mundra Zhu-Hua Luo Tanay Bose Tanel Vahter Tarquin Netherway Teng Yang Tom May Torda Varga Wei Li Victor Rafael Matos Coimbra Virton Rodrigo Targino de Oliveira Vitor Xavier de Lima Vladimir S.Mikryukov Yongzhong Lu Yosuke Matsuda Yumiko Miyamoto Urm Institute of Ecology and Earth Sciences University of Tartu14A Ravila50411 TartuEstonia Natural History Museum University of Tartu46 Vanemuise Str51003 TartuEstonia Gothenburg Global Biodiversity Centre Box 46140530 GothenburgSweden Department of Biological and Environmental Sciences University of GothenburgGothenburgSweden Department of Soil and Environment Swedish University of Agricultural SciencesBox 701475007 UppsalaSweden Department of Forest Mycology and Plant Pathology Swedish University of Agricultural SciencesBox 702675007 UppsalaSweden Section for Genetics and Evolutionary Biology(EvoGene) Department of BiosciencesUniversity of OsloP.O.Box 1066BlindernNO-0316 OsloNorway University of Hawaiʻi at Mānoa 3190 Maile WaySt.John 102HonoluluHIUSA Department of Biology University of CopenhagenUniversitetsparken 152100 CopenhagenØDenmark Purdue University Northwest WestvilleIN 46391USA Institute of Microbiology Czech Academy of SciencesVidenska 108314220 Praha 4Czech Republic GLOBE Institute University of CopenhagenØster Farimagsgade 5KH7.2.321353 CopenhagenDenmark Dipartimento di Scienze della Vita e Biologia dei Sistemi Universitàdi TorinoViale Mattioli 2510125 TorinoItaly Department of Organismic and Evolutionary Biology and Farlow Library and Herbarium Harvard University22 Divinity AveCambridgeMA 02138USA Blaihofstr.42 72074 TübingenGermany SYNLAB Estonia Veerenni 53aTallinn 11313Estonia Escuela de Tecnología Médica Universidad Santo TomásLos Carreras 753OsornoChile Centro de Genómica y Bioinformática Universidad MayorCamino La Pirámide 5750HuechurabaSantiagoChile Norwegian Institute for Nature Research(NINA) Sognsveien 680855 OsloNorway School of Life Science and Technology University of Electronic Science and Technology of ChinaChengdu 611731People’s Republic of China Evolutionary Biology Faculty of BiologyBiological and Chemical Research CentreUniversity of Warsawul.Zwirki i Wigury 10102-089 WarsawPoland Department of Botany Swedish Museum of

The cryptic lifestyle of most fungi necessitates molecular identification of the guild in environmental *** the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and ***,in spite of the progress of molecular methods,knowledge about functional properties of the fungal taxa is vague and interpretation of environmental studies in an ecologically meaningful manner remains *** order to facilitate functional assignments and ecological interpretation of environmental studies we introduce a user friendly traits and character database FungalTraits operating at genus and species hypothesis *** the information from previous efforts such as FUNGuild and FunFun together with involvement of expert knowledge,we reannotated 10,210 and 151 fungal and Stramenopila genera,*** resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental *** order to assign the trait states to fungal species hypotheses,the scientific community of experts manually categorised and assigned available trait information to 697,413 fungal ITS *** the basis of those sequences we were able to summarise trait and host information into 92,623 fungal species hypotheses at 1%dissimilarity threshold.

关键词： Fungal traits Trophic modes Function Guild Bioinformatics High-throughput sequencing Community ecology

Diversity of Endophytic Diaporthe associated with Citrus grandis cv“Tomentosa”in China

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Diversity of Endophytic Diaporthe associated with Citrus gra...

Epitypification and neotypification:guidelines with appropriate and inappropriate examples

中国植物病理学会2021年学术年会

作者：董章勇 MANAWASINGHE Ishara Sandeepani HUANG Yinghua SHU Yongxin PHILLIPS Alan John Lander DISSANAYAKE Asha Janadaree hyde kevin david XIANG Meimei 罗梅 Innovative Institute for Plant Health Zhongkai University of Agriculture and Engineering Center of Excellence in Fungal Research Mae Fah Luang University Faculdade de Ciencias Biosystems and Integrative Sciences Institute(BioISI)Universidade de Lisboa School of Life Sciences and Technology University of Electronic Science and Technology of China

Diaporthe species are associated with Citrus as endophytes,pathogens,and saprobes ***,little is known about Diaporthe as endophytes in Citrus grandis in *** this study,24 endophytic Diaporthe isolates were obtained from cultivated *** cv."Tomentosa" in Huazhou,Guangdong Province in *** nuclear ribosomal internal transcribed spacer（ITS）,partial sequences of translation elongation factor 1-a（tef1）,b-tubulin（tub2）,and partial calmodulin（cal） gene regions were sequenced and employed to construct phylogenetic *** on morphology and combined multigene phylogeny,eleven Diaporthe species were identified including two new species,Diaporthe endocitricola and *** are the first report of ***,***,***,***,***,***,***,***,and *** on *** study provides the first intensive study of endophytic Diaporthe species on *** *** in *** results will improve the current knowledge of Diaporthe species associated with *** results obtained in this study will also help to understand the potential pathogens and biocontrol agents and to develop a platform in disease management.

关键词： new host records new species Diaporthales phylogeny taxonomy

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Fungal Diversity 2014年第6期69卷 57-91页

作者： Hiran A.Ariyawansa david L.Hawksworth kevin D.hyde E.B.Gareth Jones Sajeewa S.N.Maharachchikumbura Dimuthu S.Manamgoda Kasun M.Thambugala Dhanushka Udayanga Erio Camporesi Anupama Daranagama Ruvishika Jayawardena Jian-Kui Liu Eric H.C.McKenzie Rungtiwa Phookamsak Indunil C.Senanayake Roger G.Shivas Qing Tian Jian-Chu Xu Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanChina World Agroforestry Centre East and Central AsiaKunming 650201YunnanChina Institute of Excellence in Fungal Research School of ScienceMae Fah Luang UniversityChiang Rai 57100Thailand Departamento de Biología Vegetal II Facultad de FarmaciaUniversidad Complutense de MadridPlaza Ramón y CajalMadrid 28040Spain Department of Life Sciences The Natural History MuseumCromwell RoadLondon SW75BDUK Mycology Section Royal Botanic GardensKewRichmond Surrey TW93DSUK Department of Botany and Microbiology King Saudi UniversityRiyadhSaudi Arabia A.M.B.Gruppo Micologico Forlivese“Antonio Cicognani” Via Roma18ForlìItaly Manaaki Whenua Landcare Research Private Bag 92170 AucklandNew Zealand Plant Pathology Herbarium Agri-Science Queensland40 Boggo RoadDutton ParkQld 4102Australia

review of phylogenetic studies carried out together with morphological ones shows that a major problem with most early studies is that they concentrated on techniques and used material or strains of fungi that in most cases were not carefully reference,and in a worrying number of cases wrongly *** classical species,particularly of microfungi,are not represented by adequate type material,or other authoritatively identified cultures or specimens,that can serve as DNA sources for phylogenetic study,or for developing robust identification *** classifications of fungi therefore suffer fromthe lack of reference strains in resultant phylogenetic *** some cases,epitypification and neotypification can solve this problem and these tools are increasingly used to resolve taxonomic confusion and stabilize the understanding of species,genera,families,or orders of *** manuscript discusses epitypification and neotypification,describes how to epitypify or neotypify species and examines the importance of this process.A set of guidelines for epitypification is *** where taxa have been epitypified are presented and the benefits and problems of epitypification are *** examples of epitypification,or to provide reference specimens,a new epitype is designated for Paraphaeosphaeria michotii and reference specimens are provided for Astrosphaeriella stellata,***,Phaeosphaeria elongata,Ophiobolus cirsii,and *** this way we demonstrate how to epitypify taxa and its importance,and also illustrate the value of proposing reference specimens if epitypification is not *** we provided guidelines for epitypification,the decision to epitypify or not lies with the author,who should have experience of the fungus *** responsibility is to be taken seriously,as once a later typification is made,it may not be possible to undo that,particularly in the case of epitypes,without using the lengthy and tedious f

关键词： Epitype Generic types Molecular data Nomenclature Systematics Taxonomy Typification

Early-diverging fungal phyla:taxonomy,species concept,ecology,distribution,anthropogenic impact,and novel phylogenetic proposals

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Fungal Diversity 2021年第4期109卷 59-98页

作者： Kerstin Voigt Timothy Y.James Paul M.Kirk AndréL.C.M.de A.Santiago Bruce Waldman Gareth W.Griffith Minjie Fu Renate Radek Jürgen F.H.Strassert Christian Wurzbacher Gustavo Henrique Jerônimo david R.Simmons Kensuke Seto Eleni Gentekaki Vedprakash G.Hurdeal kevin D.hyde Thuong T.T.Nguyen Hyang Burm Lee Jena Microbial Resource Collection Leibniz Institute for Natural Product Research and Infection BiologyAdolf-Reichwein-Straße 2307745 JenaGermany Institute of Microbiology Faculty of Biological SciencesFriedrich Schiller University JenaNeugasse 2507743 JenaGermany Department of Ecology and Evolutionary Biology University of MichiganAnn ArborMI 48109USA Biodiversity Informatics and Spatial Analysis Jodrell LaboratoryRoyal Botanic Gardens KewSurrey TW93DSUK Department of Mycology Federal University of PernambucoAv.Da Engenharias/nRecifePE 50740-4600Brazil School of Biological Sciences Seoul National UniversitySeoul 08826South Korea Department of Integrative Biology Oklahoma State UniversityStillwaterOK 74078USA Institute of Biological Environmentaland Rural Sciences(IBERS)Aberystwyth UniversityAberystwyth SY233DDWalesUK Institute of Biology/Zoology Evolutionary BiologyFreie Universität Berlin14195 BerlinGermany Leibniz Institute of Freshwater Ecology and Inland Fisheries Ecosystem Research12587 BerlinGermany Department of Civil Geo and Environmental EngineeringTechnical University of MunichGarchingGermany School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand Environmental Microbiology Lab Department of Agricultural Biological ChemistryCollege of Agriculture&Life SciencesChonnam National UniversityGwangju 61186South Korea

The increasing number of new fungal species described from all over the world along with the use of genetics to define taxa,has dramatically changed the classification system of early-diverging fungi over the past several *** number of phyla established for non-Dikarya fungi has increased from 2 to ***,to date,both the classification and phylogeny of the basal fungi are still *** this article,we review the recent taxonomy of the basal fungi and re-evaluate the relationships among early-diverging lineages of fungal *** also provide information on the ecology and distribu-tion in Mucoromycota and highlight the impact of chytrids on amphibian *** concepts in Chytridiomycota,Aphelidiomycota,Rozellomycota,Neocallimastigomycota are discussed in this *** preserve the current application of the genus Nephridiophaga(Chytridiomycota:Nephridiophagales),a new type species,Nephridiophaga blattellae,is proposed.

关键词： Early-diverging fungi Evolution Nuclear large subunit(LSU/28S) Nuclear small subunit(SSU/18S) Molecular phylogeny