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Using a temporal phylogenetic method to harmonize familyand genus-level classification in the largest clade of lichen-forming fungi

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Fungal Diversity 2017年第3期84卷 101-117页

作者： Pradeep K.Divakar Ana Crespo Ekaphan Kraichak Steven D.Leavitt Garima Singh Imke Schmitt h.thorsten lumbsch Departamento de Biología Vegetal II Facultad de FarmaciaUniversidad Complutense de Madrid28040 MadridSpain Department of Botany Faculty of ScienceKasetsart UniversityBangkokThailand Department of Biology and M.L.Bean Life Science Museum Brigham Young University4102 Life Science BuildingProvoUT 84602USA Department of Biological Sciences Institute of EcologyEvolution and DiversityGoethe Universitat and Senckenberg Biodiversity and Climate Research Centre(BiK-F)Frankfurt am MainGermany Science&Education The Field MuseumChicagoILUSA

Although classification at supra-specific ranks is inherently arbitrary,comparable taxonomic ranks within clades can facilitate more consistent classifications and objective comparisons among *** circumscriptions of the hyper-diverse lichen-forming fungal family Parmeliaceae and widely different generic circumscriptions among authors have been *** this study,we use a recently developed temporal approach that uses timecalibrated chronograms to identify temporal bands for specific ranks in Parmeliaceae and allied groups with the overarching goal of establishing a consistent,stable classification.A data set of 330 species,representing 73 genera in the family and 52 species of related families was used to address the circumscription of Parmeliaceae and its genera following the proposed temporal *** on the results of this study,we propose a revised,temporal-based classification for Parmeliaceae,including all clades that share a common ancestor 102.13–112.88 Ma for families and a time window of 29.45–32.55 Ma for *** of the currently accepted genera in Parmeliaceae were supported in their current *** subfamilies are accepted within Parmeliaceae:Protoparmelioideae Divakar et ***.,including Protoparmelia and the resurrected genus Maronina,and Parmelioideae,including the bulk of genera in the *** new genus Austromelanelixia Divakar et *** proposed to accommodate a clade of southern hemisphere species previously included in *** and tentatively Dolichousnea are resurrected as genera separate from *** following genera are reduced to synonymy:Allocetraria,Cetrariella,Usnocetraria,and Vulpicida with Cetraria;Arctocetraria,Cetreliopsis,Flavocetraria,Kaernefeltia,Masonhalea,Tuckermanella,and Tuckermannopsis with Nephromopsis;and the lichenicolous genera Nesolechia and Raesaenenia with the lichen-forming genera Punctelia and Protousnea,respectively.A total of 47 new combinations and

关键词： Ascomycota Gypsoplacaceae Lecanorales Lichenized fungi Parmeliaceae Phylogeny Protoparmelia Taxonomy Taxonomicranks

Phylogenomic reconstruction addressing the Peltigeralean backbone(Lecanoromycetes,Ascomycota)

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Fungal Diversity 2021年第5期110卷 59-73页

作者： Todd J.Widhelm Felix Grewe Bernard Goffinet Mats Wedin Trevor Goward Luis F.Coca Isabel Distefano Alica Košuthová· h.thorsten lumbsch Science&Education The Grainger Bioinformatics CenterNegaunee Integrative Research CenterGantz Family Collections Centerand Pritzker Laboratory for Molecular SystematicsThe Field Museum1400 S.Lake Shore DriveChicagoIL 60605USA Department of Ecology and Evolutionary Biology University of Connecticut75 North Eagleville RoadStorrsCT 06269-3043USA Department of Botany Swedish Museum of Natural HistoryP.O.Box 5000710405 StockholmSweden herbarium Beaty MuseumUniversity of British ColumbiaVancouverBC V6T 1Z4Canada herbario Univ Caldas FAUC Edificio BicentenarioCalle 6526-10275 ManizalesColombia

Rapid radiations in Fungi are only beginning to be studied with phylogenomic *** evolutionary history of the lichenized fungal order Peltigerales has not been well resolved,particularly for the ***,we used concatenation and coalescent-based species tree methods to reconstruct the phylogeny of the Peltigerales based on sequences of 125 nuclear single-copy exon sequences among 60 samples,representing 58 *** uneven,lineage-specific missing data and significant topological incongruence of individual exon trees,the resulting phylogenies were concordant and successfully resolved the phylogenetic relationships of the *** in the Collematineae were defined by short branches and lower nodal support than in other parts of the tree,due in part to conflicting signal in exon trees,suggesting rapid diversification events in the early evolution of the *** tree distance measures,we were able to identify a minimum subset of exons that could reconstruct phylogenetic relationships in Peltigerales with higher support than the 125-exon *** between the minimum and complete datasets in species tree inferences,bipartition analyses,and divergence time estimations displayed similar results,although the minimum dataset was characterized by higher levels of error in estimations of divergence *** our inferences from the complete and minimum datasets to those derived from few nuclear and mitochondrial loci reveal that our topology is concordant with topologies reconstructed using the nuclear large subunit and mitochondrial small subunit ribosomal DNA markers,but the target capture datasets had much higher support *** demonstrated how target capture approaches can effectively decipher ancient rapid radiations in cases where well resolved individual exon trees are sufficiently sampled and how to identify subsets of loci that are appropriate for fungal order-level phylogenetics.

关键词： Lichenized fungi Phylogenomics Rapid radiations high-throughput sequencing

Outline of Ascomycota: 2017

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Fungal Diversity 2018年第1期88卷 167-263页

作者： Nalin N.Wijayawardene Kevin D.hyde h.thorsten lumbsch Jian Kui Liu Sajeewa S.N.Maharachchikumbura Anusha h.Ekanayaka Qing Tian Rungtiwa Phookamsak Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of ScienceKunming 650201YunnanPeople’s Republic of China Science&Education The Field Museum1400 S.Lake Shore DriveChicagoIL 60605USA Guizhou Institute of Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006People’s Republic of China Department of Crop Sciences College of Agricultural and Marine SciencesSultan Qaboos UniversityPO Box 34123 AlkhoudOman Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand

Taxonomic placement of genera have been changing rapidly as taxonomists widely use DNA sequence data in phylogenetic and evolutionary studies. It is essential to update existing databases/outlines based on recent studies, since thesesources are widely used as a foundation for other research. In this outline, we merge both asexual and sexual genera intoone outline. The phylum Ascomycota comprises of three subphyla viz. Pezizomycotina (including 13 classes, 124 ordersand 507 families), Saccharomycotina (including one class, one order and 13 families) and Taphrinomycotina (five classes,five orders and six families). Approximately, 6600 genera have been listed under different taxonomic ranks includingauxiliary (intermediate) taxonomic ranks.

关键词： Asexual genera Classification Sexual genera Systematic Taxonomic ranks

Phylogenomic analysis of 2556 single-copy protein-coding genes resolves most evolutionary relationships for the major clades in the most diverse group of lichen-forming fungi

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Fungal Diversity 2018年第5期92卷 31-41页

作者： David Pizarro Pradeep K.Divakar Felix Grewe Steven D.Leavitt Jen-Pan huang Francesco Dal Grande Imke Schmitt Mats Wedin Ana Crespo h.thorsten lumbsch Departamento de Farmacologı́a Farmacognosia y BotánicaFacultad de FarmaciaUniversidad Complutense de Madrid28040 MadridSpain Science&Education The Field Museum1400 S.Lake Shore DriveChicagoILUSA Department of Biology and M.L.Bean Life Science Museum Brigham Young UniversityLife Science Building 4102ProvoUT 84602USA Senckenberg Biodiversity and Climate Research Centre(SBiK-F) Senckenberganlage 2560325 Frankfurt am MainGermany Institute of Ecology Evolution and DiversityGoethe UniversityFrankfurt am MainMax-von-Laue-Str.960438 Frankfurt am MainGermany Department of Botany Swedish Museum of Natural HistoryPO Box 5000710405 StockholmSweden

Phylogenomic datasets continue to enhance our understanding of evolutionary relationships in many lineages of ***,genome-scale data have not been widely implemented in reconstructing relationships in lichenized *** we generate a data set comprised of 2556 single-copy protein-coding genes to reconstruct previously unresolved rela-tionships in the most diverse family of lichen-forming fungi,*** sampling included 51 taxa,mainly from the subfamily Parmelioideae,and represented six of the seven previously identified major clades within the *** results provided strong support for the monophyly of each of these major clades and most backbone relationships in the topology were recovered with high nodal support based on concatenated dataset and species tree *** alectorioid clade was strongly supported as sister-group to all remaining clades,which were divided into two major *** the first major clade the anzioid and usneoid clades formed a strongly supported sister-group relationship with the cetrarioid?hypogymnioid *** sister-group relationship of Evernia with the cetrarioid clade was also strongly supported,whereas that between the anzioid and usneoid clades needs further *** the second major clade Oropogon and Platismatia were sister to the parmelioid group,while the position of Omphalora was not fully *** study demonstrates the power of genome-scale data sets to resolve long-standing,ambiguous phylogenetic rela-tionships of lichen-forming ***,the topology inferred in this study will provide a valuable framework for better understanding diversification in the most diverse lineage of lichen-forming fungi,Parmeliaceae.

关键词： Fungi Lecanorales Lichenized fungi Parmeliaceae Parmelioideae Phylogeny Systematics

Towards a revised generic classification of lecanoroid lichens(Lecanoraceae,Ascomycota)based on molecular,morphological and chemical evidence

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Fungal Diversity 2016年第3期78卷 293-304页

作者： Xin Zhao Steven D.Leavitt Zun Tian Zhao Lu Lu Zhang Ulf Arup Martin Grube Sergio Pérez-Ortega Christian Printzen LucynaŚliwa Ekaphan Kraichak Pradeep K.Divakar Ana Crespo h.thorsten lumbsch College of Life Sciences Shandong Normal UniversityJinan 250014People’s Republic of China Science&Education The Field MuseumChicagoILUSA Biological Museum Lund UniversityBox 117SE-22100 LundSweden Institute of Plant Sciences Karl-Franzens-University GrazHolteigasse 68010 GrazAustria Departamento Biogeoquímica y Ecología Microbiana Museo Nacional de Ciencias NaturalesMadridSpain Present address:Real Jardín Botánico Plaza de Murillo 228014 MadridSpain Department of Botany and Molecular Evolution Senckenberg Research Institute and Natural History Museum FrankfurtSenckenberganlage 25D-60325 Frankfurt am MainGermany Laboratory of Lichenology W.Szafer Institute of BotanyPolish Academy of SciencesLubicz 4631–512 KrakówPoland Department of Botany Faculty of ScienceKasetsart University10900 BangkokThailand Departamento de Biología Vegetal II Facultad de FarmaciaUniversidad Complutense de Madrid28040 MadridSpain

Abstract The phylogenetic relationship of lecanoroid lichens is studied using two data sets:1)a 2-locus data set including 251 OTUs representing 150 species,and 2)a 6-locus data set with 82 OTUs representing 53 *** genus Lecanora as currently circumscribed is shown to be highly polyphyletic and several genera,including Adelolecia,Arctopeltis,Bryonora,Carbonea,Frutidella,Lecidella,Miriquidica,Palicella,Protoparmeliopsis,Pyrrhospora,and Rhizoplaca are nested within Lecanora sensu lato.A core group of Lecanora is supported as monophyletic and includes species of the ***,***,and *** groups,and a core group of the *** *** monophyletic clades that are well supported in our analyses and well characterized by phenotypical characters are accepted here:1)Myriolecis to accommodate the Lecanora dispersa group and Arctopeltis;2)Protoparmeliopsis for the *** group;and 3)Rhizoplaca is emended to include three placodioid taxa previously classified in Lecanora(***,***),whereas *** and *** are excluded from *** latter is transferred into *** is strongly supported as a monophyletic *** studies indicate the presence of additional clades of species currently placed in Lecanora sensu lato that warrant taxonomic recognition but additional data will be necessary before the circumscription of these entities is fully understood.37 new combinations are proposed into the genera Myriolecis(30),Protoparmeliopsis(2),and Rhizoplaca(5).

关键词： Arctopeltis Classification Generic concept Lecanora Lichenized fungi Myriolecis Rhizoplaca Protoparmeliopsis Rhizoplaca Taxonomy

基于多基因序列分析的锈菌类酵母的分类系统重建

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基于多基因序列分析的锈菌类酵母的分类系统重建

The Faces of Fungi database:fungal names linked with morphology,phylogeny and human impacts

中国菌物学会2015年学术年会

作者：王启明 Marizeth Groenewald Masako Takashima Markus G?ker h.thorsten lumbsch Andrey M.Yurkov Teun Boekhout 白逢彦中国科学院微生物研究所真菌学国家重点实验室

柄锈菌亚门（Pucciniomycotina,Basidiomycota）除了包括植物病原菌（锈菌）外,还包括以单细胞为主要繁殖方式的酵母菌（锈菌类酵母）。近年来基于rDNA的序列分析表明当前的锈菌类酵母分类系统存在很多问题,特别是很多属都是异源的。我... 详细信息

柄锈菌亚门（Pucciniomycotina,Basidiomycota）除了包括植物病原菌（锈菌）外,还包括以单细胞为主要繁殖方式的酵母菌（锈菌类酵母）。近年来基于rDNA的序列分析表明当前的锈菌类酵母分类系统存在很多问题,特别是很多属都是异源的。我们使用了7个基因片段（SSU rDNA、LSU D1/D2区、ITS1+5.8S rDNA+ITS2、RPB1、RPB、TEF1和CYTB）对184个种的模式菌株进行了多基因的序列分析。根据最新命名法规中一个真菌一个名称（One Fungus=One Name）规定,我们对那些异源的属进行了重新的划分和界定,对一些有性型属和无性型属进行了合并,重建了锈菌类酵母的分类系统。在此基础上,创建了1个新纲、6个新科、24个新属和112个新组合。

关键词：真菌担子菌门柄锈菌亚门酵母多基因序列分析分类系统

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Fungal Diversity 2015年第5期74卷 3-18页

作者： Subashini C.Jayasiri Kevin D.hyde hiran A.Ariyawansa Jayarama Bhat Bart Buyck Lei Cai Yu-Cheng Dai Kamel A.Abd-Elsalam Damien Ertz Iman hidayat Rajesh Jeewon E.B.Gareth Jones Ali h.Bahkali Samantha C.Karunarathna Jian-Kui Liu J.Jennifer Luangsa-ard h.thorsten lumbsch Sajeewa S.N.Maharachchikumbura Eric h.C.McKenzie Jean-Marc Moncalvo Masoomeh Ghobad-Nejhad henrik Nilsson Ka-Lai Pang Olinto L.Pereira Alan J.L.Phillips Olivier Raspé Adam W.Rollins Andrea I.Romero Javier Etayo Faruk Selçuk Steven L.Stephenson Satinee Suetrong Joanne E.Taylor Clement K.M.Tsui Alfredo Vizzini Mohamed A.Abdel-Wahab Ting-Chi Wen Saranyaphat Boonmee Dong Qin Dai Dinushani A.Daranagama Asha J.Dissanayake Anusha h.Ekanayaka S.C.Fryar Sinang hongsanan Ruvishika S.Jayawardena Wen-Jing Li Rekhani h.Perera R.Phookamsak Nimali Ide Silva Kasun M.T.hambugala Qing Tian Nalin N.Wijayawardene Rui-Lin Zhao Qi Zhao Ji-Chuan Kang Itthayakorn Promputtha Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand World Agro forestry Centre East and Central Asia Office 132 Lanhei RoadKunming 650201China Botany and Microbiology Department College of ScienceKing Saud UniversityRiyadh 1145Saudi Arabia Guizhou Key Laboratory of Agricultural Biotechnology Guizhou Academy of Agricultural SciencesGuiyang 550006GuizhouChina No.128/1-J Azad Housing SocietyCurcaP.O.Goa Velha403108 GoaIndia Department of Botany Goa UniversityGoa 403206India Muséum National d’histoire Naturelle Département Systématique et EvolutionCP 39ISYEBUMR 7205 CNRS MNHN UPMC EPHE12 Rue BuffonF-75005 ParisFrance State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesWest Beicheng RdBeijingChina Institute of Microbiology Beijing Forestry UniversityPO Box 61Beijing 100083China Plant Pathology Research Institute Agricultural Research Center(ARC)12619 GizaEgypt Botanic Garden Meise Department Bryophytes-Thallophytes(BT)Nieuwelaan 38B-1860 MeiseBelgium Fédération Wallonie-Bruxelles Direction Générale de l’Enseignement non obligatoire et de la Recherche scientifiqueRue A.Lavallée 11080 BruxellesBelgium Microbiology Division Research Center for BiologyIndonesian Institute of Sciences(LIPI)Jl.Raya Jakarta-Bogor KM 46Cibinong 16911West JavaIndonesia Department of health Sciences Faculty of ScienceUniversity of MauritiusReduitMauritius Microbe Interaction Laboratory(BMIT) BIOTECNational Science and Technology Development Agency(NSTDA)113 Thailand Science ParkThanon PhahonyothinTombon Khlong NuengAmphoe Khlong LuangPathum Thani 12120Thailand Science&Education The Field Museum1400 S.Lake Shore DriveChicagoIL 60605USA Manaaki Whenua Landcare Research Private Bag 92170AucklandNew Zealand Department of Natural history Royal Ontario Museumand Department of Ecology and Evolutionary BiologyUniversity of Toronto100 Queen’s ParkTorontoON M5S2C6Canada Department of Biotechnology Iranian Research Organiza

Taxonomic names are key links between various databases that store information on different *** global fungal nomenclural and taxonomic databases(notably Index Fungorum,Species Fungorum and MycoBank)can be sourced to find taxonomic details about fungi,while DNA sequence data can be sourced from NCBI,EBI and UNITE *** the sequence data may be linked to a name,the quality of the metadata is variable and generally there is no corresponding link to images,descriptions or herbarium *** is generally no way to establish the accuracy of the names in these genomic databases,other than whether the submission is from a reputable *** tackle this problem,a new database(FacesofFungi),accessible at ***(FoF)has been *** fungal database allows deposition of taxonomic data,phenotypic details and other useful data,which will enhance our current taxonomic understanding and ultimately enable mycologists to gain better and updated insights into the current fungal classification *** addition,the database will also allow access to comprehensive metadata including descriptions of voucher and type *** database is user-friendly,providing links and easy access between taxonomic ranks,with the classification system based primarily on molecular data(from the literature and via updated web-based phylogenetic trees),and to a lesser extent on morphological data when molecular data are *** FoF species are not only linked to the closest phylogenetic representatives,but also relevant data is provided,wherever available,on various applied aspects,such as ecological,industrial,quarantine and chemical *** data include the three main fungal groups(Ascomycota,Basidiomycota,Basal fungi)and fungus-like *** FoF webpage is an output funded by the Mushroom Research Foundation which is an NGO with seven directors with mycological *** webpage has 76 curators,and with the help of these s

关键词： Classification Database Faces of Fungi Fungi Phylogeny Taxonomy

New perspectives on biology,disease progression,and therapy response of head and neck cancer gained from single cell RNA sequencing and spatial transcriptomics

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Oncology Research 2024年第1期32卷 1-17页

作者： GERWIN hELLER thorsten FUEREDER ALEXANDER MIChAEL GRANDITS ROTRAUD WIESER Division of Oncology Department of Medicine IMedical University of ViennaVienna1090Austria Ludwig Boltzmann Institute for hematology and Oncology Medical University of ViennaVienna1090Austria

head and neck squamous cell carcinoma(hNSCC)is one of the most frequent cancers *** main risk factors are consumption of tobacco products and alcohol,as well as infection with human papilloma *** therapeutic options comprise surgery,radiation,chemotherapy,targeted therapy through epidermal growth factor receptor inhibition,and immunotherapy,but outcome has remained unsatisfactory due to recurrence rates of~50%and the frequent occurrence of second *** availability of the human genome sequence at the beginning of the millennium heralded the omics era,in which rapid technological progress has advanced our knowledge of the molecular biology of malignant diseases,including hNSCC,at an unprecedented ***,microarray-based methods,followed by approaches based on next-generation sequencing,were applied to study the genetics,epigenetics,and gene expression patterns of bulk *** recently,the advent of single-cell RNA sequencing(scRNAseq)and spatial transcriptomics methods has facilitated the investigation of the heterogeneity between and within different cell populations in the tumor microenvironment(e.g.,cancer cells,fibroblasts,immune cells,endothelial cells),led to the discovery of novel cell types,and advanced the discovery of cell-cell communication within *** review provides an overview of scRNAseq,spatial transcriptomics,and the associated bioinformatics methods,and summarizes how their application has promoted our understanding of the emergence,composition,progression,and therapy responsiveness of,and intercellular signaling within,hNSCC.

关键词： head and neck squamous cell carcinoma Tumor microenvironment Immunotherapy Gene expression Omics

Insights into the kinetics–morphology relationship of 1-, 2-, and 3D TiNb_(2)O_(7) anodes for Li-ion storage

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Nano Research 2024年第4期17卷 2770-2780页

作者： Wenlei Xu Yaolin Xu Veronika Grzimek Andrea Martin thorsten Schultz Patrícia ARusso Yan Lu Norbert Koch Nicola Pinna Department of Chemistry IRIS Adlershof and the Center for the Science of Materials BerlinHumboldt-Universität zu BerlinBrook-Taylor-Str.212489 BerlinGermany Department of Electrochemical Energy Storage Helmholtz-Zentrum Berlin für Materialien und EnergieHahn-Meitner-Platz 114109 BerlinGermany Institut für Physik and IRIS Adlershof Humboldt-Universität zu BerlinBrook-Taylor-Str.212489 BerlinGermany Joint Research Group of Molecular Systems Helmholtz-Zentrum Berlin für Materialien und Energie12489 BerlinGermany

Understanding the influence of electrode material’s morphology on electrochemical behavior is of great significance for the development of rechargeable batteries,however,such studies are often limited by the inability to precisely control the morphology of electrode ***,nanostructured titanium niobium oxides(TiNb_(2)O_(7))with three different morphologies(one-dimensional(1D),two-dimensional(2D),and three-dimensional(3D))were synthesized via a facile microwave-assisted solvothermal *** influence of the morphological dimension of TiNb_(2)O_(7) as electrode material on the electrochemical performance in Li-ion batteries(LIBs)and the underlying correlation with the electrochemical kinetics were studied in detail.2D TiNb_(2)O_(7)(TNO-2D)shows a superior rate capability and cycling stability,associated with improved kinetics for charge transfer and Li-ion diffusion,compared to the 1D and 3D *** X-ray diffraction measurements reveal the structural stability and crystallographic evolution of TNO-2D upon lithiation and delithiation and correlate the Li-ion diffusion kinetics with the lattice evolution during battery charge and ***,carbon-coated TNO-2D achieves enhanced rate capability(205 mAh·g^(-1) at 50 C)and long-term cycling stability(87%after 1000 cycles at 5 C).This work provides insights into the rational morphology design of electrode materials for accelerated charge transfer and enhanced fast-charging capability,pushing forward the development of electrode materials for high-power rechargeable batteries in future energy storage.

关键词： morphological dimension electrochemical kinetics lithium-ion batteries TiNb_(2)O_(7) structural evolution