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

Fungal Diversity 2020年第2期107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 studies.Over the past decades,rapid development and affordability of molecular tools have tremendously improved insights of the fungal diversity in all ecosystems and habitats.Yet,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 challenging.In 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 levels.Combining 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,respectively.This resulted in a stand-alone spreadsheet dataset covering 17 lifestyle related traits of fungal and Stramenopila genera,designed for rapid functional assignments of environmental stud-ies.In 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 sequences.On 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

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Improving ITS sequence data for identification of plant pathogenic fungi

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Fungal Diversity 2014年第4期67卷 11-19页

作者： R.Henrik Nilsson Kevin D.Hyde Julia Pawlowska Martin Ryberg Leho Tedersoo Anders Bjornsgard Aas Siti A.Alias Artur Alves Cajsa Lisa Anderson Alexandre Antonelli A.Elizabeth Arnold Barbara Bahnmann Mohammad Bahram Johan Bengtsson-Palme Anna Berlin Sara Branco Putarak Chomnunti Asha Dissanayake Rein Drenkhan Hanna friberg tobias guldberg froslev Bettina Halwachs Martin Hartmann Beatrice Henricot Ruvishika Jayawardena Ari Jumpponen Havard Kauserud Sonja Koskela Tomasz Kulik Kare Liimatainen Bjorn D.Lindahl Daniel Lindner Jian-Kui Liu Sajeewa Maharachchikumbura Dimuthu Manamgoda Svante Martinsson Maria Alice Neves Tuula Niskanen Stephan Nylinder Olinto Liparini Pereira Danilo Batista Pinho Teresita M.Porter Valentin Queloz Taavi Riit Marisol Sánchez-García Filipe de Sousa Emil Stefańczyk Mariusz Tadych Susumu Takamatsu Qing Tian Dhanushka Udayanga Martin Unterseher Zheng Wang Saowanee Wikee Jiye Yan Ellen Larsson Karl-Henrik Larsson Urmas Koljalg Kessy Abarenkov Department of Biological and Environmental Sciences University of GothenburgBox 46140530 GothenburgSweden Institute of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand School of Science Mae Fah Luang UniversityChiang Rai 57100Thailand Department of Plant Systematics and Geography Faculty of BiologyUniversity of WarsawAl.Ujazdowskie 400-478 WarsawPoland Department of Organismal Biology Uppsala UniversityNorbyvagen 18D75236 UppsalaSweden Institute of Ecology and Earth Sciences University of TartuLai 40Tartu 51005Estonia Microbial Evolution Research Group University of OsloBlindernveien 310371 OsloNorway Institute of Biological Sciences University of Malaya50603 Kuala LumpurMalaysia Department of Biology CESAMUniversity of Aveiro3810-193 AveiroPortugal School of Plant Sciences The University of Arizona1140 E South Campus DriveForbes 303TucsonAZ 85721USA Laboratory of Environmental Microbiology Institute of Microbiology ASCRVídeňská108314220 Prague 4Czech Republic Department of Infectious Diseases Institute of BiomedicineSahlgrenska AcademyUniversity of GothenburgGuldhedsgatan 1041346 GoteborgSweden Department of Forest Mycology and Plant Pathology Swedish University of Agricultural SciencesBox 702675007 UppsalaSweden University of California at Berkeley 321 Koshland Hall University of CaliforniaBerkeleyCA 94720-3102USA Agriculture and Forestry Sciences Beijing 100097China Institute of Forestry and Rural Engineering Estonian University of Life SciencesKreutzwaldi551014 TartuEstonia Natural History Museum of Denmark Øster Voldgade 5-71350 København KDenmark Institute for Genomics and Bioinformatics Graz University of Technology8010 GrazAustria Core Facility Bioinformatics Austrian Centre of Industrial Biotechnology8010 GrazAustria Forest Soils and Biogeochemistry Swiss Federal Research Institute WSLZuercherstrasse 1118903 BirmensdorfSwitzerland Molecular Ecology Institute for Sustainability SciencesAgroscopeReckenholzstrasse 191

Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours.These taxa often have complex and poorly understood life cycles,lack observable,discriminatory morphological characters,and may not be amenable to in vitro culturing.As a result,species identification is frequently difficult.Molecular(DNA sequence)data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi,with the nuclear ribosomal internal transcribed spacer(ITS)region being the most popular marker.However,international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality,making their use in the molecular identification of plant pathogenic fungi problematic.Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages.A third objective was to enrich the sequences with geographical and ecological metadata.The results-a total of 31,954 changes-are incorporated in and made available through the UNITE database for molecular identification of fungi(http://unite.***.ee),including standalone FASTA files of sequence data for local BLAST searches,use in the next-generation sequencing analysis platforms QIIME and mothur,and related applications.The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi,and we invite all researchers with pertinent expertise to join the annotation effort.

关键词： Phytopathogenic fungi Molecular identification ITS Taxonomy Annotation

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西57号街公寓

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城市环境设计 2019年第2期118卷 228-239页

作者： David Brown Aleksander Tokarz Alessandro Ronfini Alessio Valmori Alvaro Mendive Benjamin Schulte Birk Daugaard Celine Jeanne Christoffer Gotfredsen Daniel Sundlin Dominyka Mineikyte Eivor Davidsen Felicia guldberg Florian Oberschneider Soren Grunert Gabrielle Nadeau Gül Ertekin Ho Kyung Lee Hongyi Jin Julian Liang Julianne Gola Laura Youf Lucian Racovitan Marcella Martinez Maria Nikolova Maya Shopova Mitesh Dixit Nicklas A.Rasch Ola Hariri Riccardo Mariano Steffan Heath Stanley Lung Tara Hagan Thilani Rajarathna Tyler Polich Valentina Mele Valerie Lechene Xu Li Yi Li Aaron Hales Alessandro Ronfini Brian Foster Christoffer Gotfredsen francesca Portesine Ho Kyung Lee Hongyi Jin Ivy Hume Jenny Chang Lauren Turner Mina Rafiee Rakel Karlsdottir Tara Hagan Thomas Fagan Tiago Barros Valentina Mele Iwan Baan 朱翰林

西57号街公寓结合了欧洲庭院建筑和传统曼哈顿高层的特点,并兼具两者的优点:通透的院落建筑的紧凑与高效性以及摩天楼拥有的广阔视野。通过让建筑三个角保持较低姿态而仅将东北角提升至450英尺(约137.2米),使得庭院面向哈德逊河的视野开... 详细信息

西57号街公寓结合了欧洲庭院建筑和传统曼哈顿高层的特点,并兼具两者的优点:通透的院落建筑的紧凑与高效性以及摩天楼拥有的广阔视野。通过让建筑三个角保持较低姿态而仅将东北角提升至450英尺(约137.2米),使得庭院面向哈德逊河的视野开阔,让较低的夕阳也能照进街区深处,并优雅地为一旁的Helena Tower保留河景。建筑的形式随着观察者的位置而不断变换。从西侧的高速公路上看,它

关键词： Section 局部剖面图

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丹麦国家海事博物馆

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城市环境设计 2019年第2期118卷 142-159页

作者： John Pries Jensen Henrik Kania Ariel Joy Norback Wallner Rasmus Pedersen Annette Jensen Dennis Rasmussen Jan Magasanik Jeppe Ecklon Karsten Hammer Hansen Rasmus Rodam Rune Hansen Alina Tamosiunaite Alysen Hiller Ana Merino Armen Menendian Andy Yu Andreas Johansen Baptiste Blot Christian Alvarez Christin Svensson Claudia Hertrich Claudio Moretti Cory Mattheis Eskild Nordbud Felicia guldberg Finn N?rkj?r Gül Ertekin Jan Borgstr?m James Schrader Johan Cool Jonas M?nster Kirstine Ragnhild Malte Kloe Michael Andersen Michal Kristof Marc Jay Maria Mavriku Masatoshi Oka Oana Simionescu Pablo Labra Peter Rieff Qianyi Lim Sara Sosio Sebastian Latz Tina Lund H?jgaard Tina Troster Todd Bennet Xi Chen Xing Xiong Xu Li Zoltan Kalaszi Iwan Baan Rasmus Hjortshoj Luca Santiago Mora Dragoer Luftfoto Jens Lindhe Lorenzon Boddi Thiks Wolzak 陈子钰

丹麦海事博物馆位于独特的历史和空间环境中:在丹麦最重要和最著名的建筑之一克伦堡城堡和文化庭院——一个新的、雄心勃勃的文化中心之间。BIG建议将博物馆放在地下,就在船坞的墙壁外侧,以便将船坞保留为开放的户外展示空间,保存其强... 详细信息

丹麦海事博物馆位于独特的历史和空间环境中:在丹麦最重要和最著名的建筑之一克伦堡城堡和文化庭院——一个新的、雄心勃勃的文化中心之间。BIG建议将博物馆放在地下,就在船坞的墙壁外侧,以便将船坞保留为开放的户外展示空间,保存其强有力的结构作为海事博物馆中心。将博物馆这样设置,使它在成为与克伦堡城堡和邻近的文化庭院相联系的文化环境的一部分的同时,彰显自身,成为一个独立

关键词：海事博物馆铝覆层 Section 重钢结构

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深圳能源大厦

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建筑实践 2019年第6期2卷 26-33页

作者： Bjarke Ingels Andreas Klok Pedersen Martin Voelkle He Song Andre Schmidt Alessio Zenaro Alina Tamosiunaite Alysen Hiller Ana Merino Andreas Geisler Johansen Annette Jensen Armor Rivas Balaj IIulian Brian Yang Baptiste Blot Buster Christiansen Cecilia Ho Christian Alvarez Christin Svensson Claudia Hertrich Claudio Moretti Cory Mattheis Dave Brown Dennis Rasmussen Doug Stechschulte Eskild Nordbud Felicia guldberg fred Zhou Gaetan Brunet Gül Ertekin Henrik Kania Iris Van der Heide James Schrader Jan Magasanik Jan Borgstr?m Jeppe Ecklon Jelena Vucic Jo?o Albuquerque Jonas M?nster Karsten Hansen Malte Kloe Mikkel Marcker Stubgaard Michael Andersen Michal Kristof Min Ter Lim Oana Simionescu Nicklas A. Rasch Philip Sima Rasmus Pedersen Rune Hansen Rui Huang Sofia Gaspar Stanley Lung Sun Ming Lee Takuya Hosokai Todd Bennett Xi Chen Xing Xiong Xiao Lu Xu Li Yijie Dan Zoltan Kalaszi BIG

深圳能源公司办公楼项目总建筑面积为96000m^2,旨在让人在深圳的文化、政治和商业中心感到亲切的同时,在城市主轴线上建造一座可持续的新公共地标。本项目的体量和高度由中心区城市总体规划决定。主体建筑由两座塔楼组成,北楼高220m,南... 详细信息

深圳能源公司办公楼项目总建筑面积为96000m^2,旨在让人在深圳的文化、政治和商业中心感到亲切的同时,在城市主轴线上建造一座可持续的新公共地标。本项目的体量和高度由中心区城市总体规划决定。主体建筑由两座塔楼组成,北楼高220m,南楼高120m,两座塔楼与邻近建筑的塔楼一起在深圳的中心形成一个连续的弧形天际线。

关键词：城市总体规划商业中心主轴线天际线邻近建筑主体建筑塔楼公司办公楼

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