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      Fusarium and allied fusarioid taxa (FUSA). 1

      1 , 2 , * , 1 , 1 , 1 , 1 , 1 , 1 , 1 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 , 12 , 14 , 15 , 16 , 16 , 17 , 18 , 19 , 20 , 21 , 15 , 22 , 11 , 11 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 11 , 28 , 32 , 33 , 34 , 35 , 36 , 32 , 37 , 38 , 39 , 9 , 40 , 41 , 42 , 42 , 42 , 42 , 43 , 43 , 44 , 44 , 43 , 3 , 45 , 46
      Fungal Systematics and Evolution
      Fungal Systematics and Evolution
      Longinectria, multi-gene phylogeny, Nectriaceae, Neocosmospora, new taxa, systematics, typification

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          Seven Fusarium species complexes are treated, namely F. aywerte species complex (FASC) (two species), F. buharicum species complex (FBSC) (five species), F. burgessii species complex (FBURSC) (three species), F. camptoceras species complex (FCAMSC) (three species), F. chlamydosporum species complex (FCSC) (eight species), F. citricola species complex (FCCSC) (five species) and the F. concolor species complex (FCOSC) (four species). New species include Fusicolla elongata from soil (Zimbabwe), and Neocosmospora geoasparagicola from soil associated with Asparagus officinalis (Netherlands). New combinations include Neocosmospora akasia, N. awan, N. drepaniformis, N. duplosperma, N. geoasparagicola, N. mekan, N. papillata, N. variasi and N. warna. Newly validated taxa include Longinectria gen. nov., L. lagenoides, L. verticilliforme, Fusicolla gigas and Fusicolla guangxiensis. Furthermore, Fusarium rosicola is reduced to synonymy under N. brevis. Finally, the genome assemblies of Fusarium secorum (CBS 175.32) , Microcera coccophila (CBS 310.34), Rectifusarium robinianum (CBS 430.91), Rugonectria rugulosa (CBS 126565), and Thelonectria blattea (CBS 952.68) are also announced here.

          Citation: Crous PW, Sandoval-Denis M, Costa MM, Groenewald JZ, van Iperen AL, Starink-Willemse M, Hernández-Restrepo M, Kandemir H, Ulaszewski B, de Boer W, Abdel-Azeem AM, Abdollahzadeh J, Akulov A, Bakhshi M, Bezerra JDP, Bhunjun CS, Câmara MPS, Chaverri P, Vieira WAS, Decock CA, Gaya E, Gené J, Guarro J, Gramaje D, Grube M, Gupta VK, Guarnaccia V, Hill R, Hirooka Y, Hyde KD, Jayawardena RS, Jeewon R, Jurjević Ž, Korsten L, Lamprecht SC, Lombard L, Maharachchikumbura SSN, Polizzi G, Rajeshkumar KC, Salgado-Salazar C, Shang Q-J, Shivas RG, Summerbell RC, Sun GY, Swart WJ, Tan YP, Vizzini A, Xia JW, Zare R, González CD, Iturriaga T, Savary O, Coton M, Coton E, Jany J-L, Liu C, Zeng Z-Q, Zhuang W-Y, Yu Z-H, Thines M (2022). Fusarium and allied fusarioid taxa (FUSA). 1. Fungal Systematics and Evolution 9: 161–200. doi: 10.3114/fuse.2022.09.08

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          Most cited references82

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          Trimmomatic: a flexible trimmer for Illumina sequence data

          Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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            IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

            Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether the best tree is found. Thus, there is need for additional approaches that employ different search strategies to find ML trees and that are at the same time as fast as currently available ML programs. We show that a combination of hill-climbing approaches and a stochastic perturbation method can be time-efficiently implemented. If we allow the same CPU time as RAxML and PhyML, then our software IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3-97.1%.
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              IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

              Abstract IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have continuously expanded IQ-TREE to integrate a plethora of new models of sequence evolution and efficient computational approaches of phylogenetic inference to deal with genomic data. Here, we describe notable features of IQ-TREE version 2 and highlight the key advantages over other software.

                Author and article information

                Fungal Syst Evol
                Fungal Syst Evol
                Fungal Systematics and Evolution
                Fungal Systematics and Evolution
                23 June 2022
                June 2022
                : 9
                : 161-200
                [1 ]Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
                [2 ]Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
                [3 ]Senckenberg Biodiversity and Climate Research Center, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
                [4 ]Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
                [5 ]Soil Biology Group, Wageningen University, Wageningen, Netherlands
                [6 ]Systematic Mycology Lab., Botany and Microbiology Department, Faculty of Science, Suez Canal University, Ismailia 41522, Egypt
                [7 ]Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj, Iran
                [8 ]Department of Mycology and Plant Resistance, V. N. Karazin Kharkiv National University, Maidan Svobody 4, 61022 Kharkiv, Ukraine
                [9 ]Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 19395-1454, Tehran, Iran
                [10 ]Setor de Micologia / Departamento de Biociências e Tecnologia, Instituto de Patologia Tropical e Saúde Pública, Rua 235 - s/n – Setor Universitário - CEP: 74605-050, Universidade Federal de Goiás / Federal University of Goiás, Goiânia, Brasil / Goiânia, Brazil
                [11 ]Center of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
                [12 ]Departamento de Agronomia, Universidade Federal Rural de Pernambuco, Recife, 52171-900, PE, Brazil
                [13 ]Escuela de Biología and Centro de Investigaciones en Productos Naturales, Universidad de Costa Rica, San Pedro, Costa Rica
                [14 ]Mycothèque de l’Université catholique de Louvain (MUCL, BCCMTM), Earth and Life Institute – ELIM – Mycology, Université catholique de Louvain, Croix du Sud 2 bte L7.05.06, B-1348 Louvain-la-Neuve, Belgium
                [15 ]Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK
                [16 ]Unitat de Micologia, Facultat de Medicina i Ciències de la Salut i Institut d’Investigació Sanitària Pere Virgili (IISPV), Universitat Rovira i Virgili, 43201 Reus, Spain
                [17 ]Institute of Grapevine and Wine Sciences (ICVV), Spanish National Research Council (CSIC)-University of La Rioja-Government of La Rioja, Logroño 26007, Spain
                [18 ]Institut für Biologie, Karl-Franzens-Universität Graz, Holteigasse 6, 8010 Graz, Austria
                [19 ]Center for Safe and Improved Food, Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
                [20 ]Biorefining and Advanced Materials Research Center, Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
                [21 ]Department of Agricultural, Forestry and Food Sciences (DISAFA), University of Torino, Largo P. Braccini 2, 10095 Grugliasco (TO), Italy
                [22 ]Department of Clinical Plant Science, Faculty of Bioscience, Hosei University3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
                [23 ]Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Reduit, Mauritius
                [24 ]EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, NJ 08077, USA
                [25 ]Department of Plant and Soil Sciences, University of Pretoria, P. Bag X20 Hatfield, Pretoria 0002, South Africa
                [26 ]ARC-Plant Health and Protection, Private Bag X5017, Stellenbosch 7599, Western Cape, South Africa
                [27 ]Dutch General Inspection Service for agricultural seeds and seed potatoes (NAK), Randweg 14, 8304 AS, Emmeloord, The Netherlands
                [28 ]School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 611731, People’s Republic of China
                [29 ]Dipartimento di Agricoltura, Alimentazione e Ambiente, sez. Patologia vegetale, University of Catania, Via S. Sofia 100, 95123 Catania, Italy
                [30 ]National Fungal Culture Collection of India (NFCCI), Biodiversity and Palaeobiology (Fungi) Group, Agharkar Research Institute, Pune, Maharashtra 411 004, India
                [31 ]USDA-ARS Mycology & Nematology Genetic Diversity & Biology Laboratory, Bldg. 010A, Rm. 212, BARC-West, 10300 Baltimore Ave. Beltsville, MD 20705, USA
                [32 ]Centre for Crop Health, University of Southern Queensland, Toowoomba 4350, Queensland, Australia
                [33 ]Sporometrics, Toronto, ON, Canada
                [34 ]Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
                [35 ]College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
                [36 ]Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa
                [37 ]Queensland Plant Pathology Herbarium, Department of Agriculture and Fisheries, Dutton Park, Queensland 4102, Australia
                [38 ]Department of Life Sciences and Systems Biology, University of Torino and Institute for Sustainable Plant Protection (IPSP-SS Turin), C.N.R, Viale P.A. Mattioli, 25, I-10125 Torino, Italy
                [39 ]Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian, 271018, China
                [40 ]Lab. Salud de Bosques, Fac. de Ciencias Forestales y RRNN, Universidad Austral de Chile, Chile
                [41 ]Curator, Cornell University Plant Pathology Herbarium, Ithaca, NY, USA
                [42 ]Univ Brest, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France
                [43 ]College of Life Sciences, Yangtze University, Jingzhou, Hubei 434025, China
                [44 ]State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
                [45 ]Goethe-University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue Str. 13, D-60438 Frankfurt am Main, Germany
                [46 ]LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
                Author notes
                *Corresponding author: p.crous@ 123456wi.knaw.nl
                Corresponding editor: A.J.L. Phillips
                © 2022 Westerdijk Fungal Biodiversity Institute

                Fungal Systematics and Evolution is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License

                : 21 March 2022
                : 14 June 2022

                longinectria,multi-gene phylogeny,nectriaceae,neocosmospora,new taxa,systematics,typification


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