title: Evaluation of two novel barcodes for species recognition of opportunistic pathogens in Fusarium.
abstract: The genus Fusarium includes more than 200 species of which 73 have been isolated from human infections. Fusarium species are opportunistic human pathogens with variable aetiology. Species determination is best made with the combined phylogeny of protein-coding genes such as elongation factor (TEF1), RNA polymerase (RPB2) and the partial β-tubulin (BT2) gene. The internal transcribed spacers 1, 2 and 5.8S rRNA gene (ITS) have also been used, however, ITS cannot discriminate several closely related species and has nonorthologous copies in Fusarium. Currently, morphological approaches and tree-building methods are in use to define species and to discover hitherto undescribed species. Aftter a species is defined, DNA barcoding approaches can be used to identify species by the presence or absence of discrete nucleotide characters. We demonstrate the potential of two recently discovered DNA barcode loci, topoisomerase I (TOP1) and phosphoglycerate kinase (PGK), in combination with other routinely used markers such as TEF1, in an analysis of 144 Fusarium strains belonging to 52 species. Our barcoding study using TOP1 and PKG provided concordance of molecular data with TEF1. The currently accepted Fusarium species sampled were well supported in phylogenetic trees of both new markers.
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands; Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands; Directorate General of Health Services, Ibri Hospital, Ministry of Health, P.C.: 100, P.O. Box : 393, Ibri, Oman. Electronic address: a.alhatmi@cbs.knaw.nl.
authors.forename: Abdullah M S
authors.initials: AM
authors.lastname: Al-Hatmi
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.
authors.forename: A H G Gerrits
authors.initials: AH
authors.lastname: Van Den Ende
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.
authors.forename: J Benjamin
authors.initials: JB
authors.lastname: Stielow
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands.
authors.forename: Anne D
authors.initials: AD
authors.lastname: Van Diepeningen
authors.affiliation: Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Seifert
authors.affiliation: Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada.
authors.forename: Wayne
authors.initials: W
authors.lastname: McCormick
authors.affiliation: Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada.
authors.forename: Rafik
authors.initials: R
authors.lastname: Assabgui
authors.affiliation: Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada.
authors.forename: Tom
authors.initials: T
authors.lastname: Gräfenhan
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, P.O. Box 85167, 3508 AD Utrecht, The Netherlands; Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands; Peking University Health Science Center, Research Center for Medical Mycology, Beijing 100034, PR China; Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yanjiang W Rd, Guangzhou, China; Shanghai Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China; Basic Pathology Department, Federal University of Paraná State, Curitiba 81531-990, Paraná, Brazil; King Abdulaziz University, Jeddah 22254, Saudi Arabia.
authors.forename: G Sybren
authors.initials: GS
authors.lastname: De Hoog
authors.affiliation: Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, Ontario K1A 0C6, Canada.
authors.forename: C André
authors.initials: CA
authors.lastname: Levesque
mesh_terms: D058893:DNA Barcoding, Taxonomic / Q000379:methods*; D004271:DNA, Fungal / Q000235:genetics; D005656:Fungal Proteins / Q000235:genetics; D060585:Fusariosis / Q000382:microbiology*; D005670:Fusarium / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D006801:Humans; D010802:Phylogeny
chemical_list: D004271:DNA, Fungal; D005656:Fungal Proteins
keywords: Character-based DNA barcoding; Fusarium; Intra- and inter-specific variation; Phosphoglycokinase (PGK); Topoisomerase I (TOP1)