title: The 'species complex' issue in clinically relevant fungi: A case study in Scedosporium apiospermum.
abstract: The genus Scedosporium currently comprises six species, Scedosporium apiospermum, Scedosporium boydii, Pseudallescheria angusta, Scedosporium minutisporum, Scedosporium dehoogii, and Scedosporium aurantiacum, most of which can be distinguished with the primary fungal DNA barcode, the ITS1/2 region of the rDNA gene cluster. In the present study, four additional genetic loci were explored from a phylogenetic point of view enabling a barcoding approach based on K2P pairwise distances to resolve the taxa Scedosporium. We included partial γ-actin (ACT), β-tubulin (BT2), elongation factor 1α (TEF1), and the small ribosomal protein 60S L10 (L1) (RP60S). Phylogenetic inference of each marker individually showed that four out of six species within Scedosporium can be distinguished unambiguously, while strains of S. apiospermum, S. boydii, and P. angusta showed occasional recombination, and accordingly, no genealogical concordance between markers was obtainable. We defined S. apiospermum, S. boydii, and P. angusta as the 'S. apiospermum species complex' since observed differences were not consistent between lineages, and no clinical differences are known between entities within the complex. While BT2 revealed the best performance among the genetic loci tested at the lineage level, barcoding of the ITS region is sufficient for distinction of all entities in Scedosporium at the species or 'complex' level.
authors.affiliation: Shanghai Institute of Medical Mycology, Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Changzheng Hospital, Shanghai 200003, China; CBS-KNAW Fungal Biodiversity Centre, Utrecht 3584 CT, The Netherlands; Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam 1012 WX, The Netherlands.
authors.forename: Min
authors.initials: M
authors.lastname: Chen
authors.affiliation: Department of Dermatology and Venereology, Union Hospital, Tongji Medical College, Huazhong Science and Technology University, Wuhan 430000, China. Electronic address: wuhanzjs@aliyun.com.
authors.forename: Jingsi
authors.initials: J
authors.lastname: Zeng
authors.affiliation: Shanghai Institute of Medical Mycology, Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Changzheng Hospital, Shanghai 200003, China; CBS-KNAW Fungal Biodiversity Centre, Utrecht 3584 CT, The Netherlands; Institute of Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam 1012 WX, The Netherlands; Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510630, China; Department of Dermatology, Peking University First Hospital, Research Center for Medical Mycology, Beijing, 100034, China; Biological Sciences Department, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Department of Basic Biology, University of Paraná, Curitiba 80060-000, Brazil.
authors.forename: G Sybren
authors.initials: GS
authors.lastname: De Hoog
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, Utrecht 3584 CT, The Netherlands.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Stielow
authors.affiliation: CBS-KNAW Fungal Biodiversity Centre, Utrecht 3584 CT, The Netherlands.
authors.forename: A H G
authors.initials: AH
authors.lastname: Gerrits Van Den Ende
authors.affiliation: Shanghai Institute of Medical Mycology, Shanghai Key Laboratory of Molecular Medical Mycology, Department of Dermatology, Shanghai Changzheng Hospital, Shanghai 200003, China.
authors.forename: Wanqing
authors.initials: W
authors.lastname: Liao
authors.affiliation: Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck 6020, Austria. Electronic address: Michaela.Lackner@i-med.ac.at.
authors.forename: Michaela
authors.initials: M
authors.lastname: Lackner
mesh_terms: D000199:Actins / Q000235:genetics; D005656:Fungal Proteins / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D016533:Mycological Typing Techniques; D009181:Mycoses / Q000382:microbiology*; D010802:Phylogeny; D021681:Scedosporium / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D014404:Tubulin / Q000235:genetics
chemical_list: D000199:Actins; D005656:Fungal Proteins; D014404:Tubulin
keywords: ITS rDNA; Populations; Primary barcode; Secondary barcode