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      The divorce of Sporothrix and Ophiostoma: solution to a problematic relationship

      research-article
      1 , , 2 , 1
      Studies in Mycology
      CBS Fungal Biodiversity Centre
      Sporothrix schenckii, Sporotrichosis, Taxonomy, Nomenclature, One fungus one name, Sporothrix abietina (Marm. & Butin) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. aurorae (X.D. Zhou & M.J. Wingf.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. bragantina (Pfenning & Oberw.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. candida (Kamgan et al.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. cantabriensis (P. Romón et al.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. dentifunda (Aghayeva & M.J. Wingf.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. epigloea (Guerrero) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. eucalyptigena (Barber & Crous) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. eucastaneae (R.W. Davidson) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. euskadiensis (P. Romón et al.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. fumea (Kamgan et al.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. fusiformis (Aghayeva & M.J. Wingf.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. gemella (Roets et al.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. gossypina (R.W. Davidson) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. lunata (Aghayeva & M.J. Wingf.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. narcissi (Limber) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. nebularis (P. Romón et al.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. nigrograna (Masuya) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. palmiculminata (Roets et al.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. phasma (Roets et al.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. polyporicola (Constant. & Ryman) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. prolifera (Kowalski & Butin) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. protea-sedis (Roets et al.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. stenoceras (Robak) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. thermara (J.A. van der Linde et al.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. zambiensis (Roets et al.) Z.W. de Beer, T.A. Duong & M.J. Wingf., S. dombeyi Z.W. de Beer, T.A. Duong & M.J. Wingf., S. rossii Z.W. de Beer, T.A. Duong & M.J. Wingf

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          Abstract

          One of the causal agents of human sporotrichosis, Sporothrix schenckii, is the type species of the genus Sporothrix. During the course of the last century the asexual morphs of many Ophiostoma spp. have also been treated in Sporothrix. More recently several DNA-based studies have suggested that species of Sporothrix and Ophiostoma converge in what has become known as Ophiostoma s. lat. Were the one fungus one name principles adopted in the Melbourne Code to be applied to Ophiostoma s. lat., Sporothrix would have priority over Ophiostoma, resulting in more than 100 new combinations. The consequence would be name changes for several economically important tree pathogens including O. novo-ulmi. Alternatively, Ophiostoma could be conserved against Sporothrix, but this would necessitate changing the names of the important human pathogens in the group. In this study, we sought to resolve the phylogenetic relationship between Ophiostoma and Sporothrix. DNA sequences were determined for the ribosomal large subunit and internal transcribed spacer regions, as well as the beta-tubulin and calmodulin genes in 65 isolates. The results revealed Sporothrix as a well-supported monophyletic lineage including 51 taxa, distinct from Ophiostoma s. str. To facilitate future studies exploring species level resolution within Sporothrix, we defined six species complexes in the genus. These include the Pathogenic Clade containing the four human pathogens, together with the S. pallida-, S. candida-, S. inflata-, S. gossypina- and S. stenoceras complexes, which include environmental species mostly from soil, hardwoods and Protea infructescences. The description of Sporothrix is emended to include sexual morphs, and 26 new combinations. Two new names are also provided for species previously treated as Ophiostoma.

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          Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous.

          The evolutionary history of the phytopathogenic Gibberella fujikuroi complex of Fusarium and related species was investigated by cladistic analysis of DNA sequences obtained from multiple unlinked loci. Gene phylogenies inferred from the mitochondrial small subunit (mtSSU) rDNA, nuclear 28S rDNA, and beta-tubulin gene were generally concordant, providing strong support for a fully resolved phylogeny of all biological and most morphological species. Discordance of the nuclear rDNA internal transcribed spacer 2 (ITS2) gene tree is due to paralogous or xenologous ITS2 sequences. PCR and sequence analysis demonstrated that every strain of the ingroup species tested possesses two highly divergent nonorthologous ITS2 types designated type I and type II. Only the major ITS2 type, however, is discernable when PCR products are amplified and sequenced directly with conserved primers. The minor ITS2 type was recovered using ITS2 type-specific PCR primers. Distribution of the major ITS2 type within the species lineages exhibits a homoplastic pattern of evolution, thus obscuring true phylogenetic relationships. The results suggest that the ancestral ITS2 types may have arisen following an ancient interspecific hybridization or gene duplication which occurred prior to the evolutionary radiation of the Gibberella fujikuroi complex and related species of Fusarium. The results also indicate that current morphological-based taxonomic schemes for these fungi are unnatural and a new classification is required.
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            Sporothrix brasiliensis, S. globosa, and S. mexicana, three new Sporothrix species of clinical interest.

            Sporothrix schenckii is the species responsible for sporotrichosis, a fungal infection caused by the traumatic implantation of this dimorphic fungus. Recent molecular studies have demonstrated that this species constitutes a complex of numerous phylogenetic species. Since the delineation of such species could be of extreme importance from a clinical point of view, we have studied a total of 127 isolates, most of which were received as S. schenckii, including the available type strains of species currently considered synonyms, and also some close morphological species. We have phenotypically characterized all these isolates using different culture media, growth rates at different temperatures, and numerous nutritional tests and compared their calmodulin gene sequences. The molecular analysis revealed that Sporothrix albicans, S. inflata, and S. schenckii var. luriei are species that are clearly different from S. schenckii. The combination of these phenetic and genetic approaches allowed us to propose the new species Sporothrix brasiliensis, S. globosa, and S. mexicana. The key phenotypic features for recognizing these species are the morphology of the sessile pigmented conidia, growth at 30, 35, and 37 degrees C, and the assimilation of sucrose, raffinose, and ribitol.
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              One fungus, one name promotes progressive plant pathology.

              The robust and reliable identification of fungi underpins virtually every element of plant pathology, from disease diagnosis to studies of biology, management/control, quarantine and, even more recently, comparative genomics. Most plant diseases are caused by fungi, typically pleomorphic organisms, for which the taxonomy and, in particular, a dual nomenclature system have frustrated and confused practitioners of plant pathology. The emergence of DNA sequencing has revealed cryptic taxa and revolutionized our understanding of relationships in the fungi. The impacts on plant pathology at every level are already immense and will continue to grow rapidly as new DNA sequencing technologies continue to emerge. DNA sequence comparisons, used to resolve a dual nomenclature problem for the first time only 19 years ago, have made it possible to approach a natural classification for the fungi and to abandon the confusing dual nomenclature system. The journey to a one fungus, one name taxonomic reality has been long and arduous, but its time has come. This will inevitably have a positive impact on plant pathology, plant pathologists and future students of this hugely important discipline on which the world depends for food security and plant health in general. This contemporary review highlights the problems of a dual nomenclature, especially its impact on plant pathogenic fungi, and charts the road to a one fungus, one name system that is rapidly drawing near. © 2011 The Authors. Molecular Plant Pathology © 2011 BSPP and Blackwell Publishing Ltd.
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                Author and article information

                Contributors
                Journal
                Stud Mycol
                Stud. Mycol
                Studies in Mycology
                CBS Fungal Biodiversity Centre
                0166-0616
                1872-9797
                27 July 2016
                2016
                27 July 2016
                : 83
                : 165-191
                Affiliations
                [1 ]Department of Microbiology and Plant Pathology, Forestry and Agricultural Research Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
                [2 ]Department of Genetics, Forestry and Agricultural Research Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
                Author notes
                [] Correspondence: Z.W. de Beer wilhelm.debeer@ 123456fabi.up.ac.za
                Article
                S0166-0616(16)30003-3
                10.1016/j.simyco.2016.07.001
                5007658
                27616802
                61bab683-0385-4b55-8cea-a7834a903bb2
                Copyright © 2016, CBS-KNAW Fungal Biodiversity Centre. Production and hosting by ELSEVIER B.V.

                This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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                Categories
                Research Paper

                Plant science & Botany
                sporothrix schenckii,sporotrichosis,taxonomy,nomenclature,one fungus one name,sporothrix abietina (marm. & butin) z.w. de beer, t.a. duong & m.j. wingf.,s. aurorae (x.d. zhou & m.j. wingf.) z.w. de beer, t.a. duong & m.j. wingf.,s. bragantina (pfenning & oberw.) z.w. de beer, t.a. duong & m.j. wingf.,s. candida (kamgan et al.) z.w. de beer, t.a. duong & m.j. wingf.,s. cantabriensis (p. romón et al.) z.w. de beer, t.a. duong & m.j. wingf.,s. dentifunda (aghayeva & m.j. wingf.) z.w. de beer, t.a. duong & m.j. wingf.,s. epigloea (guerrero) z.w. de beer, t.a. duong & m.j. wingf.,s. eucalyptigena (barber & crous) z.w. de beer, t.a. duong & m.j. wingf.,s. eucastaneae (r.w. davidson) z.w. de beer, t.a. duong & m.j. wingf.,s. euskadiensis (p. romón et al.) z.w. de beer, t.a. duong & m.j. wingf.,s. fumea (kamgan et al.) z.w. de beer, t.a. duong & m.j. wingf.,s. fusiformis (aghayeva & m.j. wingf.) z.w. de beer, t.a. duong & m.j. wingf.,s. gemella (roets et al.) z.w. de beer, t.a. duong & m.j. wingf.,s. gossypina (r.w. davidson) z.w. de beer, t.a. duong & m.j. wingf.,s. lunata (aghayeva & m.j. wingf.) z.w. de beer, t.a. duong & m.j. wingf.,s. narcissi (limber) z.w. de beer, t.a. duong & m.j. wingf.,s. nebularis (p. romón et al.) z.w. de beer, t.a. duong & m.j. wingf.,s. nigrograna (masuya) z.w. de beer, t.a. duong & m.j. wingf.,s. palmiculminata (roets et al.) z.w. de beer, t.a. duong & m.j. wingf.,s. phasma (roets et al.) z.w. de beer, t.a. duong & m.j. wingf.,s. polyporicola (constant. & ryman) z.w. de beer, t.a. duong & m.j. wingf.,s. prolifera (kowalski & butin) z.w. de beer, t.a. duong & m.j. wingf.,s. protea-sedis (roets et al.) z.w. de beer, t.a. duong & m.j. wingf.,s. stenoceras (robak) z.w. de beer, t.a. duong & m.j. wingf.,s. thermara (j.a. van der linde et al.) z.w. de beer, t.a. duong & m.j. wingf.,s. zambiensis (roets et al.) z.w. de beer, t.a. duong & m.j. wingf.,s. dombeyi z.w. de beer, t.a. duong & m.j. wingf.,s. rossii z.w. de beer, t.a. duong & m.j. wingf
                Plant science & Botany
                sporothrix schenckii, sporotrichosis, taxonomy, nomenclature, one fungus one name, sporothrix abietina (marm. & butin) z.w. de beer, t.a. duong & m.j. wingf., s. aurorae (x.d. zhou & m.j. wingf.) z.w. de beer, t.a. duong & m.j. wingf., s. bragantina (pfenning & oberw.) z.w. de beer, t.a. duong & m.j. wingf., s. candida (kamgan et al.) z.w. de beer, t.a. duong & m.j. wingf., s. cantabriensis (p. romón et al.) z.w. de beer, t.a. duong & m.j. wingf., s. dentifunda (aghayeva & m.j. wingf.) z.w. de beer, t.a. duong & m.j. wingf., s. epigloea (guerrero) z.w. de beer, t.a. duong & m.j. wingf., s. eucalyptigena (barber & crous) z.w. de beer, t.a. duong & m.j. wingf., s. eucastaneae (r.w. davidson) z.w. de beer, t.a. duong & m.j. wingf., s. euskadiensis (p. romón et al.) z.w. de beer, t.a. duong & m.j. wingf., s. fumea (kamgan et al.) z.w. de beer, t.a. duong & m.j. wingf., s. fusiformis (aghayeva & m.j. wingf.) z.w. de beer, t.a. duong & m.j. wingf., s. gemella (roets et al.) z.w. de beer, t.a. duong & m.j. wingf., s. gossypina (r.w. davidson) z.w. de beer, t.a. duong & m.j. wingf., s. lunata (aghayeva & m.j. wingf.) z.w. de beer, t.a. duong & m.j. wingf., s. narcissi (limber) z.w. de beer, t.a. duong & m.j. wingf., s. nebularis (p. romón et al.) z.w. de beer, t.a. duong & m.j. wingf., s. nigrograna (masuya) z.w. de beer, t.a. duong & m.j. wingf., s. palmiculminata (roets et al.) z.w. de beer, t.a. duong & m.j. wingf., s. phasma (roets et al.) z.w. de beer, t.a. duong & m.j. wingf., s. polyporicola (constant. & ryman) z.w. de beer, t.a. duong & m.j. wingf., s. prolifera (kowalski & butin) z.w. de beer, t.a. duong & m.j. wingf., s. protea-sedis (roets et al.) z.w. de beer, t.a. duong & m.j. wingf., s. stenoceras (robak) z.w. de beer, t.a. duong & m.j. wingf., s. thermara (j.a. van der linde et al.) z.w. de beer, t.a. duong & m.j. wingf., s. zambiensis (roets et al.) z.w. de beer, t.a. duong & m.j. wingf., s. dombeyi z.w. de beer, t.a. duong & m.j. wingf., s. rossii z.w. de beer, t.a. duong & m.j. wingf

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