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Zerouki C, Chakraborty K, Kuittinen S, Pappinen A, Turunen O. Whole-genome sequence and mass spectrometry study of the snow blight fungus Phacidium infestans (Karsten) DSM 5139 growing at freezing temperatures. Mol Genet Genomics 2023; 298:1449-1466. [PMID: 37815644 PMCID: PMC10657286 DOI: 10.1007/s00438-023-02073-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023]
Abstract
Phacidium infestans (synonym Gremmenia infestans) is a significant pathogen that impacts Pinus species across the northern regions of Europe and Asia. This study introduces the genome sequence of P. infestans Karsten DSM 5139 (Phain), obtained through Pacbio technology. The assembly resulted in 44 contigs, with a total genome size of 36,805,277 bp and a Guanine-Cytosine content of 46.4%. Genome-mining revealed numerous putative biosynthetic gene clusters that code for virulence factors and fungal toxins. The presence of the enzyme pisatin demethylase was indicative of the potential of Phain to detoxify its environment from the terpenoid phytoalexins produced by its host as a defense mechanism. Proteomic analysis revealed the potential survival strategies of Phain under the snow, which included the production of antifreeze proteins, trehalose synthesis enzymes, desaturases, proteins related to elongation of very long-chain fatty acids, and stress protein responses. Study of protein GH11 endoxylanase expressed in Escherichia coli showed an acidic optimum pH (pH 5.0) and a low optimum temperature (45 °C), which is reflective of the living conditions of the fungus. Mass spectrometry analysis of the methanol extract of Phain, incubated at - 3 °C and 22 °C, revealed differences in the produced metabolites. Both genomic and mass spectrometry analyses showed the ability of Phain to adapt its metabolic processes and secretome to freezing temperatures through the production of osmoprotectant and cryoprotectant metabolites. This comprehensive exploration of Phain's genome sequence, proteome, and secretome not only advances our understanding of its unique adaptive mechanisms but also expands the possibilities of biotechnological applications.
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Affiliation(s)
- C Zerouki
- School of Forest Sciences, University of Eastern Finland, Yliopistokatu 7, 80101, Joensuu, Finland.
| | - K Chakraborty
- School of Forest Sciences, University of Eastern Finland, Yliopistokatu 7, 80101, Joensuu, Finland
| | - S Kuittinen
- School of Forest Sciences, University of Eastern Finland, Yliopistokatu 7, 80101, Joensuu, Finland
| | - A Pappinen
- School of Forest Sciences, University of Eastern Finland, Yliopistokatu 7, 80101, Joensuu, Finland
| | - O Turunen
- School of Forest Sciences, University of Eastern Finland, Yliopistokatu 7, 80101, Joensuu, Finland
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Cho SE, Kim HS, Kwag YN, Lee DH, Han JG, Kim CS. Mitrula aurea sp. nov., A New Aero-Aquatic Species from the Republic of Korea. MYCOBIOLOGY 2022; 50:213-218. [PMID: 36158040 PMCID: PMC9467578 DOI: 10.1080/12298093.2022.2097770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 06/16/2023]
Abstract
The genus Mitrula (Mitrulaceae, Helotiales), as also known as swamp beacons, inhabits submerged, decaying vegetation in standing or decaying needles, twigs, leaves, and shallow water. They play an important role in carbon cycling in some freshwater ecosystems. In the herbarium of the Korea National Arboretum (KH), seven Mitrula specimens were collected during mushroom forays in the period from 2019 to 2021. The Korean collections were found to be macromorphologically closely related to M. paludosa and M. elegans, but micromorphologically they could be distinguished by characteristics of slightly narrower asci and aseptate ascospores. Our molecular phylogenetic analyses of the internal transcribed spacer (ITS) and 28S rDNA regions also revealed that our specimens were related to M. paludosa and M. elegans, but formed a distinct clade. Based on these results, we reported our specimens as new to science and discussed the phylogeny and diversity of Mitrula species.
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Affiliation(s)
- Sung-Eun Cho
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Hyung So Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Young-Nam Kwag
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
| | - Dong-Hyeon Lee
- Divison of Forest Insect Pests and Diseases, National Institute of Forest Science, Seoul, South Korea
| | - Jae-Gu Han
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, South Korea
| | - Chang Sun Kim
- Forest Biodiversity Division, Korea National Arboretum, Pocheon, South Korea
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Li WJ, McKenzie EHC, Liu JK(J, Bhat DJ, Dai DQ, Camporesi E, Tian Q, Maharachchikumbura SSN, Luo ZL, Shang QJ, Zhang JF, Tangthirasunun N, Karunarathna SC, Xu JC, Hyde KD. Taxonomy and phylogeny of hyaline-spored coelomycetes. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00440-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Gernandt DS, Stone JK. Phylogenetic analysis of nuclear ribosomal DNA places the nematode parasite, Drechmeria coniospora, in Clavicipitaceae. Mycologia 2019. [DOI: 10.1080/00275514.1999.12061109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- David S. Gernandt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331–2902
| | - Jeffrey K. Stone
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331–2902
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Gernandt DS, Platt JL, Stone JK, Spatafor JW, Holst-Jensen A, Hamelin RC, Kohn LM. Phylogenetics of Helotiales and Rhytismatales based on partial small subunit nuclear ribosomal DNA sequences. Mycologia 2019. [DOI: 10.1080/00275514.2001.12063226] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- David S. Gernandt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331–2902
| | - Jamie L. Platt
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331–2902
| | - Jeffrey K. Stone
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331–2902
| | - Joseph W. Spatafor
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331–2902
| | - Arne Holst-Jensen
- National Veterinary Institute, Section of Food & Feed Microbiology, Ullevålsveien 68, P.O. Box 8156 Dep. 0033 Oslo, Norway
| | - Richard C. Hamelin
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, P.O. Box 3800, 1055 rue du P.E.P.S., Sainte-Foy, QC G1V 4C7 Canada
| | - Linda M. Kohn
- Department of Botany, University of Toronto, Erindale Campus, Mississauga, Ontario L5L 1C6 Canada
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Johnston PR, Seifert KA, Stone JK, Rossman AY, Marvanová L. Recommendations on generic names competing for use in Leotiomycetes (Ascomycota). IMA Fungus 2014; 5:91-120. [PMID: 25083411 PMCID: PMC4107902 DOI: 10.5598/imafungus.2014.05.01.11] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 05/31/2014] [Indexed: 11/18/2022] Open
Abstract
In advancing to one scientific name for fungi, this paper treats genera competing for use in the phylogenetically defined class Leotiomycetes except for genera of Erysiphales. Two groups traditionally included in the so-called "inoperculate discomycetes" have been excluded from this class and are also not included here, specifically Geoglossomycetes and Orbiliomycetes. A recommendation is made about the generic name to use in cases in which two or more generic names are synonyms or taxonomically congruent along with the rationale for the recommendation. In some cases the recommended generic name does not have priority or is based on an asexual type species, thus needs to be protected and ultimately approved according to Art. 57.2 of the International Code of Nomenclature for algae, fungi and plants (ICN). A table is presented listing all competing generic names and their type species noting the recommended generic name. New combinations are introduced for the oldest epithet in the recommended genus including Ascocalyx berenice, Ascoconidium purpurascens, Ascocoryne albida, A. trichophora, Blumeriella filipendulae, B. ceanothi, Botrytis arachidis, B. fritillariae-pallidoflori, Calloria urticae, Calycellina aspera, Dematioscypha delicata, Dermea abietinum, D. boycei, D. stellata, Diplocarpon alpestre, D. fragariae, Godroniopsis peckii, Grovesinia moricola, Heterosphaera sublineolata, Hyphodiscus brachyconium, H. brevicollaris, H. luxurians, Leptotrochila campanulae, Monilinia polystroma, Neofabraea actinidae, N. citricarpa, N. vagabunda, Oculimacula aestiva, O. anguioides, Pezicula brunnea, P. californiae, P. cornina, P. diversispora, P. ericae, P. melanogena, P. querciphila, P. radicicola, P. rhizophila, Phialocephala piceae, Pilidium lythri, Rhabdocline laricis, Streptotinia streptothrix, Symphyosirinia parasitica, S. rosea, Unguiculariopsis caespitosa, and Vibrissea laxa.
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Affiliation(s)
| | - Keith A. Seifert
- Biodiversity (Mycology and Microbiology), Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jeffrey K. Stone
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
| | - Amy Y. Rossman
- Systematic Mycology & Microbiology Laboratory, Agricultural Research Service-USDA, Beltsville, MD 20705, USA
| | - Ludmila Marvanová
- Czech Collection of Microorganisms, Institute of Experimental Biology, Masaryk University, 625 00 Brno, Czech Republic
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Vrålstad T, Myhre E, Schumacher T. Molecular diversity and phylogenetic affinities of symbiotic root-associated ascomycetes of the Helotiales in burnt and metal polluted habitats. THE NEW PHYTOLOGIST 2002; 155:131-148. [PMID: 33873290 DOI: 10.1046/j.1469-8137.2002.00444.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
• The diversity and phylogenetic affinities of symbiotic root-associated ascomycetes of the Helotiales are reported here based on ITS1-5.8S-ITS2 (internal transcribed spacer, ITS) nrDNA sequences. • Mycobionts were obtained from roots of ericoid plants and grasses and from Piceirhiza bicolorata ectomycorrhizas (pbECM) on conifers and hardwoods, predominantly in burnt and metal-polluted habitats. The mycobionts were sequenced through the ITS and compared with sequences of known helotialean taxa. • We recognized 132 fungal ITS-sequences with affinity to the Helotiales, of which 75% (54 different ITS-genotypes) grouped within the Hymenoscyphus ericae aggregate including Phialophora finlandia. This aggregate showed stronger affinity to members of the Hyaloscyphaceae and Dermateaceae than to Hymenoscyphus fructigenus (genus-type species; Helotiaceae). Most of the pbECM mycobionts grouped with P. finlandia, although some grouped with H. ericae. Two genotypes co-occurred in ericoid and ectomycorrhizal roots. • The H. ericae aggregate may be referable to a generic unit, and includes a diverse group of closely related, more or less darkly pigmented, root-associated ascomycetes where the borders between intra- and interspecific ITS-sequence variation, as well as different mycorrhizal and nonmycorrhizal root-symbioses, remains unclear.
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Affiliation(s)
- Trude Vrålstad
- Ascomycete Research group, Oslo, Norway (ARON), Division of Botany and Plant Physiology, Department of Biology, University of Oslo, PO Box 1045 Blindern, N-0316 Oslo, Norway
| | - Elin Myhre
- Ascomycete Research group, Oslo, Norway (ARON), Division of Botany and Plant Physiology, Department of Biology, University of Oslo, PO Box 1045 Blindern, N-0316 Oslo, Norway
| | - Trond Schumacher
- Ascomycete Research group, Oslo, Norway (ARON), Division of Botany and Plant Physiology, Department of Biology, University of Oslo, PO Box 1045 Blindern, N-0316 Oslo, Norway
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