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Oba Y, Hosaka K. The Luminous Fungi of Japan. J Fungi (Basel) 2023; 9:615. [PMID: 37367550 DOI: 10.3390/jof9060615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/17/2023] [Accepted: 05/24/2023] [Indexed: 06/28/2023] Open
Abstract
Luminous fungi have long attracted public attention in Japan, from old folklore and fiction to current tourism, children's toys, games, and picture books. At present, 25 species of luminous fungi have been discovered in Japan, which correspond to approximately one-fourth of the globally recognized species. This species richness is arguably due to the abundant presence of mycophiles looking to find new mushroom species and a tradition of night-time activities, such as firefly watching, in Japan. Bioluminescence, a field of bioscience focused on luminous organisms, has long been studied by many Japanese researchers, including the biochemistry and chemistry of luminous fungi. A Japanese Nobel Prize winner, Osamu Shimomura (1928-2018), primarily focused on the bioluminescence system of luminous fungi in the latter part of his life, and total elucidation of the mechanism was finally accomplished by an international research team with representatives from Russia, Brazil, and Japan in 2018. In this review, we focused on multiple aspects related to luminous fungi of Japan, including myth, taxonomy, and modern sciences.
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Affiliation(s)
- Yuichi Oba
- Department of Environmental Biology, Chubu University, Kasugai 487-8501, Aichi, Japan
| | - Kentaro Hosaka
- Department of Botany, National Museum of Nature and Science, Tsukuba 305-0005, Ibaraki, Japan
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Coetzee MPA, Wingfield BD, Wingfield MJ. Armillaria Root-Rot Pathogens: Species Boundaries and Global Distribution. Pathogens 2018; 7:E83. [PMID: 30356027 PMCID: PMC6313743 DOI: 10.3390/pathogens7040083] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/21/2018] [Accepted: 10/21/2018] [Indexed: 11/16/2022] Open
Abstract
This review considers current knowledge surrounding species boundaries of the Armillaria root-rot pathogens and their distribution. In addition, a phylogenetic tree using translation elongation factor subunit 1-alpha (tef-1α) from isolates across the globe are used to present a global phylogenetic framework for the genus. Defining species boundaries based on DNA sequence-inferred phylogenies has been a central focus of contemporary mycology. The results of such studies have in many cases resolved the biogeographic history of species, mechanisms involved in dispersal, the taxonomy of species and how certain phenotypic characteristics have evolved throughout lineage diversification. Such advances have also occurred in the case of Armillaria spp. that include important causal agents of tree root rots. This commenced with the first phylogeny for Armillaria that was based on IGS-1 (intergenic spacer region one) DNA sequence data, published in 1992. Since then phylogenies were produced using alternative loci, either as single gene phylogenies or based on concatenated data. Collectively these phylogenies revealed species clusters in Armillaria linked to their geographic distributions and importantly species complexes that warrant further research.
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Affiliation(s)
- Martin P A Coetzee
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
| | - Brenda D Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology (BGM), Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa.
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Elías-Román RD, Medel-Ortiz R, Alvarado-Rosales D, Hanna JW, Ross-Davis AL, Kim MS, Klopfenstein NB. Armillaria mexicana, a newly described species from Mexico. Mycologia 2018; 110:347-360. [PMID: 29608410 DOI: 10.1080/00275514.2017.1419031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Armillaria mexicana (Agaricales, Physalacriaceae) is described as a new species based on morphology, DNA sequence data, and phylogenetic analyses. It clearly differs from previously reported Armillaria species in North, Central, and South America. It is characterized by the absence of fibulae in the basidioma, abundant cheilocystidia, and ellipsoidal, hyaline basidiospores that are apparently smooth under light microscope, but slightly to moderately rugulose under scanning electron microscope. It is differentiated from other Armillaria species by macromorphological characters, including annulus structure, pileus and stipe coloration, and other structures. DNA sequence data (nuc rDNA internal transcribed spacers [ITS1-5.8S-ITS2 = ITS], 28S D-domain, 3' end of 28S intergenic spacer 1, and translation elongation factor 1-α [TEF1]) show that A. mexicana sequences are quite distinct from sequences of analogous Armillaria species in GenBank. In addition, sequences of ITS of the A. mexicana ex-type culture reveal an ITS1 of 1299 bp and an ITS2 of 582 bp, the longest ITS regions reported thus far in fungi. Phylogenetic analysis based on TEF1 sequences place A. mexicana in a well-separated, monophyletic clade basal to the polyphyletic A. mellea complex.
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Affiliation(s)
- Rubén Damián Elías-Román
- a Departamento de Agronomía, División de Ciencias de la Vida (DICIVA) , Campus Irapuato-Salamanca, Universidad de Guanajuato, C.P. 36824 , Irapuato , Guanajuato , México
| | - Rosario Medel-Ortiz
- b Instituto de Investigaciones Forestales, Universidad Veracruzana , Xalapa , Veracruz , México
| | | | - John W Hanna
- d US Department of Agriculture Forest Service , Rocky Mountain Research Station, 1221 S. Main Street, Moscow , Idaho 83843
| | - Amy L Ross-Davis
- d US Department of Agriculture Forest Service , Rocky Mountain Research Station, 1221 S. Main Street, Moscow , Idaho 83843
| | - Mee-Sook Kim
- e U.S. Department of Agriculture Forest Service, Pacific Northwest Research Station , 3200 SW Jefferson Way , Corvallis , Oregon 97331
| | - Ned B Klopfenstein
- d US Department of Agriculture Forest Service , Rocky Mountain Research Station, 1221 S. Main Street, Moscow , Idaho 83843
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Klopfenstein NB, Stewart JE, Ota Y, Hanna JW, Richardson BA, Ross-Davis AL, Elías-Román RD, Korhonen K, Keča N, Iturritxa E, Alvarado-Rosales D, Solheim H, Brazee NJ, Łakomy P, Cleary MR, Hasegawa E, Kikuchi T, Garza-Ocañas F, Tsopelas P, Rigling D, Prospero S, Tsykun T, Bérubé JA, Stefani FOP, Jafarpour S, Antonín V, Tomšovský M, McDonald GI, Woodward S, Kim MS. Insights into the phylogeny of Northern Hemisphere Armillaria: Neighbor-net and Bayesian analyses of translation elongation factor 1-α gene sequences. Mycologia 2017; 109:75-91. [PMID: 28402796 DOI: 10.1080/00275514.2017.1286572] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Armillaria possesses several intriguing characteristics that have inspired wide interest in understanding phylogenetic relationships within and among species of this genus. Nuclear ribosomal DNA sequence-based analyses of Armillaria provide only limited information for phylogenetic studies among widely divergent taxa. More recent studies have shown that translation elongation factor 1-α (tef1) sequences are highly informative for phylogenetic analysis of Armillaria species within diverse global regions. This study used Neighbor-net and coalescence-based Bayesian analyses to examine phylogenetic relationships of newly determined and existing tef1 sequences derived from diverse Armillaria species from across the Northern Hemisphere, with Southern Hemisphere Armillaria species included for reference. Based on the Bayesian analysis of tef1 sequences, Armillaria species from the Northern Hemisphere are generally contained within the following four superclades, which are named according to the specific epithet of the most frequently cited species within the superclade: (i) Socialis/Tabescens (exannulate) superclade including Eurasian A. ectypa, North American A. socialis (A. tabescens), and Eurasian A. socialis (A. tabescens) clades; (ii) Mellea superclade including undescribed annulate North American Armillaria sp. (Mexico) and four separate clades of A. mellea (Europe and Iran, eastern Asia, and two groups from North America); (iii) Gallica superclade including Armillaria Nag E (Japan), multiple clades of A. gallica (Asia and Europe), A. calvescens (eastern North America), A. cepistipes (North America), A. altimontana (western USA), A. nabsnona (North America and Japan), and at least two A. gallica clades (North America); and (iv) Solidipes/Ostoyae superclade including two A. solidipes/ostoyae clades (North America), A. gemina (eastern USA), A. solidipes/ostoyae (Eurasia), A. cepistipes (Europe and Japan), A. sinapina (North America and Japan), and A. borealis (Eurasia) clade 2. Of note is that A. borealis (Eurasia) clade 1 appears basal to the Solidipes/Ostoyae and Gallica superclades. The Neighbor-net analysis showed similar phylogenetic relationships. This study further demonstrates the utility of tef1 for global phylogenetic studies of Armillaria species and provides critical insights into multiple taxonomic issues that warrant further study.
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Affiliation(s)
- Ned B Klopfenstein
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Jane E Stewart
- b Department of Bioagricultural Sciences and Pest Management , Colorado State University , 307 University Avenue, Ft. Collins , Colorado 80523
| | - Yuko Ota
- c College of Bioresource Sciences , Nihon University , 1866 Kameino, Fujisawa, Kanagawa 252-0880 , Japan
| | - John W Hanna
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Bryce A Richardson
- d United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 735 North 500 East, Provo , Utah 84606
| | - Amy L Ross-Davis
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Rubén D Elías-Román
- e Departamento de Agronomía, División de Ciencias de la Vida , Campus Irapuato-Salamanca, Universidad de Guanajuato , C.P. 36824 , Apdo. Postal 311, Irapuato , Guanajuato , México
| | | | - Nenad Keča
- g Faculty of Forestry , University of Belgrade , Kneza Viseslava 1, 11030 Belgrade , Serbia
| | - Eugenia Iturritxa
- h Neiker Tecnalia, Production and Plant Protection , Granja Modelo de Arkaute , 46 Post, Vitoria-Gasteiz , 01080 , Spain
| | - Dionicio Alvarado-Rosales
- i Colegio de Postgraduados, Campus Montecillo , Instituto de Fitosanidad-Fitopatología , Texcoco 56230 , México
| | - Halvor Solheim
- j Norwegian Institute of Bioeconomy Research , Pb 115, NO-1431 Ås, Norway
| | - Nicholas J Brazee
- k UMass Extension, Center for Agriculture, Food and the Environment , University of Massachusetts , Amherst , Massachusetts 01002
| | - Piotr Łakomy
- l Department of Forest Pathology , Poznan University of Life Sciences , Wojska Polskiego 71c, 60-625 Poznań , Poland
| | - Michelle R Cleary
- m Sveriges Lantbruksuniversitet , Swedish University of Agricultural Sciences, Southern Swedish Forest Research Centre , 230 53 Alnarp , Sweden
| | - Eri Hasegawa
- n Kansai Research Center , Forestry and Forest Products Research Institute , 68 Nagai-Kyutaro, Momoyama, Fushimi , Kyoto 612-0855 , Japan
| | - Taisei Kikuchi
- o Department of Infectious Diseases, Faculty of Medicine , University of Miyazaki, Miyazaki 889-1692, Japan and Forestry and Forest Products Research Institute , Matsunosato 1, Tsukuba , Ibaraki 305-8687 , Japan
| | - Fortunato Garza-Ocañas
- p Facultad de Ciencias Forestales , Universidad Autónoma de Nuevo León , Linares , Nuevo León , Mexico
| | - Panaghiotis Tsopelas
- q NAGREF-Institute of Mediterranean Forest Ecosystems , Terma Alkmanos , 11528 Athens, B.O. 14180 , Greece
| | - Daniel Rigling
- r Swiss Federal Research Institute WSL , Zuercherstrasse 111 , CH-8903 Birmensdorf , Switzerland
| | - Simone Prospero
- r Swiss Federal Research Institute WSL , Zuercherstrasse 111 , CH-8903 Birmensdorf , Switzerland
| | - Tetyana Tsykun
- r Swiss Federal Research Institute WSL , Zuercherstrasse 111 , CH-8903 Birmensdorf , Switzerland
| | - Jean A Bérubé
- s Canadian Forest Service , Natural Resources Canada , PO Box 10380 Stn Sainte-Foy, Quebec City , Quebec G1V 4C7 , Canada
| | - Franck O P Stefani
- t Agriculture and Agri-Food Canada , KW Neatby Bldg , Ottawa , Ontario K1A 0C6 Canada
| | - Saeideh Jafarpour
- u Department of Plant Protection, Faculty of Agricultural Science and Engineering, College of Agriculture and Natural Resources , University of Tehran , Karaj , 31587-77871 , Iran
| | - Vladimír Antonín
- v Moravian Museum , Department of Botany , Zelny trh 6, 659 37 Brno , Czech Republic
| | - Michal Tomšovský
- w Faculty of Forestry and Wood Technology , Mendel University in Brno , Zemědělská 3, CZ-613 00 Brno , Czech Republic
| | - Geral I McDonald
- a United States Department of Agriculture Forest Service , Rocky Mountain Research Station , 1221 South Main Street, Moscow , Idaho 83843
| | - Stephen Woodward
- x Department of Plant and Soil Sciences, Institute of Biological and Environmental Sciences , University of Aberdeen , Aberdeen AB24 2TZ , Scotland , UK
| | - Mee-Sook Kim
- y Department of Forestry, Environment and Systems , Kookmin University , Seoul 02707 , Republic of Korea
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Tsykun T, Rigling D, Prospero S. A new multilocus approach for a reliable DNA-based identification of Armillaria species. Mycologia 2013; 105:1059-76. [PMID: 23449075 DOI: 10.3852/12-209] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In this paper we highlight and critically discuss limitations to molecular methods for identification of fungi via the example of the basidiomycete genus Armillaria. We analyzed a total of 144 sequences of three DNA regions commonly used for identifying fungi (ribosomal IGS-1 and ITS regions, translation elongation factor-1 alpha gene) from 48 specimens of six Armillaria species occurring in Europe (A. cepistipes, A. ostoyae, A. gallica, A. borealis, A. mellea, A. tabescens). Species were identified by comparing newly obtained sequences with those from the NCBI database, phylogenetic analyses and PCR-RFLP analyses of the three regions considered. When analyzed separately, no single gene region could unambiguously identify all six Armillaria species because of low interspecific and high intrasequence variability. We therefore developed a multilocus approach, which involves the stepwise use of the three regions. Following this scheme, all six species could be clearly discriminated. Our study suggests that, to improve the reliability of DNA-based techniques for species identification, multiple genes or intergenic regions should be analyzed.
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