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Nguyen HDT, Dodge A, Dadej K, Rintoul TL, Ponomareva E, Martin FN, de Cock AWAM, Lévesque CA, Redhead SA, Spies CFJ. Whole genome sequencing and phylogenomic analysis show support for the splitting of genus Pythium. Mycologia 2022; 114:501-515. [PMID: 35522547 DOI: 10.1080/00275514.2022.2045116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The genus Pythium (nom. cons.) sensu lato (s.l.) is composed of many important species of plant pathogens. Early molecular phylogenetic studies suggested paraphyly of Pythium, which led to a formal proposal by Uzuhashi and colleagues in 2010 to split the genus into Pythium sensu stricto (s.s.), Elongisporangium, Globisporangium, Ovatisporangium (= Phytopythium), and Pilasporangium using morphological characters and phylogenies of the mt cytochrome c oxidase subunit 2 (cox2) and D1-D2 domains of nuc 28S rDNA. Although the split was fairly justified by the delineating morphological characters, there were weaknesses in the molecular analyses, which created reluctance in the scientific community to adopt these new genera for the description of new species. In this study, this issue was addressed using phylogenomics. Whole genomes of 109 strains of Pythium and close relatives were sequenced, assembled, and annotated. These data were combined with 10 genomes sequenced in previous studies. Phylogenomic analyses were performed with 148 single-copy genes represented in at least 90% of the taxa in the data set. The results showed support for the division of Pythium s.l. The status of alternative generic names that have been used for species of Pythium in the past (e.g., Artotrogus, Cystosiphon, Eupythium, Nematosporangium, Rheosporangium, Sphaerosporangium) was investigated. Based on our molecular analyses and review of the Pythium generic concepts, we urge the scientific community to adopt the generic names Pythium, Elongisporangium, Globisporangium, and their concepts as proposed by Uzuhashi and colleagues in 2010 in their work going forward. In order to consolidate the taxonomy of these genera, some of the recently described Pythium spp. are transferred to Elongisporangium and Globisporangium.
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Affiliation(s)
- Hai D T Nguyen
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Annette Dodge
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Kasia Dadej
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Tara L Rintoul
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Ekaterina Ponomareva
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Frank N Martin
- Crop Improvement and Protection Research, Agricultural Research Service, United States Department of Agriculture, Salinas, California 93905, USA
| | - Arthur W A M de Cock
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - C André Lévesque
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Scott A Redhead
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6 Canada
| | - Christoffel F J Spies
- Plant Microbiology, Agricultural Research Council - Plant Health and Protection, Private Bag X5017, Stellenbosch, 7599, South Africa
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Chen JJ, Feng H, Yu J, Ye W, Zheng X. Pythium huanghuaiense sp. nov. isolated from soybean: morphology, molecular phylogeny and pathogenicity. Biodivers Data J 2021; 9:e65227. [PMID: 33935560 PMCID: PMC8084853 DOI: 10.3897/bdj.9.e65227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/18/2021] [Indexed: 11/12/2022] Open
Abstract
Background Soybean (Glycine max) is a major source of edible oil and protein. A novel species of the genus Pythium, Pythium huanghuaiense, isolated from soybean seedlings in China, is described and illustrated on the basis of morphological characters and molecular evidence. New information Pythium huanghuaiense sp. nov. is closely related to species of the genus Pythium in clade F, as evidenced by the presence of hyphal swellings and its relatively rapid morphological growth. However, it differs by having relatively small sporangia and plerotic or nearly plerotic and thin-walled oospores. A pathogenicity test confirmed the newly-identified species as a pathogen of soybean.
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Affiliation(s)
- Jia-Jia Chen
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry Zhenjiang 212400 China
| | - Hui Feng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China Department of Plant Pathology, Nanjing Agricultural University Nanjing 210095 China
| | - Jian Yu
- College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry, Zhenjiang 212400, China College of Landscape Architecture, Jiangsu Vocational College of Agriculture and Forestry Zhenjiang 212400 China
| | - Wenwu Ye
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China Department of Plant Pathology, Nanjing Agricultural University Nanjing 210095 China
| | - Xiaobo Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China Department of Plant Pathology, Nanjing Agricultural University Nanjing 210095 China
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Badali F, Abrinbana M, Abdollahzadeh J. Morphological and Molecular Taxonomy of Pythium monoclinum Abrinbana, Abdollahz. & Badali, Sp. Nov., and P. iranense, Sp. Nov., from Iran. CRYPTOGAMIE MYCOL 2020. [DOI: 10.5252/cryptogamie-mycologie2020v41a11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Farzaneh Badali
- Department of Plant Protection, Faculty of Agriculture and Natural Resources, Urmia University, P.O. Box 165, Urmia (Iran)
| | - Masoud Abrinbana
- Department of Plant Protection, Faculty of Agriculture and Natural Resources, Urmia University, P.O. Box 165, Urmia (Iran)
| | - Jafar Abdollahzadeh
- Department of Plant Protection, Faculty of Agriculture, University of Kurdistan, P.O. Box 416, Sanandaj (Iran)
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Li GJ, Zhao RL, Zhang CL, Lin FC. A preliminary DNA barcode selection for the genus Russula (Russulales, Basidiomycota). Mycology 2019; 10:61-74. [PMID: 31069120 PMCID: PMC6493256 DOI: 10.1080/21501203.2018.1500400] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 07/10/2018] [Indexed: 11/20/2022] Open
Abstract
Russula is a worldwid genus which has a high species diversity . Aiming accurate and rapid species identification, candidate genes nLSU (28S), ITS, tef-1α, mtSSU, rpb1, and rpb2, were analysed as potential DNA barcodes. This analysis included 433 sequences from 38 well-circumscribed Russula species of eight subgenera. Two vital standards were analysed for success species identification using DNA barcodes, specifically inter- and intra-specific variations together with the success rates of PCR amplification and sequencing. Although the gap between inter- and intra-specific variations was narrow, ITS met the qualification standards for a target DNA barcode. Overlapping inter- and intra-specific pairwise distances were observed in nLSU, tef-1α, mtSSU, and rpb2. The success rates of PCR amplification and sequencing in mtSSU and rpb1 were lower than those of others. Gene combinations were also investigated for resolution of species recognition. ITS-rpb2 was suggested as the likely target DNA barcode for Russula, owing to the two viatal standards above. Since nLSU has the lowest minimum of inter-specific variation, and tef-1α has the highest overlap between intra- and inter-species variations among the candidate genes, they are disqualified from the selection for DNA barcode of Russula.
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Affiliation(s)
- Guo-Jie Li
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Rui-Lin Zhao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Huairou District, Beijing, China
| | - Chu-Long Zhang
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Fu-cheng Lin
- State Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Rahman MZ, Abdelzaher HMA, Mingzhu L, Motohashi K, Suga H, Kageyama K. Pythium rishiriense sp. nov. from water and P. alternatum sp. nov. from soil, two new species from Japan. FEMS Microbiol Lett 2015; 362:fnv086. [PMID: 26062753 DOI: 10.1093/femsle/fnv086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2015] [Indexed: 11/14/2022] Open
Abstract
In an investigation of Pythium species in natural ecosystems of Rishiri Island in Northern Japan, two new species, Pythium rishiriense and P. alternatum, were identified based on morphological and molecular analyses. Pythium rishiriense differed morphologically from other Pythium species by its characteristic oogonial formation which occasionally arranged in chains. Pythium alternatum differed morphologically from other Pythium species by its distinguishing sexual organs where oogonia occasionally arranged alternately with antheridia in chains. Pythium rishiriense is a fast growing, high-temperature loving species, while P. alternatum is a slow growing species. Phylogenetic analyses based on the internal transcribed spacer region and cytochrome c oxidase 1 gene sequences showed that these two species are clearly separate from morphologically similar species.
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Affiliation(s)
| | | | - Li Mingzhu
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Keiichi Motohashi
- Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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Four new Pythium species from aquatic environments in Japan. Antonie van Leeuwenhoek 2014; 107:375-91. [DOI: 10.1007/s10482-014-0336-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 11/14/2014] [Indexed: 10/24/2022]
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