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Prencipe S, Schiavon G, Rosati M, Nari L, Schena L, Spadaro D. Characterization of Phytopythium Species Involved in the Establishment and Development of Kiwifruit Vine Decline Syndrome. Microorganisms 2023; 11:microorganisms11010216. [PMID: 36677508 PMCID: PMC9862930 DOI: 10.3390/microorganisms11010216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Since 2012, the kiwifruit vine decline syndrome (KVDS) has progressively compromised Italian kiwifruit orchards. Different abiotic and biotic factors have been associated with the establishment and development of KVDS. During monitoring of orchards affected by KVDS in north-western Italy during 2016-2019, 71 Phytopythium spp. were isolated. Based on maximum likelihood concatenated phylogeny on the ITS1-5.8S-ITS2 region of the rDNA, large subunit rDNA, and cytochrome oxidase I, isolates were identified as P. vexans (52), P. litorale (10), P. chamaehyphon (7) and P. helicoides (2). Phytopythium litorale and P. helicoides are reported for the first time as agents of KVDS in Italy. To demonstrate pathogenicity and fulfil Koch's postulates, representative isolates of P. vexans, P. litorale, P. chamaehyphon and P. helicoides were inoculated in potted plants. In these trials, waterlogging was applied to stress plant with a temporary anoxia and to favour the production of infective zoospores by the oomycetes. In experiments in vitro, the four species showed the highest growth at 25-30 °C, depending on the media used. P. helicoides was able to grow also at 40 °C. The four species were able to grow in vitro at a pH ranging from 5.0 to 8.0, showing that pH had less effect on growth than temperature. The present study suggests a strong role of different species of Phytopythium in the establishment and development of KVDS. Phytopythium spp. could be favoured by the average increase in soil temperatures during summer, associated with global warming.
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Affiliation(s)
- Simona Prencipe
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Via Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Giada Schiavon
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Via Paolo Braccini 2, 10095 Grugliasco, Italy
- Centre of Competence for the Innovation in the Agro-Environmental Sector—AGROINNOVA, University of Turin, Via Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Marco Rosati
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Via Paolo Braccini 2, 10095 Grugliasco, Italy
- Centre of Competence for the Innovation in the Agro-Environmental Sector—AGROINNOVA, University of Turin, Via Paolo Braccini 2, 10095 Grugliasco, Italy
| | - Luca Nari
- Fondazione Agrion, Via Falicetto, 24, 12030 Manta, Italy
| | - Leonardo Schena
- Dipartimento di AGRARIA, Università Mediterranea di Reggio Calabria, Feo di Vito, 89122 Reggio Calabria, Italy
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Via Paolo Braccini 2, 10095 Grugliasco, Italy
- Centre of Competence for the Innovation in the Agro-Environmental Sector—AGROINNOVA, University of Turin, Via Paolo Braccini 2, 10095 Grugliasco, Italy
- Correspondence:
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Intragenomic variation in nuclear ribosomal markers and its implication in species delimitation, identification and barcoding in fungi. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Langer JAF, Sharma R, Nam B, Hanic L, Boersma M, Schwenk K, Thines M. Cox2 community barcoding at Prince Edward Island reveals long-distance dispersal of a downy mildew species and potentially marine members of the Saprolegniaceae. Mycol Prog 2021. [DOI: 10.1007/s11557-021-01687-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AbstractMarine oomycetes are highly diverse, globally distributed, and play key roles in marine food webs as decomposers, food source, and parasites. Despite their potential importance in global ocean ecosystems, marine oomycetes are comparatively little studied. Here, we tested if the primer pair cox2F_Hud and cox2-RC4, which is already well-established for phylogenetic investigations of terrestrial oomycetes, can also be used for high-throughput community barcoding. Community barcoding of a plankton sample from Brudenell River (Prince Edward Island, Canada), revealed six distinct oomycete OTU clusters. Two of these clusters corresponded to members of the Peronosporaceae—one could be assigned to Peronospora verna, an obligate biotrophic pathogen of the terrestrial plant Veronica serpyllifolia and related species, the other was closely related to Globisporangium rostratum. While the detection of the former in the sample is likely due to long-distance dispersal from the island, the latter might be a bona fide marine species, as several cultivable species of the Peronosporaceae are known to withstand high salt concentrations. Two OTU lineages could be assigned to the Saprolegniaceae. While these might represent marine species of the otherwise terrestrial genus, it is also conceivable that they were introduced on detritus from the island. Two additional OTU clusters were grouped with the early-diverging oomycete lineages but could not be assigned to a specific family. This reflects the current underrepresentation of cox2 sequence data which will hopefully improve with the increasing interest in marine oomycetes.
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Afandi A, Murayama E, Yin-Ling, Hieno A, Suga H, Kageyama K. Population structures of the water-borne plant pathogen Phytopythium helicoides reveal its possible origins and transmission modes in Japan. PLoS One 2018; 13:e0209667. [PMID: 30586460 PMCID: PMC6306214 DOI: 10.1371/journal.pone.0209667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/10/2018] [Indexed: 11/19/2022] Open
Abstract
The purpose of this study was to clarify the genetic diversity of Phytopythium helicoides and to understand the transmission mode of the pathogen in Japan. In total, 232 P. helicoides isolates were collected from various host plants and geographic origins, including farms and natural environments. We developed 6 novel microsatellite markers for use in the study and found 90 alleles among the 6 markers in the 232 isolates. The analysis of molecular variance suggested that P. helicoides has high variance within individuals and low fixation indices between populations. A phylogenetic analysis revealed that isolates collected from the same hosts and/or geographic origins were often grouped together. For example, several isolates from natural environments were grouped with isolates from nearby agricultural areas. On the other hand, 2 geographically distant populations collected from the same host plant had similar genotypes. Our results suggested that migration of the pathogen could be facilitated naturally via drainage systems or by human activity in the transport of agricultural materials.
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Affiliation(s)
- Auliana Afandi
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan
- Biotechnology Study Program, Graduate School of Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Emi Murayama
- River Basin Research Center, Gifu University, Gifu, Japan
| | - Yin-Ling
- Inner Mongolia University for Nationalities, Tongliao, China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu, Japan
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Le DP, Smith MK, Aitken EAB. Genetic variation in Pythium myriotylum based on SNP typing and development of a PCR-RFLP detection of isolates recovered from Pythium soft rot ginger. Lett Appl Microbiol 2017; 65:319-326. [PMID: 28736938 DOI: 10.1111/lam.12779] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 07/14/2017] [Accepted: 07/14/2017] [Indexed: 11/30/2022]
Abstract
Pythium myriotylum is responsible for severe losses in both capsicum and ginger crops in Australia under different regimes. Intraspecific genomic variation within the pathogen might explain the differences in aggressiveness and pathogenicity on diverse hosts. In this study, whole genome data of four P. myriotylum isolates recovered from three hosts and one Pythium zingiberis isolate were derived and analysed for sequence diversity based on single nucleotide polymorphisms (SNPs). A higher number of true and unique SNPs occurred in P. myriotylum isolates obtained from ginger with symptoms of Pythium soft rot (PSR) in Australia compared to other P. myriotylum isolates. Overall, SNPs were discovered more in the mitochondrial genome than those in the nuclear genome. Among the SNPs, a single substitution from the cytosine (C) to the thymine (T) in the partially sequenced CoxII gene of 14 representatives of PSR P. myriotylum isolates was within a restriction site of HinP1I enzyme which was used in the PCR-RFLP for detection and identification of the isolates without sequencing. The PCR-RFLP was also sensitive to detect PSR P. myriotylum strains from artificially infected ginger without the need for isolation for pure cultures. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first study of intraspecific variants of Pythium myriotylum isolates recovered from different hosts and origins based on single nucleotide polymorphism (SNP) genotyping of multiple genes. The SNPs discovered provide valuable makers for detection and identification of P. myriotylum strains initially isolated from Pythium soft rot (PSR) ginger by using PCR-RFLP of the CoxII locus. The PCR-RFLP was also sensitive to detect P. myriotylum directly from PSR ginger sampled from pot trials without the need of isolation for pure cultures.
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Affiliation(s)
- D P Le
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - M K Smith
- Maroochy Research Station, Queensland Department of Agriculture and Fisheries, Nambour, QLD, Australia
| | - E A B Aitken
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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He XL, Li Q, Peng WH, Zhou J, Cao XL, Wang D, Huang ZQ, Tan W, Li Y, Gan BC. Intra- and inter-isolate variation of ribosomal and protein-coding genes in Pleurotus: implications for molecular identification and phylogeny on fungal groups. BMC Microbiol 2017. [PMID: 28651582 PMCID: PMC5485676 DOI: 10.1186/s12866-017-1046-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background The internal transcribed spacer (ITS), RNA polymerase II second largest subunit (RPB2), and elongation factor 1-alpha (EF1α) are often used in fungal taxonomy and phylogenetic analysis. As we know, an ideal molecular marker used in molecular identification and phylogenetic studies is homogeneous within species, and interspecific variation exceeds intraspecific variation. However, during our process of performing ITS, RPB2, and EF1α sequencing on the Pleurotus spp., we found that intra-isolate sequence polymorphism might be present in these genes because direct sequencing of PCR products failed in some isolates. Therefore, we detected intra- and inter-isolate variation of the three genes in Pleurotus by polymerase chain reaction amplification and cloning in this study. Results Results showed that intra-isolate variation of ITS was not uncommon but the polymorphic level in each isolate was relatively low in Pleurotus; intra-isolate variations of EF1α and RPB2 sequences were present in an unexpectedly high amount. The polymorphism level differed significantly between ITS, RPB2, and EF1α in the same individual, and the intra-isolate heterogeneity level of each gene varied between isolates within the same species. Intra-isolate and intraspecific variation of ITS in the tested isolates was less than interspecific variation, and intra-isolate and intraspecific variation of RPB2 was probably equal with interspecific divergence. Meanwhile, intra-isolate and intraspecific variation of EF1α could exceed interspecific divergence. These findings suggested that RPB2 and EF1α are not desirable barcoding candidates for Pleurotus. We also discussed the reason why rDNA and protein-coding genes showed variants within a single isolate in Pleurotus, but must be addressed in further research. Conclusions Our study demonstrated that intra-isolate variation of ribosomal and protein-coding genes are likely widespread in fungi. This has implications for studies on fungal evolution, taxonomy, phylogenetics, and population genetics. More extensive sampling of these genes and other candidates will be required to ensure reliability as phylogenetic markers and DNA barcodes. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1046-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiao-Lan He
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Qian Li
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.,Jilin Agricultural University, Changchun, 130118, China.,Mianyang Institute of Agricultural Sciences, Mianyang, 621023, China
| | - Wei-Hong Peng
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Jie Zhou
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Xue-Lian Cao
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Di Wang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Zhong-Qian Huang
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Wei Tan
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Yu Li
- Jilin Agricultural University, Changchun, 130118, China
| | - Bing-Cheng Gan
- Soil and Fertilizer Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
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Species delimitation in Pythium species complexes: the case of Pythium myriotylum Drechsler and Pythium zingiberis Takahashi. Mycol Prog 2017. [DOI: 10.1007/s11557-017-1272-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Nirenberg HI, Gerlach WF, Gräfenhan T. Phytophthora × pelgrandis, a new natural hybrid pathogenic toPelargonium grandiflorumhort. Mycologia 2017; 101:220-31. [DOI: 10.3852/06-157] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Helgard I. Nirenberg
- Julius Kühn Institute-Federal Research Center for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Berlin-Dahlem, Germany
| | | | - Tom Gräfenhan
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, Biodiversity (Mycology and Botany), Ottawa, Ontario
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Pannecoucque J, Höfte M. Detection of rDNA ITS polymorphism inRhizoctonia solaniAG 2-1 isolates. Mycologia 2017; 101:26-33. [DOI: 10.3852/08-084] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | - Monica Höfte
- Ghent University, Department of Crop Protection, Laboratory of Phytopathology, Coupure Links 653, B-9000 Ghent, Belgium
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10
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DNA Barcoding for Diagnosis and Monitoring of Fungal Plant Pathogens. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Paradigm Shift in Plant Disease Diagnostics: A Journey from Conventional Diagnostics to Nano-diagnostics. Fungal Biol 2016. [DOI: 10.1007/978-3-319-27312-9_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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12
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Baten MA, Mingzhu L, Motohashi K, Ishiguro Y, Rahman MZ, Suga H, Kageyama K. Two new species, Phytopythium iriomotense sp. nov. and P. aichiense sp. nov., isolated from river water and water purification sludge in Japan. Mycol Prog 2015. [DOI: 10.1007/s11557-015-1027-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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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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14
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Two new species, Pythium agreste and P. wuhanense, based on morphological characteristics and DNA sequence data. Mycol Prog 2013. [DOI: 10.1007/s11557-013-0901-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Schroeder KL, Martin FN, de Cock AWAM, Lévesque CA, Spies CFJ, Okubara PA, Paulitz TC. Molecular Detection and Quantification of Pythium Species: Evolving Taxonomy, New Tools, and Challenges. PLANT DISEASE 2013; 97:4-20. [PMID: 30722255 DOI: 10.1094/pdis-03-12-0243-fe] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The genus Pythium is one of the most important groups of soilborne plant pathogens, present in almost every agricultural soil and attacking the roots of thousands of hosts, reducing crop yield and quality. Most species are generalists, necrotrophic pathogens that infect young juvenile tissue. In fact, Cook and Veseth have called Pythium the "common cold" of wheat, because of its chronic nature and ubiquitous distribution. Where Pythium spp. are the cause of seedling damping-off or emergence reduction, the causal agent can easily be identified based on symptoms and culturing. In more mature plants, however, infection by Pythium spp. is more difficult to diagnose, because of the nonspecific symptoms that could have abiotic causes such as nutrient deficiencies or be due to other root rotting pathogens. Molecular methods that can accurately identify and quantify this important group are needed for disease diagnosis and management recommendations and to better understand the epidemiology and ecology of this important group. The purpose of this article is to outline the current state-of-the-art in the detection and quantification of this important genus. In addition, we will introduce the reader to new changes in the taxonomy of this group.
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Affiliation(s)
| | | | | | - C André Lévesque
- Agriculture and Agri-Food Canada, Central Experimental Farm, Ottawa, ON
| | | | - Patricia A Okubara
- USDA-ARS, Root Disease and Biological Control Research Unit, Pullman, WA
| | - Timothy C Paulitz
- USDA-ARS, Root Disease and Biological Control Research Unit, Pullman, WA
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Solieri L, Chand Dakal T, Giudici P. Zygosaccharomyces sapae sp. nov., isolated from Italian traditional balsamic vinegar. Int J Syst Evol Microbiol 2013; 63:364-371. [DOI: 10.1099/ijs.0.043323-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Fourteen yeast isolates were recovered from two traditional balsamic vinegar (TBV) samples collected in the provinces of Modena and Reggio Emilia, Italy. Microsatellite-primed-PCR (MSP-PCR) was used to de-replicate the isolate collection into two representative strains, ABT301T and ABT601. Phylogenetic analysis based on the D1/D2 domains of the 26S rRNA gene indicated that these strains represented a distinct species of the genus Zygosaccharomyces, closely related to Zygosaccharomyces rouxii and Zygosaccharomyces mellis. Physiological and morphological tests supported the recognition of a novel taxon of halotolerant, osmotolerant, non-psychrotolerant and maltose-fermentation-negative yeasts showing a chain or star-shaped pattern of budding cells, which remained attached to each other. Morphological observations offered evidence of ascospore formation. A novel species, Zygosaccharomyces sapae sp. nov., is proposed to accommodate these strains, with strain ABT301T ( = CBS 12607T = MUCL 54092T) as the type strain. Based on D1/D2 domain phylogenetic analysis, the novel strains shared the highest sequence similarity (100 %) with Zygosaccharomyces sp. strain NCYC 3042, previously isolated from sugar [James, S. A., Bond, C. J., Stratford, M. & Roberts, I. N. (2005). FEMS Yeast Res 5, 747–755]. However, based on phylogenetic (internal transcribed spacers, ITS), PCR fingerprinting and physiological analyses, marked differences were observed between the novel species and strain NCYC 3042, and these results are discussed in more detail.
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Affiliation(s)
- Lisa Solieri
- Department of Life Sciences, via Amendola 2, Padiglione Besta, University of Modena and Reggio Emilia, 42121 Reggio Emilia, Italy
| | - Tikam Chand Dakal
- Department of Life Sciences, via Amendola 2, Padiglione Besta, University of Modena and Reggio Emilia, 42121 Reggio Emilia, Italy
| | - Paolo Giudici
- Department of Life Sciences, via Amendola 2, Padiglione Besta, University of Modena and Reggio Emilia, 42121 Reggio Emilia, Italy
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Molecular analyses of Pythium irregulare isolates from grapevines in South Africa suggest a single variable species. Fungal Biol 2011; 115:1210-24. [DOI: 10.1016/j.funbio.2011.08.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 08/10/2011] [Accepted: 08/23/2011] [Indexed: 11/19/2022]
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18
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Alper I, Frenette M, Labrie S. Ribosomal DNA polymorphisms in the yeast Geotrichum candidum. Fungal Biol 2011; 115:1259-69. [PMID: 22115445 DOI: 10.1016/j.funbio.2011.09.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Revised: 09/08/2011] [Accepted: 09/10/2011] [Indexed: 10/17/2022]
Abstract
The dimorphic yeast Geotrichum candidum (teleomorph: Galactomyces candidus) is commonly used to inoculate washed-rind and bloomy-rind cheeses. However, little is known about the phylogenetic lineage of this microorganism. We have sequenced the complete 18S, 5.8S, 26S ribosomal RNA genes and their internal transcribed spacers (ITS1) and ITS2 regions (5126 nucleotides) from 18 G. candidum strains from various environmental niches, with a focus on dairy strains. Multiple sequence alignments revealed the presence of 60 polymorphic sites, which is generally unusual for ribosomal DNA (rDNA) within a given species because of the concerted evolution mechanism. This mechanism drives genetic homogenization to prevent the divergent evolution of rDNA copies within individuals. While the polymorphisms observed were mainly substitutions, one insertion/deletion (indel) polymorphism was detected in ITS1. No polymorphic sites were detected downstream from this indel site, that is, in 5.8S and ITS2. More surprisingly, many sequence electrophoregrams generated during the sequencing of the rDNA had dual peaks, suggesting that many individuals exhibited intragenomic rDNA variability. The ITS1-5.8S-ITS2 regions of four strains were cloned. The sequence analysis of 68 clones revealed 32 different ITS1-5.8S-ITS2 variants within these four strains. Depending on the strain, from four to twelve variants were detected, indicating that multiple rDNA copies were present in the genomes of these G. candidum strains. These results contribute to the debate concerning the use of the ITS region for barcoding fungi and suggest that community profiling techniques based on rDNA should be used with caution.
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Affiliation(s)
- Iraz Alper
- Nutraceuticals and Functional Foods Institute, STELA Dairy Research Centre, Department of Food Sciences and Nutrition, Université Laval, Quebec City, QC, Canada G1V 0A6
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20
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Robideau GP, De Cock AWAM, Coffey MD, Voglmayr H, Brouwer H, Bala K, Chitty DW, Désaulniers N, Eggertson QA, Gachon CMM, Hu CH, Küpper FC, Rintoul TL, Sarhan E, Verstappen ECP, Zhang Y, Bonants PJM, Ristaino JB, Lévesque CA. DNA barcoding of oomycetes with cytochrome c oxidase subunit I and internal transcribed spacer. Mol Ecol Resour 2011; 11:1002-11. [PMID: 21689384 PMCID: PMC3195333 DOI: 10.1111/j.1755-0998.2011.03041.x] [Citation(s) in RCA: 295] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Oomycete species occupy many different environments and many ecological niches. The genera Phytophthora and Pythium for example, contain many plant pathogens which cause enormous damage to a wide range of plant species. Proper identification to the species level is a critical first step in any investigation of oomycetes, whether it is research driven or compelled by the need for rapid and accurate diagnostics during a pathogen outbreak. The use of DNA for oomycete species identification is well established, but DNA barcoding with cytochrome c oxidase subunit I (COI) is a relatively new approach that has yet to be assessed over a significant sample of oomycete genera. In this study we have sequenced COI, from 1205 isolates representing 23 genera. A comparison to internal transcribed spacer (ITS) sequences from the same isolates showed that COI identification is a practical option; complementary because it uses the mitochondrial genome instead of nuclear DNA. In some cases COI was more discriminative than ITS at the species level. This is in contrast to the large ribosomal subunit, which showed poor species resolution when sequenced from a subset of the isolates used in this study. The results described in this paper indicate that COI sequencing and the dataset generated are a valuable addition to the currently available oomycete taxonomy resources, and that both COI, the default DNA barcode supported by GenBank, and ITS, the de facto barcode accepted by the oomycete and mycology community, are acceptable and complementary DNA barcodes to be used for identification of oomycetes.
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Affiliation(s)
- Gregg P Robideau
- Biology Department, Carleton University, 1125 Colonel By Dr., Ottawa, Ontario, Canada
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Spies CF, Mazzola M, Botha WJ, Van Der Rijst M, Mostert L, Mcleod A. Oogonial biometry and phylogenetic analyses of the Pythium vexans species group from woody agricultural hosts in South Africa reveal distinct groups within this taxon. Fungal Biol 2011; 115:157-68. [DOI: 10.1016/j.funbio.2010.11.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 11/26/2010] [Accepted: 11/26/2010] [Indexed: 10/18/2022]
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Bezuidenhout C, Denman S, Kirk S, Botha W, Mostert L, McLeod A. Phytophthora taxa associated with cultivated Agathosma, with emphasis on the P. citricola complex and P. capensis sp. nov. PERSOONIA 2010; 25:32-49. [PMID: 21339965 PMCID: PMC3028514 DOI: 10.3767/003158510x538371] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 09/03/2010] [Indexed: 11/25/2022]
Abstract
Agathosma species, which are indigenous to South Africa, are also cultivated for commercial use. Recently growers experienced severe plant loss, and symptoms shown by affected plants suggested that a soilborne disease could be the cause of death. A number of Phytophthora taxa were isolated from diseased plants, and this paper reports their identity, mating type, and pathogenicity to young Agathosma plants. Using morphological and sequence data seven Phytophthora taxa were identified: the A1 mating type of P. cinnamomi var. cinnamomi, P. cinnamomi var. parvispora and P. cryptogea, the A2 mating type of P. drechsleri and P. nicotianae, and two homothallic taxa from the P. citricola complex. The identity of isolates in the P. citricola complex was resolved using reference isolates of P. citricola CIT groups 1 to 5 sensu Oudemans et al. (1994) along with multi-locus phylogenies (three nuclear and two mitochondrial regions), isozyme analyses, morphological characteristics and temperature-growth studies. These analyses revealed the isolates from Agathosma to include P. multivora and a putative novel species, P. taxon emzansi. Furthermore, among the P. citricola reference isolates the presence of a new species was revealed, described here as P. capensis. Findings of our study, along with some recent other studies, have contributed to resolving some of the species complexity within the P. citricola complex, resulting in the identification of a number of phylogenetically distinct taxa. The pathogenicity of representative isolates of the taxa from Agathosma was tested on A. betulina seedlings. The putative novel species, P. taxon emzansi, and P. cinnamomi var. parvispora were non-pathogenic, whereas the other species were pathogenic to this host.
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Affiliation(s)
- C.M. Bezuidenhout
- Agricultural Research Council, Infruitec-Nietvoorbij, Private Bag X5026, Stellenbosch 7599, South Africa
| | - S. Denman
- Forest Research, Alice Holt Lodge, Farnham, Surrey, GU104LH, England
| | - S.A. Kirk
- Forest Research, Alice Holt Lodge, Farnham, Surrey, GU104LH, England
| | - W.J. Botha
- Agricultural Research Council, Plant Protection Research Institute, P. Bag X134, Queenswood, Pretoria, 0121, South Africa
| | - L. Mostert
- Department of Plant Pathology, University of Stellenbosch, P. Bag X1, Matieland, 7602, South Africa
| | - A. McLeod
- Department of Plant Pathology, University of Stellenbosch, P. Bag X1, Matieland, 7602, South Africa
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Ahonsi MO, Ling Y, Kageyama K. Development of SCAR markers and PCR assays for single or simultaneous species-specific detection of Phytophthora nicotianae and Pythium helicoides in ebb-and-flow irrigated kalanchoe. J Microbiol Methods 2010; 83:260-5. [DOI: 10.1016/j.mimet.2010.08.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Accepted: 08/29/2010] [Indexed: 11/24/2022]
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24
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25
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Naher M, Motohash K, Watanabe H, Chikuo Y, Senda M, Suga H, Brasier C, Kageyama K. Phytophthora chrysanthemi sp. nov., a new species causing root rot of chrysanthemum in Japan. Mycol Prog 2010. [DOI: 10.1007/s11557-010-0670-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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26
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Li M, Senda M, Komatsu T, Suga H, Kageyama K. Development of real-time PCR technique for the estimation of population density of Pythium intermedium in forest soils. Microbiol Res 2010; 165:695-705. [PMID: 20116230 DOI: 10.1016/j.micres.2009.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 11/14/2009] [Accepted: 11/21/2009] [Indexed: 10/19/2022]
Abstract
Pythium intermedium is known to play an important role in the carbon cycling of cool-temperate forest soils. In this study, a fast, precise and effective real-time PCR technique for estimating the population densities of P. intermedium from soils was developed using species-specific primers. Specificity was confirmed both with conventional PCR and real-time PCR. The detection limit (sensitivity) was determined and amplification standard curves were generated using SYBR Green II fluorescent dye. A rapid and accurate assay for quantification of P. intermedium in Takayama forest soils of Japan was developed using a combination of a new DNA extraction method and PCR primers were developed for real-time PCR. And the distribution of P. intermedium in forest soil was investigated with both soil plating method and the developed real-time PCR technique. This new technique will be a useful tool and can be applied to practical use for studying the role of Pythium species in forest and agricultural ecosystems.
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Affiliation(s)
- Mingzhu Li
- The United Graduate School of Agriculture Science, Gifu University, Gifu 501-1193, Japan.
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Senda M, Kageyama K, Suga H, Lévesque CA. Two new species of Pythium, P. senticosum and P. takayamanum,isolated from cool-temperate forest soil in Japan. Mycologia 2009; 101:439-48. [PMID: 19623925 DOI: 10.3852/08-104] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Pythium senticosum and P. takayamanum spp. nov. were isolated from cool-temperate forest soil in Japan. P. senticosum can grow at 5 C and is fast growing at 25 C with a radial growth of 22.2 mm 24 h(-1). The species is morphologically characterized by ovoid to ellipsoid sporangia with apical papilla, ornamented oogonia with acute conical spines, and antheridia with broad attachment to oogonia. P. takayamanum is very different and can grow at 35 C. This species is morphologically characterized by its wavy antheridial stalks and ellipsoidal oogonia with constricted areas. Phylogenetic analyses of the ITS rDNA region and the partial COX2 gene showed that the two species are genetically distinct from each other and from their closest relatives. P. senticosum is closely related to P. dimorphum and P. undulatum whereas P. takayamanum is closely related to P. rhizosaccharum and P. parvum.
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Affiliation(s)
- Masako Senda
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan.
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28
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Connell LB, Redman R, Rodriguez R, Barrett A, Iszard M, Fonseca Á. Dioszegia antarctica sp. nov. and Dioszegia cryoxerica sp. nov., psychrophilic basidiomycetous yeasts from polar desert soils in Antarctica. Int J Syst Evol Microbiol 2009; 60:1466-1472. [PMID: 19671723 DOI: 10.1099/ijs.0.015412-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a survey of the culturable soil fungal population in samples collected in Taylor Valley, South Victoria Land, Antarctica, 13 basidiomycetous yeast strains with orange-coloured colonies were isolated. Phylogenetic analyses of internal transcribed spacer (ITS) and partial LSU rRNA gene sequences showed that the strains belong to the Dioszegia clade of the Tremellales (Tremellomycetes, Agaricomycotina), but did not correspond to any of the hitherto recognized species. Two novel species, Dioszegia antarctica sp. nov. (type strain ANT-03-116(T) =CBS 10920(T) =PYCC 5970(T)) and Dioszegia cryoxerica sp. nov. (type strain ANT-03-071(T) =CBS 10919(T) =PYCC 5967(T)), are described to accommodate ten and three of these strains, respectively. Analysis of ITS sequences demonstrated intrastrain sequence heterogeneity in D. cryoxerica. The latter species is also notable for producing true hyphae with clamp connections and haustoria. However, no sexual structures were observed. The two novel species can be considered obligate psychrophiles, since they failed to grow above 20 degrees C and grew best between 10 and 15 degrees C.
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Affiliation(s)
- Laurie B Connell
- School of Marine Sciences, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, USA
| | - Regina Redman
- Adaptive Symbiotic Technologies, Seattle, WA 98125, USA.,College of Forest Resources, University of Washington, Seattle, WA 98195, USA
| | - Russel Rodriguez
- Department of Biology, University of Washington, Seattle, WA 98195, USA.,US Geological Survey, Western Fisheries Research Center, Seattle, WA 98115, USA
| | - Anne Barrett
- School of Marine Sciences, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, USA
| | - Melissa Iszard
- School of Marine Sciences, University of Maine, 5735 Hitchner Hall, Orono, ME 04469, USA
| | - Álvaro Fonseca
- Centro de Recursos Microbiológicos (CREM), Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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29
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Uzuhashi S, Kakishima M, Imazu M. Structure and organization of the rDNA intergenic spacer region in Pythium ultimum. MYCOSCIENCE 2009. [DOI: 10.1007/s10267-008-0473-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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31
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Yin-Ling, Zhou W, Motohashi K, Suga H, Fukui H, Kageyama K. Development of microsatellite markers for Pythium helicoides. FEMS Microbiol Lett 2009; 293:85-91. [PMID: 19278526 DOI: 10.1111/j.1574-6968.2009.01518.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
A strategy combining dual-suppression PCR and thermal asymmetric interlaced PCR was used to determine sequences flanking microsatellite regions in Pythium helicoides. The primer pairs were designed to amplify loci containing (AC)n, (GA)n, (AGC)n, (CAC)n(CAA)n, (TCA)n and (CTTT)n repeats from the P. helicoides nuclear genome. The PCR products of each primer pair, amplified from three representative isolates collected from different hosts and locations, were cloned and sequenced. Different degrees of polymorphism were detected among these microsatellite markers. The numbers of alleles were 6, 2, 4, 11, 4 and 4 in YL-AC, YL-AGC, YL-CAA, YL-CTTT, YL-GA and YL-TCA, respectively. Allele analysis of 30 P. helicoides isolates showed length polymorphisms in all loci, except for YL-AC, using capillary electrophoresis. Thus, we have developed a simple method for designing PCR primers to amplify microsatellite markers from P. helicoides.
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Affiliation(s)
- Yin-Ling
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan.
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32
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Belbahri L, McLeod A, Paul B, Calmin G, Moralejo E, Spies CFJ, Botha WJ, Clemente A, Descals E, Sánchez-Hernández E, Lefort F. Intraspecific and within-isolate sequence variation in the ITS rRNA gene region ofPythium mercurialesp. nov. (Pythiaceae). FEMS Microbiol Lett 2008; 284:17-27. [DOI: 10.1111/j.1574-6968.2008.01168.x] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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High-frequency intragenomic heterogeneity of the ribosomal DNA intergenic spacer region in Trichophyton violaceum. EUKARYOTIC CELL 2008; 7:721-6. [PMID: 18296618 DOI: 10.1128/ec.00441-07] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The intergenic spacer (IGS) of the rRNA genes was analyzed from the dermatophyte Trichophyton violaceum isolated from cases of tinea capitis in Taiwan and Iran. T. violaceum strains were cultured from different colonies, from single conidial colonies derived by dilution plating, and from micromanipulation of single conidia from clinical samples. A ribosomal DNA probe hybridizing to multiple EcoRI fragments was used to compare restriction fragment length polymorphisms in different T. violaceum isolates. The arthroconidia of T. violaceum that form in vivo during infection were shown to contain a single nucleus by 4',6'-diamidino-2-phenylindole staining. IGS regions from an isolate cultured from a single conidium were amplified, cloned, and sequenced. The results identified that heterogeneity exists between IGS regions within a single T. violaceum genome due to different copy numbers of a 171-bp tandem repeat. This suggests that the IGS of T. violaceum is partially excluded from the concerted evolution of the rRNA gene locus. The heterogeneous character of the IGS regions in T. violaceum contrasts with the closely related dermatophyte Trichophyton rubrum, posing further questions on the phylogeny and the evolution of dermatophyte fungi.
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