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Dos Santos TT, de Souza Leite T, de Queiroz CB, de Araújo EF, Pereira OL, de Queiroz MV. High genetic variability in endophytic fungi from the genus Diaporthe isolated from common bean (Phaseolus vulgaris L.) in Brazil. J Appl Microbiol 2016; 120:388-401. [PMID: 26541097 DOI: 10.1111/jam.12985] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/26/2015] [Accepted: 09/07/2015] [Indexed: 01/11/2023]
Abstract
AIMS The goals of the present study were to identify, to analyse the phylogenetic relations and to evaluate the genetic variability in Diaporthe endophytic isolates from common bean. METHODS AND RESULTS Diaporthe sp., D. infecunda and D. phaseolorum strains were identified using multilocus phylogeny (rDNA ITS region; EF1-α, β-tubulin, and calmodulin genes). IRAP (Inter-Retrotransposon Amplified Polymorphism) and REMAP (Retrotransposon-Microsatellite Amplified Polymorphism) molecular markers reveal the existence of high genetic variability, especially among D. infecunda isolates. CONCLUSIONS It was concluded that the multilocus phylogenetic approach was more effective than individual analysis of ITS sequences, in identifying the isolates to species level, and that IRAP and REMAP markers can be used for studying the genetic variability in the genus Diaporthe particularly at the intraspecific level. SIGNIFICANCE AND IMPACT OF THE STUDY The combined use of molecular tools such as multilocus phylogenetic approach and molecular markers, as performed in this study, is the best way to distinguish endophytic strains of Diaporthe isolated from common bean (Phaseolus vulgaris L.).
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Affiliation(s)
- T T Dos Santos
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil.,Instituto de Ciências e Tecnologia das Águas, Universidade Federal do Oeste do Pará, Santarém, Brazil
| | - T de Souza Leite
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - C B de Queiroz
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - E F de Araújo
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - O L Pereira
- Department of Phytopathology, Universidade Federal de Viçosa, Viçosa, Brazil
| | - M V de Queiroz
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Brazil
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Biodiversity, Phylogeny, and Antifungal Functions of Endophytic Fungi Associated with Zanthoxylum bungeanum. Int J Mol Sci 2016; 17:ijms17091541. [PMID: 27649145 PMCID: PMC5037815 DOI: 10.3390/ijms17091541] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/29/2016] [Accepted: 09/07/2016] [Indexed: 11/27/2022] Open
Abstract
This study investigated the biodiversity, phylogeny, and antifungal activity of endophytic fungi isolated from Zanthoxylum bungeanum. A total of 940 isolates obtained were grouped into 93 morphotypes, 43 species, and 23 genera, which were authenticated by molecular identification based on rDNA internal transcribed spacer (ITS) sequence analysis. A high diversity of endophytic fungi from Z. bungeanum are observed with high species richness S (43), Margalef index D′ (6.1351), Shannon–Wiener index H′ (3.2743), Simpson diversity index Ds (0.9476), PIE index (0.9486), and evenness Pielou index J (0.8705) but a low dominant index λ (0.0524). Significant tissue specificity of the endophytic fungi was observed in Z. bungeanum, and the highest species richness and diversity indexes were obtained in the stem. Phylogenetic analyses of the 93 endophytic isolates were carried out by the neighbor-joining (NJ) method to demonstrate their evolutionary processes. Antifungal activities of endophytic fungi were assayed and eight endophytic isolates showed strong and long-lasting inhibition against host pathogenic fungi Fusarium sambucinum and Pseudocercospora zanthoxyli. Here, for the first time, we systematically demonstrate the biodiversity, phylogeny, and antifungal activity of endophytic fungi associated with Z. bungeanum and reveal the value of sampling different tissues of a given plant to obtain the greatest endophyte species diversity, which might offer a framework for further investigation and utilization of endophytic fungi as aunique source of interesting and useful bioactive compounds.
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Mating type markers reveal high levels of heterothallism in Leptographium sensu lato. Fungal Biol 2016; 120:538-546. [PMID: 27020155 DOI: 10.1016/j.funbio.2016.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/23/2015] [Accepted: 01/03/2016] [Indexed: 01/16/2023]
Abstract
Species of Leptographium sensu lato are sap-stain fungi vectored by bark beetles and some species cause or are associated with tree diseases. Sexual states have been reported for more than 30 species in this group and these have been treated in the sexual genus Grosmannia. No sexual state is known for at least 59 additional species and these reside in the genus Leptographium. The discovery of sexual states for species of Leptographium relies mainly on the presence of fruiting bodies on host tissue at the time of isolation and/or intensive laboratory mating studies, which commonly have low levels of success. We developed mating-type markers to study sexual compatibility of species in Leptographium sensu lato. Using these markers, it was possible to identify mating types for 42 species and to determine thallism in many species for the first time. Surprisingly, the results showed that heterothallic and putatively heterothallic species are abundant (39 out of 42 species) in Leptographium sensu lato, and only three species were confirmed to be homothallic. The mating type markers developed in this study will be useful for future studies concerning mating type and sexual compatibility of species in this genus.
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Affiliation(s)
- Yahui Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
- University of Chinese Academy of Sciences, Shijingshan Rd, Shijingshan, Beijing 100049, P.R. China
| | - Fang Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, P. R. China
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Bai Q, Zhai L, Chen X, Hong N, Xu W, Wang G. Biological and Molecular Characterization of Five Phomopsis Species Associated with Pear Shoot Canker in China. PLANT DISEASE 2015; 99:1704-1712. [PMID: 30699520 DOI: 10.1094/pdis-03-15-0259-re] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In recent years, a widespread canker disease that infects the branches of pear trees has been observed in many provinces in China; it kills the branches and results in high losses in fruit production. Symptomatic branches were collected for etiological isolation from 11 varieties of three pear species and from Malus pumila. Samples were collected from six provinces in China. In total, 143 Phomopsis isolates were obtained from 181 samples and these were identified as belonging to five species: Phomopsis fukushii (n = 69 isolates), Diaporthe eres (n = 31), P. amygdali (n = 22), P. longicolla (n = 13), and D. neotheicola (n = 8). Pathogenicity tests showed that only the first three species induced lesions on nonwounded branches of Pyrus pyrifolia var. Cuiguan. All the fungal species induced branch cankers following wound inoculations, and tests with additional pear varieties showed significantly higher virulence levels for the first three species than the latter two. A host range evaluation suggested that the five species could infect most fruit trees belonging to the Rosaceae family as well as some non-Rosaceous species. Virulence varied depending on the species of both host and pathogen. Isolates of Phomopsis amygdali had significantly higher virulence in all the tested Rosaceae plants. Correlations among the host, pathogen, and sampling regions were noted, and the morphology, growth rate, and sporulation of these species in varied media were also characterized. This study presents the first attempt to perform a broad survey and characterization of the Phomopsis spp. associated with the pear shoot cankers in China. This study shows that D. eres and P. amygdali are just as responsible for the pear shoot canker diseases as P. fukushii, and it expands the host and geographic ranges of the five species. This report provides useful information for understanding and improving management strategies for controlling this economically important disease.
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Affiliation(s)
- Qing Bai
- State Key Laboratory of Agricultural Microbiology; College of Plant Science and Technology, Huazhong Agricultural University; and National Indoor Conservation Center of Virus-free Germplasms of Fruit Crops, Wuham, Hubei 430070, China
| | - Lifeng Zhai
- State Key Laboratory of Agricultural Microbiology; College of Plant Science and Technology, Huazhong Agricultural University; and National Indoor Conservation Center of Virus-free Germplasms of Fruit Crops, Wuham, Hubei 430070, China
| | - Xiaoren Chen
- State Key Laboratory of Agricultural Microbiology; College of Plant Science and Technology, Huazhong Agricultural University; and National Indoor Conservation Center of Virus-free Germplasms of Fruit Crops, Wuham, Hubei 430070, China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology; College of Plant Science and Technology, Huazhong Agricultural University; and National Indoor Conservation Center of Virus-free Germplasms of Fruit Crops, Wuham, Hubei 430070, China
| | - Wenxing Xu
- State Key Laboratory of Agricultural Microbiology; College of Plant Science and Technology, Huazhong Agricultural University; and National Indoor Conservation Center of Virus-free Germplasms of Fruit Crops, Wuham, Hubei 430070, China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology; College of Plant Science and Technology, Huazhong Agricultural University; and National Indoor Conservation Center of Virus-free Germplasms of Fruit Crops, Wuham, Hubei 430070, China
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Thompson S, Tan Y, Shivas R, Neate S, Morin L, Bissett A, Aitken E. Green and brown bridges between weeds and crops reveal novel Diaporthe species in Australia. PERSOONIA 2015; 35:39-49. [PMID: 26823627 PMCID: PMC4713110 DOI: 10.3767/003158515x687506] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 10/30/2014] [Indexed: 01/05/2023]
Abstract
Diaporthe (syn. Phomopsis) species are well-known saprobes, endophytes or pathogens on a range of plants. Several species have wide host ranges and multiple species may sometimes colonise the same host species. This study describes eight novel Diaporthe species isolated from live and/or dead tissue from the broad acre crops lupin, maize, mungbean, soybean and sunflower, and associated weed species in Queensland and New South Wales, as well as the environmental weed bitou bush (Chrysanthemoides monilifera subsp. rotundata) in eastern Australia. The new taxa are differentiated on the basis of morphology and DNA sequence analyses based on the nuclear ribosomal internal transcribed spacer region, and part of the translation elongation factor-1α and ß-tubulin genes. The possible agricultural significance of live weeds and crop residues ('green bridges') as well as dead weeds and crop residues ('brown bridges') in aiding survival of the newly described Diaporthe species is discussed.
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Affiliation(s)
- S.M. Thompson
- Centre for Crop Health, University of Southern Queensland, West Street, Toowoomba. Queensland 4350 Australia
- School of Agriculture and Food Science, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Y.P. Tan
- Plant Pathology Herbarium, Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia
| | - R.G. Shivas
- Plant Pathology Herbarium, Department of Agriculture, Fisheries and Forestry, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia
| | - S.M. Neate
- Centre for Crop Health, University of Southern Queensland, West Street, Toowoomba. Queensland 4350 Australia
| | - L. Morin
- CSIRO Ecosystem Sciences and Biosecurity Flagship, G.P.O. Box 1700, Canberra, Australian Capital Territory 2601, Australia
| | - A. Bissett
- CSIRO Plant Industry, G.P.O. Box 1600, Canberra, Australian Capital Territory 2601, Australia
| | - E.A.B. Aitken
- School of Agriculture and Food Science, The University of Queensland, St Lucia, Queensland 4072, Australia
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Lawrence DP, Travadon R, Baumgartner K. Diversity of Diaporthe species associated with wood cankers of fruit and nut crops in northern California. Mycologia 2015; 107:926-40. [PMID: 26240309 DOI: 10.3852/14-353] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 06/23/2015] [Indexed: 11/10/2022]
Abstract
Diaporthe ampelina, causal agent of Phomopsis cane and leaf spot of grapevine (Vitis vinifera L.) is isolated frequently from grapevine wood cankers, causing Phomopsis dieback. The latter disease is associated with four other Diaporthe species, three of which also are reported from hosts other than grape. To better understand the role of this Diaporthe community in Phomopsis dieback of grapevine and the potential for infection routes among alternate hosts, 76 Diaporthe isolates were recovered from wood cankers of cultivated grape, pear, apricot, almond and the wild host willow in four California counties. Isolates were characterized morphologically and assigned to species based on multigene sequence analyses. This study identified eight Diaporthe species from grapevine and one novel taxon from willow, D. benedicti. We report the first findings of D. australafricana and D. novem in North America. Our findings also expand the host ranges of D. ambigua to apricot and willow, D. australafricana to almond and willow, D. chamaeropis to grapevine and willow, D. foeniculina to willow and D. novem to almond. The generalists D. ambigua and D. eres were the most genetically diverse species, based on high nucleotide and haplotypic diversity, followed by the grapevine specialist D. ampelina. Analyses based on multilocus linkage disequilibrium could not reject the hypothesis of random mating for D. ambigua, which is further supported by relatively high haplotypic diversity, reports of both mating types and reports of successful matings in vitro. Pathogenicity assays revealed that D. ampelina was the most pathogenic species to grapevine wood.
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Affiliation(s)
- Daniel P Lawrence
- Department of Plant Pathology, University of California, Davis, California 95616
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, California 95616
| | - Kendra Baumgartner
- United States Department of Agriculture, Agricultural Research Service, Crops Pathology and Genetics Research Unit, Davis, California 95616
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58
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59
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Udayanga D, Castlebury LA, Rossman AY, Chukeatirote E, Hyde KD. The Diaporthe sojae species complex: Phylogenetic re-assessment of pathogens associated with soybean, cucurbits and other field crops. Fungal Biol 2015; 119:383-407. [PMID: 25937066 DOI: 10.1016/j.funbio.2014.10.009] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 10/28/2014] [Indexed: 01/25/2023]
Abstract
Phytopathogenic species of Diaporthe are associated with a number of soybean diseases including seed decay, pod and stem blight and stem canker and lead to considerable crop production losses worldwide. Accurate morphological identification of the species that cause these diseases has been difficult. In this study, we determined the phylogenetic relationships and species boundaries of Diaporthe longicolla, Diaporthe phaseolorum, Diaporthe sojae and closely related taxa. Species boundaries for this complex were determined based on combined phylogenetic analysis of five gene regions: partial sequences of calmodulin (CAL), beta-tubulin (TUB), histone-3 (HIS), translation elongation factor 1-α (EF1-α), and the nuclear ribosomal internal transcribed spacers (ITS). Phylogenetic analyses revealed that this large complex of taxa is comprised of soybean pathogens as well as species associated with herbaceous field crops and weeds. Diaporthe arctii, Diaporthe batatas, D. phaseolorum and D. sojae are epitypified. The seed decay pathogen D. longicolla was determined to be distinct from D. sojae. D. phaseolorum, originally associated with stem and leaf blight of Lima bean, was not found to be associated with soybean. A new species, Diaporthe ueckerae on Cucumis melo, is introduced with description and illustrations.
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Affiliation(s)
- Dhanushka Udayanga
- Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture - Agricultural Research Service, Beltsville, MD 20705, USA; Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand; School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Lisa A Castlebury
- Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture - Agricultural Research Service, Beltsville, MD 20705, USA.
| | - Amy Y Rossman
- Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture - Agricultural Research Service, Beltsville, MD 20705, USA
| | - Ekachai Chukeatirote
- Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand; School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand
| | - Kevin D Hyde
- Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai, 57100, Thailand; School of Science, Mae Fah Luang University, Chiang Rai, 57100, Thailand; Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China; World Agroforestry Centre, East and Central Asia, Kunming 650201, People's Republic of China
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60
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Identification of Acremonium isolates from grapevines and evaluation of their antagonism towards Plasmopara viticola. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1082-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Ferreira MC, Vieira MDLA, Zani CL, Alves TMDA, Junior PAS, Murta SM, Romanha AJ, Gil LHVG, Carvalho AGDO, Zilli JE, Vital MJS, Rosa CA, Rosa LH. Molecular phylogeny, diversity, symbiosis and discover of bioactive compounds of endophytic fungi associated with the medicinal Amazonian plant Carapa guianensis Aublet ( Meliaceae ). BIOCHEM SYST ECOL 2015. [DOI: 10.1016/j.bse.2014.12.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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63
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Udayanga D, Castlebury LA, Rossman AY, Chukeatirote E, Hyde KD. Insights into the genus Diaporthe: phylogenetic species delimitation in the D. eres species complex. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0297-2] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Gao Y, Su Y, Sun W, Cai L. Diaporthe species occurring on Lithocarpus glabra in China, with descriptions of five new species. Fungal Biol 2014; 119:295-309. [PMID: 25937059 DOI: 10.1016/j.funbio.2014.06.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 05/12/2014] [Accepted: 06/08/2014] [Indexed: 11/18/2022]
Abstract
The Diaporthe species include important plant pathogenic fungi with wide host ranges and geographic distributions. In this paper, species associated with Lithocarpus glabra were examined using a multi-locus phylogeny based on a combined rDNA-internal transcribed spacer (ITS), and partial translation elongation factor 1-alpha (TEF1), beta tubulin (TUB), and calmodulin (CAL) regions. The phylogenies inferred from combined multi-locus sequences grouped isolates from L. glabra into seven distinct lineages with high branch support, which corresponded to two previously described species and five novel species described in this paper. Our results indicate a high species diversity of Diaporthe associated with L. glabra, and host association is further proved not reliable for species delimitation. Three species previously described in Phomopsis were transferred to Diaporthe in the present paper. A synopsis of morphological characters of the 14 species currently known from Fagaceae is provided.
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Affiliation(s)
- YaHui Gao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1, West Beicheng Rd, Chaoyang District, Beijing 100101, PR China; University of Chinese Academy of Sciences, Shijingshan Rd, Shijingshan, Beijing 100049, PR China
| | - YuanYing Su
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1, West Beicheng Rd, Chaoyang District, Beijing 100101, PR China
| | - Wei Sun
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1, West Beicheng Rd, Chaoyang District, Beijing 100101, PR China
| | - Lei Cai
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, No. 1, West Beicheng Rd, Chaoyang District, Beijing 100101, PR China.
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Geng Y, Li Z, Xia LY, Wang Q, Hu XM, Zhang XG. Characterization and phylogenetic analysis of the mating-type loci in the asexual ascomycete genus Ulocladium. Mycologia 2014; 106:649-65. [PMID: 24891417 DOI: 10.3852/13-383] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The genus Ulocladium is thought to be strictly asexual. Mating-type (MAT) loci regulate sexual reproduction in fungi and their study may help to explain the apparent lack of sexual reproduction in Ulocladium. We sequenced the full length of two MAT genes in 26 Ulocladium species and characterized the entire MAT idiomorphs plus flanking regions of Ulocladium botrytis. The MAT1-1 ORF encodes a protein with an alpha-box motif by the MAT1-1-1 gene and the MAT1-2 ORF encodes a protein with an HMG box motif by the MAT1-2-1 gene. Both MAT1-1-1 and MAT1-2-1 genes were detected in a single strain of every species. Moreover, the results of RT-PCR revealed that both MAT genes are expressed in all 26 Ulocladium species. This demonstrates that MAT genes of Ulocladium species might be functional and that they have the potential for sexual reproduction. Phylogenies based on MAT genes were compared with GAPDH and Alt a 1 phylograms in Ulocladium using maximum parsimony (MP) and Bayesian analysis. The MAT genealogies and the non-MAT trees displayed different topologies, indicating that MAT genes are unsuitable phylogenetic markers at the species level in Ulocladium. Furthermore, the conflicting topologies between MAT1-1-1 and MAT1-2-1 phylogeny indicate separate evolutionary events for the two MAT genes. However, the intergeneric phylogeny of four closely allied genera (Ulocladium, Alternaria, Cochliobolus, Stemphylium) based on MAT alignments demonstrated that MAT genes are suitable for phylogenetic analysis among allied genera.
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Affiliation(s)
- Yun Geng
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
| | - Zhuang Li
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
| | - Li-Yun Xia
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
| | - Qun Wang
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
| | - Xian-Mei Hu
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
| | - Xiu-Guo Zhang
- Department of Plant Pathology, Shandong Agricultural University, Taian, 271018, China
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Udayanga D, Castlebury L, Rossman A, Hyde K. Species limits in Diaporthe: molecular re-assessment of D. citri, D. cytosporella, D. foeniculina and D. rudis. PERSOONIA 2014; 32:83-101. [PMID: 25264384 PMCID: PMC4150081 DOI: 10.3767/003158514x679984] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 08/09/2013] [Indexed: 11/25/2022]
Abstract
Species of Diaporthe are important plant pathogens of a wide range of hosts worldwide. In the present study the species causing melanose and stem end rot diseases of Citrus spp. are revised. Three species of Diaporthe occurring on Citrus are characterised, including D. citri, D. cytosporella and D. foeniculina. Morphology and phylogenetic analyses of the complete nuclear ribosomal internal transcribed spacer regions and partial sequences of actin, beta-tubulin, calmodulin and translation elongation factor 1-α were used to resolve species on Citrus and related Diaporthe species. Diaporthe citri occurs on Citrus throughout the Citrus-growing regions of the world. Diaporthe cytosporella is found on Citrus in Europe and California (USA). Diaporthe foeniculina, including the synonym D. neotheicola, is recognised as a species with an extensive host range including Citrus. Diaporthe medusaea, a name widely used for D. citri, was determined to be a synonym of D. rudis, a species with a broad host range. Diaporthe citri is delimited based on molecular phylogenetic analysis with the inclusion of the conserved ex-type and additional collections from different geographic locations worldwide. Diaporthe cytosporella, D. foeniculina and D. rudis are epitypified, fully described and illustrated with a review of all synonyms based on molecular data and morphological studies. Newly designed primers are introduced to optimise the amplification and sequencing of calmodulin and actin genes in Diaporthe. A discussion is provided of the utility of genes and the need for multi-gene phylogenies when distinguishing species of Diaporthe or describing new species.
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Affiliation(s)
- D. Udayanga
- *Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA
- Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - L.A. Castlebury
- *Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA
| | - A.Y. Rossman
- *Systematic Mycology and Microbiology Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, 20705 USA
| | - K.D. Hyde
- Institute of Excellence in Fungal Research, Mae Fah Luang University, Chiang Rai 57100, Thailand
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
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Chen S, Morgan DP, Hasey JK, Anderson K, Michailides TJ. Phylogeny, Morphology, Distribution, and Pathogenicity of Botryosphaeriaceae and Diaporthaceae from English Walnut in California. PLANT DISEASE 2014; 98:636-652. [PMID: 30708543 DOI: 10.1094/pdis-07-13-0706-re] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Species of family Botryosphaeriaceae and genus Diaporthe (anamorph: genus Phomopsis, family Diaporthaceae) were reported and caused diseases on various fruit and nut trees in California. In the last several years, diseases on English walnut (Juglans regia) caused by species of Botryosphaeriaceae and Diaporthe were observed frequently in California. Disease symptoms include stem canker; shoot canker and blight; twig, leaf, and fruit blight; and necrotic leaf lesions. Isolates of the pathogen were collected from English walnut in 13 counties in California. The aims of this study were to identify these isolates and to test their pathogenicity to English walnut cultivars. In total, 159 California isolates were identified based on comparisons of DNA sequence data of the internal transcribed spacer, translation elongation factor 1-α, and β-tubulin gene regions, and combined with the morphological features of the cultures and conidia. Research results revealed that isolates represent 10 species of Botryosphaeriaceae and two species of Diaporthe. These species include Botryosphaeria dothidea, Diplodia mutila, D. seriata, Dothiorella iberica, Lasiodiplodia citricola, Neofusicoccum mediterraneum, N. nonquaesitum, N. parvum, N. vitifusiforme, Neoscytalidium dimidiatum, Diaporthe neotheicola, and D. rhusicola. Pathogenicity on three English walnut cultivars ('Chandler', 'Tulare', and 'Vina') using a mycelium plug inoculation method revealed that all these species are pathogenic to all the tested cultivars, with L. citricola and N. parvum being the most pathogenic species, followed by N. mediterraneum, N. dimidiatum, and B. dothidea. Chandler was more tolerant to infection than Tulare and Vina. Results in this study determined that multiple numbers of the Botryosphaeriaceae fungi and two Diaporthe spp. cause cankers and blights of English walnut and vary in their virulence from highly to slightly virulent, respectively.
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Affiliation(s)
- ShuaiFei Chen
- Department of Plant Pathology, University of California-Davis/Kearney Agricultural Research and Extension Center, Parlier 93648
| | - David P Morgan
- Department of Plant Pathology, University of California-Davis/Kearney Agricultural Research and Extension Center, Parlier 93648
| | - Janine K Hasey
- University of California Cooperative Extension, Yuba/Sutter Co., Yuba City 95991
| | - Kathleen Anderson
- University of California Cooperative Extension, Stanislaus Co., Modesto 95358
| | - Themis J Michailides
- Department of Plant Pathology, University of California-Davis/Kearney Agricultural Research and Extension Center
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68
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Botryosphaeriaceae and Diaporthaceae associated with panicle and shoot blight of pistachio in California, USA. FUNGAL DIVERS 2014. [DOI: 10.1007/s13225-014-0285-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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69
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Gomes R, Glienke C, Videira S, Lombard L, Groenewald J, Crous P. Diaporthe: a genus of endophytic, saprobic and plant pathogenic fungi. PERSOONIA 2013; 31:1-41. [PMID: 24761033 PMCID: PMC3904044 DOI: 10.3767/003158513x666844] [Citation(s) in RCA: 301] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 02/24/2013] [Indexed: 11/25/2022]
Abstract
Diaporthe (Phomopsis) species have often been reported as plant pathogens, non-pathogenic endophytes or saprobes, commonly isolated from a wide range of hosts. The primary aim of the present study was to resolve the taxonomy and phylogeny of a large collection of Diaporthe species occurring on diverse hosts, either as pathogens, saprobes, or as harmless endophytes. In the present study we investigated 243 isolates using multilocus DNA sequence data. Analyses of the rDNA internal transcribed spacer (ITS1, 5.8S, ITS2) region, and partial translation elongation factor 1-alpha (TEF1), beta-tubulin (TUB), histone H3 (HIS) and calmodulin (CAL) genes resolved 95 clades. Fifteen new species are described, namely Diaporthe arengae, D. brasiliensis, D. endophytica, D. hongkongensis, D. inconspicua, D. infecunda, D. mayteni, D. neoarctii, D. oxe, D. paranensis, D. pseudomangiferae, D. pseudophoenicicola, D. raonikayaporum, D. schini and D. terebinthifolii. A further 14 new combinations are introduced in Diaporthe, and D. anacardii is epitypified. Although species of Diaporthe have in the past chiefly been distinguished based on host association, results of this study confirm several taxa to have wide host ranges, suggesting that they move freely among hosts, frequently co-colonising diseased or dead tissue. In contrast, some plant pathogenic and endophytic taxa appear to be strictly host specific. Given this diverse ecological behaviour among members of Diaporthe, future species descriptions lacking molecular data (at least ITS and HIS or TUB) should be strongly discouraged.
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Affiliation(s)
- R.R. Gomes
- Department of Genetics, Universidade Federal do Paraná, Centro Politécnico, Box 19071, 81531-990, Curitiba, Brazil
| | - C. Glienke
- Department of Genetics, Universidade Federal do Paraná, Centro Politécnico, Box 19071, 81531-990, Curitiba, Brazil
| | - S.I.R. Videira
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - L. Lombard
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - J.Z. Groenewald
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
| | - P.W. Crous
- CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands
- Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Wageningen University and Research Centre (WUR), Laboratory of Phytopathology, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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70
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Úrbez-Torres JR, Peduto F, Smith RJ, Gubler WD. Phomopsis Dieback: A Grapevine Trunk Disease Caused by Phomopsis viticola in California. PLANT DISEASE 2013; 97:1571-1579. [PMID: 30716818 DOI: 10.1094/pdis-11-12-1072-re] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Field surveys recently conducted in California and in other grape-growing regions in the United States showed Phomopsis viticola to be one of the most prevalent fungi isolated from grapevine perennial cankers in declining vines. The current study has not only confirmed the presence of P. viticola from grapevine cankers in California but also has for the first time revealed the occurrence of Diaporthe ambigua, D. eres, and D. neotheicola in symptomatic grapevine wood in California by means of morphological studies and multi-gene sequence analysis. Pathogenicity trials conducted on mature cordons of Vitis vinifera 'Syrah' and 'Red Globe', as well as on lignified Syrah dormant canes, showed P. viticola isolates from California to be capable of causing perennial cankers. Lengths of vascular discoloration caused by P. viticola were similar to those caused by Eutypa lata and several Botryosphaeriaceae spp., which are well-known grapevine trunk disease pathogens. Additionally, a lack of spring growth was commonly observed in dormant canes inoculated with P. viticola spore suspensions in two pathogenicity trials. As part of this study, V. vinifera 'Cabernet Sauvignon' and 'Zinfandel' wood was shown to be more susceptible to infection by P. viticola than 'Barbera', 'Chardonnay', 'Merlot', and 'Thompson Seedless' wood. After more than 40 years overlooking P. viticola as a grapevine wood pathogen, this study provides strong evidence of the role of P. viticola as a canker-causing organism, and suggests its addition to the fungi involved in the grapevine trunk disease complex. Results from this study suggest D. ambigua and D. neotheicola to be saprophytes or weak pathogens on grapevine wood.
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Affiliation(s)
- J R Úrbez-Torres
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - F Peduto
- Department of Plant Pathology, University of California, Davis, CA 95616
| | - R J Smith
- University of California Cooperative Extension, Sonoma County, Santa Rosa, CA 95403
| | - W D Gubler
- Department of Plant Pathology, University of California Davis, Davis, CA 95616
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71
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Bienapfl JC, Balci Y. Phomopsis Blight: A New Disease of Pieris japonica Caused by Phomopsis amygdali in the United States. PLANT DISEASE 2013; 97:1403-1407. [PMID: 30708459 DOI: 10.1094/pdis-03-13-0226-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Pieris japonica, also known as Japanese andromeda, is an economically valuable broadleaf evergreen used in landscapes across the United States. From spring 2010 to 2012, P. japonica 'Mountain Fire' plants growing in Maryland nurseries were observed with a high incidence of stem canker, shoot dieback, and blight symptoms. Necrosis was evident on shoot tips and often advanced into lateral shoots, as well as to the crowns, leading to plant death. Phomopsis amygdali, known as a destructive pathogen of peach and almond, was consistently isolated from symptomatic plants. P. amygdali also caused similar symptoms on Mountain Fire test plants following inoculations. P. amygdali was consistently recovered and its identity was confirmed with both morphological and molecular tools, thus fulfilling Koch's postulates. In addition, nursery sampling in 2012 revealed that P. amygdali could also be isolated from asymptomatic plants. In all instances, infected plants were shipped from a West Coast nursery, indicating that this pathogen was inadvertently introduced to new locations. P. amygdali may be emerging as an important pathogen in nurseries because this is the first known association of this pathogen with an ornamental plant species.
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Affiliation(s)
- J C Bienapfl
- University of Maryland, Plant Science & Landscape Architecture, College Park 20742
| | - Y Balci
- University of Maryland, Plant Science & Landscape Architecture, College Park 20742
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72
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Elfar K, Torres R, Díaz GA, Latorre BA. Characterization of Diaporthe australafricana and Diaporthe spp. Associated with Stem Canker of Blueberry in Chile. PLANT DISEASE 2013; 97:1042-1050. [PMID: 30722477 DOI: 10.1094/pdis-11-12-1030-re] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Stem canker and dieback are important factors that limit the longevity and reduce the yield of blueberry (Vaccinium spp.) in Chile. In this study, species of Diaporthe associated with blueberry were isolated and identified. The internal transcribed spacer (ITS) regions of ribosomal DNA of 30 isolates and the translation elongation factor 1-α (EF1-α) of 14 isolates were sequenced, analyzed, and compared with their morphological and pathological characteristics. The molecular analysis of ITS sequences by alignment with those of ex-type strains deposited in GenBank and morphological characteristics allowed the identification of Diaporthe ambigua, D. australafricana, D. neotheicola, D. passiflorae, and Diaporthe sp. 1. However, morphology alone was insufficient to identify these species. The combined analysis of ITS and EF1-α gene sequences grouped the Chilean blueberry isolates in the same five groups obtained in the ITS analysis. Pathogenicity tests conducted with attached and detached blueberry shoots (<1 year old) and stems (1 to 2 years old) confirmed that isolates of these Diaporthe spp. were pathogenic. The symptoms were reproducible and consisted of necrotic reddish-brown cankers on blueberry shoots and stems. These isolates were capable of infecting blueberry fruit, causing a soft decay, suggesting that they were tissue nonspecific and were also pathogenic on shoots of apple, grapevine, and pear. D. australafricana was the most frequently isolated species and D. ambigua, D. australafricana, and D. passiflorae were highly virulent in shoots, stems, and fruit of blueberry. This study showed that at least four species of Diaporthe are primary pathogens, capable of causing stem canker symptoms on blueberry, and this is the first report of D. ambigua, D. neotheicola, and D. passiflorae attacking this host.
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Affiliation(s)
- Karina Elfar
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile
| | - René Torres
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile
| | - Gonzalo A Díaz
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile
| | - Bernardo A Latorre
- Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile
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73
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Endophytic Diaporthe from Southeast China are genetically diverse based on multi-locus phylogeny analyses. World J Microbiol Biotechnol 2013; 30:237-43. [DOI: 10.1007/s11274-013-1446-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 07/19/2013] [Indexed: 10/26/2022]
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74
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Baumgartner K, Fujiyoshi PT, Travadon R, Castlebury LA, Wilcox WF, Rolshausen PE. Characterization of Species of Diaporthe from Wood Cankers of Grape in Eastern North American Vineyards. PLANT DISEASE 2013; 97:912-920. [PMID: 30722541 DOI: 10.1094/pdis-04-12-0357-re] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In eastern North America, Phomopsis cane and leaf spot, caused by Phomopsis viticola, is a foliar disease of grape but, in the Mediterranean climate of western North America, P. viticola is primarily associated with wood cankers, along with other Diaporthe spp. To determine the identity of wood-infecting Diaporthe spp. in eastern North America, 65 isolates were cultured from 190 wood-canker samples from 23 vineyards with a history of Phomopsis cane and leaf spot. Identification of 29 representative isolates was based initially on morphology, followed by phylogenetic analyses of DNA sequences of the ribosomal DNA internal transcribed spacer region, elongation factor subunit 1-α, and actin in comparison with those of type specimens. Three species were identified: P. viticola, P. fukushii, and Diaporthe eres. Inoculations onto woody stems of potted Vitis labruscana 'Concord' and V. vinifera 'Chardonnay' showed that D. eres and P. fukushii were pathogenic (mean lesion lengths of 7.4 and 7.1 mm, respectively, compared with 3.5 mm for noninoculated controls) but significantly less so than wood-canker and leaf-spot isolates of P. viticola (13.5 mm). All three species infected pruning wounds of Concord and Chardonnay in the field. Our finding of pathogenic, wood-infecting Diaporthe spp. in all 23 vineyards suggests a frequent co-occurrence of the foliar symptoms of Phomopsis cane and leaf spot and wood cankers, although the latter are not always due to P. viticola.
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Affiliation(s)
- Kendra Baumgartner
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Davis, CA 95616
| | - Phillip T Fujiyoshi
- Crops Pathology and Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Davis, CA 95616
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis
| | - Lisa A Castlebury
- Systematic Mycology and Microbiology Laboratory, USDA-ARS, Beltsville, MD 20705
| | - Wayne F Wilcox
- Department of Plant Pathology and Plant Microbe Biology, Cornell University, Geneva, NY 14853
| | - Philippe E Rolshausen
- Department of Plant Pathology and Microbiology, University of California, Riverside 92521
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75
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76
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Tan YP, Edwards J, Grice KRE, Shivas R. Molecular phylogenetic analysis reveals six new species of Diaporthe from Australia. FUNGAL DIVERS 2013. [DOI: 10.1007/s13225-013-0242-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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77
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78
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Úrbez-Torres JR, Peduto F, Vossen PM, Krueger WH, Gubler WD. Olive Twig and Branch Dieback: Etiology, Incidence, and Distribution in California. PLANT DISEASE 2013; 97:231-244. [PMID: 30722318 DOI: 10.1094/pdis-04-12-0390-re] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Eighteen different fungal species were isolated from symptomatic wood of olive trees (Olea europaea) affected by twig and branch dieback in California and identified by means of morphological characters and multigene sequence analyses of the internal transcribed spacer (ITS) region (ITS1-5.8S-ITS2), a partial sequence of the β-tubulin gene, and part of the translation elongation factor 1-α gene (EF1-α). These species included Diaporthe viticola, Diatrype oregonensis, Diatrype stigma, Diplodia mutila, Dothiorella iberica, Lasiodiplodia theobromae, Phaeomoniella chlamydospora, Phomopsis sp. group 1, Phomopsis sp. group 2, and Schizophyllum commune, which are for the first time reported to occur in olive trees; Eutypa lata, Neofusicoccum luteum, Neofusicoccum vitifusiforme, and Phaeoacremonium aleophilum, which are for the first time reported to occur in olive trees in the United States; and Botryosphaeria dothidea, Diplodia seriata, Neofusicoccum mediterraneum, and Trametes versicolor, which have been previously reported in olive trees in California. Pathogenicity studies conducted in olive cultivars Manzanillo and Sevillano showed N. mediterraneum and Diplodia mutila to be the most virulent species and Diatrype stigma and D. oregonensis the least virulent when inoculated in olive branches. Intermediate virulence was shown for the rest of the taxa. This study demystifies the cause of olive twig and branch dieback and elucidates most of the fungal pathogens responsible for this disease in California.
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Affiliation(s)
- J R Úrbez-Torres
- Pacific Agri-Food Research Centre, Agriculture and Agri-Food Canada, 4200 Highway 97, Box 5000, Summerland, British Columbia V0H1Z0, Canada
| | - F Peduto
- Department of Plant Pathology, University of California Davis, Davis, CA 95616, USA
| | - P M Vossen
- University of California Cooperative Extension Sonoma County, Santa Rosa, CA 95403, USA
| | - W H Krueger
- University of California Cooperative Extension Glenn County, Orland, CA 95963, USA
| | - W D Gubler
- Department of Plant Pathology, University of California Davis, Davis, CA 95616, USA
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79
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The diversity, antimicrobial and anticancer activity of endophytic fungi associated with the medicinal plant Stryphnodendron adstringens (Mart.) Coville (Fabaceae) from the Brazilian savannah. Symbiosis 2012. [DOI: 10.1007/s13199-012-0182-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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80
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Udayanga D, Liua X, Mckenzie EH, Chukeatirote E, Hyde KD. Multi-locus Phylogeny Reveals Three new Species of Diaporthe from Thailand. CRYPTOGAMIE MYCOL 2012. [DOI: 10.7872/crym.v33.iss3.2012.295] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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81
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A multi-locus backbone tree for Pestalotiopsis, with a polyphasic characterization of 14 new species. FUNGAL DIVERS 2012. [DOI: 10.1007/s13225-012-0198-1] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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82
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Udayanga D, Liu X, Crous PW, McKenzie EHC, Chukeatirote E, Hyde KD. A multi-locus phylogenetic evaluation of Diaporthe (Phomopsis). FUNGAL DIVERS 2012. [DOI: 10.1007/s13225-012-0190-9] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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83
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Linnakoski R, Puhakka-tarvainen H, Pappinen A. Endophytic fungi isolated from Khaya anthotheca in Ghana. FUNGAL ECOL 2012. [DOI: 10.1016/j.funeco.2011.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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84
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Stem cankers on sunflower (Helianthus annuus) in Australia reveal a complex of pathogenic Diaporthe (Phomopsis) species. Persoonia - Molecular Phylogeny and Evolution of Fungi 2011; 27:80-9. [PMID: 22403478 PMCID: PMC3251322 DOI: 10.3767/003158511x617110] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2011] [Accepted: 11/11/2011] [Indexed: 12/03/2022]
Abstract
The identification of Diaporthe (anamorph Phomopsis) species associated with stem canker of sunflower (Helianthus annuus) in Australia was studied using morphology, DNA sequence analysis and pathology. Phylogenetic analysis revealed three clades that did not correspond with known taxa, and these are believed to represent novel species. Diaporthe gulyae sp. nov. is described for isolates that caused a severe stem canker, specifically pale brown to dark brown, irregularly shaped lesions centred at the stem nodes with pith deterioration and mid-stem lodging. This pathogenicity of D. gulyae was confirmed by satisfying Koch’s Postulates. These symptoms are almost identical to those of sunflower stem canker caused by D. helianthi that can cause yield reductions of up to 40 % in Europe and the USA, although it has not been found in Australia. We show that there has been broad misapplication of the name D. helianthi to many isolates of Diaporthe (Phomopsis) found causing, or associated with, stem cankers on sunflower. In GenBank, a number of isolates had been identified as D. helianthi, which were accommodated in several clades by molecular phylogenetic analysis. Two less damaging species, D. kochmanii sp. nov. and D. kongii sp. nov., are also described from cankers on sunflower in Australia.
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85
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Santos J, Vrandečić K, Ćosić J, Duvnjak T, Phillips A. Resolving the Diaporthe species occurring on soybean in Croatia. PERSOONIA 2011; 27:9-19. [PMID: 22403474 PMCID: PMC3251324 DOI: 10.3767/003158511x603719] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 08/01/2011] [Indexed: 11/25/2022]
Abstract
Diaporthe (anamorph = Phomopsis) species are plant pathogens and endophytes on a wide range of hosts including economically important crops. At least four Diaporthe taxa occur on soybean and they are responsible for serious diseases and significant yield losses. Although several studies have extensively described the culture and morphological characters of these pathogens, their taxonomy has not been fully resolved. Diaporthe and Phomopsis isolates were obtained from soybean and other plant hosts throughout Croatia. Phylogenetic relationships were determined through analyses of partial translation elongation factor 1-alpha (EF1-α) gene and ITS nrDNA sequence data. By combining morphological and molecular data, four species could be distinguished on soybeans in Croatia. Diaporthe phaseolorum is described in this study and its synonyms are discussed. Diaporthe phaseolorum var. caulivora is raised to species status and the name Diaporthe caulivora is introduced to accommodate it. A species previously known as Phomopsis sp. 9 from earlier studies on sunflower, grapevine, rooibos and hydrangea is reported for the first time on soybean, and is formally described as Diaporthe novem. The well-known soybean pathogen Phomopsis longicolla was also collected in the present study and was transferred to Diaporthe longicolla comb. nov. The presence of these species on herbaceous hosts raises once more the relevance of weeds as reservoirs for pathogens of economically important plants.
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Affiliation(s)
- J.M. Santos
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal; corresponding author e-mail:
- These authors contributed equally to this work
- Present address: Instituto de Medicina Molecular, Unidade de Parasitologia Molecular, Av. Prof. Egas Moniz, 1649-028 Lisboa, Portugal
| | - K. Vrandečić
- Department of Plant Protection, Faculty of Agriculture in Osijek, J.J. University of Osijek, Trg sv. Trojstva 3, 31000 Osijek, Croatia
- These authors contributed equally to this work
| | - J. Ćosić
- Department of Plant Protection, Faculty of Agriculture in Osijek, J.J. University of Osijek, Trg sv. Trojstva 3, 31000 Osijek, Croatia
| | - T. Duvnjak
- Agriculture Institute Osijek, Juzno predgradje 17, 31000 Osijek, Croatia
| | - A.J.L. Phillips
- Centro de Recursos Microbiológicos, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Quinta da Torre, 2829-516 Caparica, Portugal; corresponding author e-mail:
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86
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Chemical and molecular characterization of Phomopsis and Cytospora-like endophytes from different host plants in Brazil. Fungal Biol 2011; 116:249-60. [PMID: 22289771 DOI: 10.1016/j.funbio.2011.11.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Revised: 11/12/2011] [Accepted: 11/16/2011] [Indexed: 11/20/2022]
Abstract
Phomopsis and related taxa comprise important endophytic and plant pathogenic species, and are known for the production of a diverse array of secondary metabolites. Species concepts within this group based on morphological characters and assumed host specificity do not reflect phylogenetic affinities. Additional phenotypic characters, such as profiles of secondary metabolites, are needed for practical species recognition. We investigated 36 strains of Phomopsis spp. and Cytospora-like fungi, obtained as endophytes of different host plants in Brazil, using metabolite profiling based on HPLC-UV/liquid chromatography -mass spectrometry (LC-MS) combined with cluster analysis of the results. Strains were also subjected to phylogenetic analyses based on internal transcribed spacer (ITS) rDNA. Six chemotypes were identified. Chemotypes 1-5 contained Phomopsis strains, while Cytospora-like strains formed the chemotype 6. Strains of chemotype 1 typically produced alternariols, altenusin, altenuene, cytosporones, and dothiorelones. Alternariol and seven unknown compounds were consistently produced by strains of chemotype 2. Members of chemotypes 3-5 produced poor metabolite profiles containing few chemical markers. Cytospora-like endophytes (chemotype 6) produced a characteristic set of metabolites including cytosporones and dothiorelones. Bayesian and Maximum Parsimony (MP) trees classified strains of each chemotype into single phylogenetic lineages or closely related groups. Strains of chemotypes 1 and 2 formed a monophyletic group along with Diaporthe neotheicola. The remaining Phomopsis strains formed monophyletic (chemotype 4) or polyphyletic (chemotypes 3 and 5) lineages inside a large and well supported clade. Cytospora-like strains formed a monophyletic lineage located at an intermediary position between Diaporthe/Phomopsis and Valsa/Cytospora clades. The combined results show that the production of secondary metabolites by Phomopsis and related Diaporthales may be species-specific, giving support to the use of metabolite profiling and chemical classification for phenotypic recognition and delimitation of species.
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The genus Phomopsis: biology, applications, species concepts and names of common phytopathogens. FUNGAL DIVERS 2011. [DOI: 10.1007/s13225-011-0126-9] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Abstract
We report a case of scleral keratitis caused by Phomopsis phoenicicola. Pterygium surgery was a predisposing factor, and the patient was treated with natamycin and fluconazole eye drops and oral fluconazole. The fungus was identified by sequencing of the internal transcribed spacer (ITS) region of the fungal ribosomal DNA (rDNA) locus and confirmed on the basis of its typical pycnidia and conidia.
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Lindner DL, Banik MT. Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus. Mycologia 2011; 103:731-40. [PMID: 21289107 DOI: 10.3852/10-331] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Regions of rDNA are commonly used to infer phylogenetic relationships among fungal species and as DNA barcodes for identification. These regions occur in large tandem arrays, and concerted evolution is believed to reduce intragenomic variation among copies within these arrays, although some variation still might exist. Phylogenetic studies typically use consensus sequencing, which effectively conceals most intragenomic variation, but cloned sequences containing intragenomic variation are becoming prevalent in DNA databases. To understand effects of using cloned rDNA sequences in phylogenetic analyses we amplified and cloned the ITS region from pure cultures of six Laetiporus species and one Wolfiporia species (Basidiomycota, Polyporales). An average of 66 clones were selected randomly and sequenced from 21 cultures, producing a total of 1399 interpretable sequences. Significant variation (≥ 5% variation in sequence similarity) was observed among ITS copies within six cultures from three species clades (L. cincinnatus, L. sp. clade J, and Wolfiporia dilatohypha) and phylogenetic analyses with the cloned sequences produced different trees relative to analyses with consensus sequences. Cloned sequences from L. cincinnatus fell into more than one species clade and numerous cloned L. cincinnatus sequences fell into entirely new clades, which if analyzed on their own most likely would be recognized as "undescribed" or "novel" taxa. The use of a 95% cut off for defining operational taxonomic units (OTUs) produced seven Laetiporus OTUs with consensus ITS sequences and 20 OTUs with cloned ITS sequences. The use of cloned rDNA sequences might be problematic in fungal phylogenetic analyses, as well as in fungal bar-coding initiatives and efforts to detect fungal pathogens in environmental samples.
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Affiliation(s)
- Daniel L Lindner
- US Forest Service, Northern Research Station, Center for Forest Mycology Research, One Gifford Pinchot Drive, Madison, Wisconsin 53726, USA.
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Diogo ELF, Santos JM, Phillips AJL. Phylogeny, morphology and pathogenicity of Diaporthe and Phomopsis species on almond in Portugal. FUNGAL DIVERS 2010. [DOI: 10.1007/s13225-010-0057-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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