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Farooq M, Nabi A, Khursheed S, Padder BA, Sofi TA, Masoodi KZ, Hamid S, Shah MD. Whole genome sequencing of Wilsonomyces carpophilus, an incitant of shot hole disease in stone fruits: insights into secreted proteins of a necrotrophic fungal repository. Mol Biol Rep 2023; 50:4061-4071. [PMID: 36877348 DOI: 10.1007/s11033-023-08243-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/03/2023] [Indexed: 03/07/2023]
Abstract
BACKGROUND Shot hole is one of the important fungal diseases in stone fruits viz., peach, plum, apricot and cherry caused by Wilsonomyces carpophilus and almond among nut crops. Fungicides significantly decrease the disease. Pathogenicity studies proved a wide host range of the pathogen infecting all stone fruits and almond among the nut crops, however, the mechanism underlying host-pathogen interaction is still unknown. Molecular detection of the pathogen using polymerase chain reaction (PCR) based simple sequence repeat (SSR) markers is also unknown due to the unavailability of the pathogen genome. METHODS AND RESULTS We examined the morphology, pathology and genomics of the Wilsonomyces carpophilus. Whole genome sequencing of the W. carpophilus was carried out by Illumina HiSeq and PacBio high throughput sequencing plate-forms through hybrid assembly. Constant selection pressure alters the molecular mechanism of the pathogen causing disease. The studies revealed that the necrotrophs are more lethal with a complex pathogenicity mechanism and little-understood effector repositories. The different isolates of necrotrophic fungus W. carpophilus causing shot hole in stone fruits namely peach, plum, apricot and cherry, and almonds among the nut crops showed a significant variation in their morphology, however, the probability value (p = 0.29) suggests in-significant difference in the pathogenicity. Here, we reported draft genome of W. carpophilus of size 29.9 Mb (Accession number: PRJNA791904). A total of 10,901 protein-coding genes were predicted, including heterokaryon incompatibility genes, cytochrome-p450 genes, kinases, sugar transporters among others. We found 2851 simple sequence repeats (SSRs), tRNAs, rRNAs and pseudogenes in the genome. The most prominent proteins showing necrotrophic lifestyle of the pathogen were hydrolases, polysaccharide-degrading enzymes, esterolytic, lipolytic, and proteolytic enzymes accounted for 225 released proteins. Among the 223 fungal species, top-hit species distribution revealed the majority of hits against the Pyrenochaeta species followed by Ascochyta rabiei and Alternaria alternata. CONCLUSION Draft genome of W. carpophilus is 29.9 Mb based on Illumina HiSeq and PacBio hybrid assembly. The necrotrophs are more lethal with a complex pathogenicity mechanism. A significant variation in morphology was observed in different pathogen isolates. A total of 10,901 protein-coding genes were predicted in the pathogen genome including heterokaryon incompatibility, cytochrome-p450 genes, kinases and sugar transporters. We found 2851 SSRs, tRNAs, rRNAs and pseudogenes, and prominent proteins showing necrotrophic lifestyle such as hydrolases, polysaccharide-degrading enzymes, esterolytic, lipolytic and proteolytic enzymes. The top-hit species distribution were against the Pyrenochaeta spp. followed by Ascochyta rabiei.
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Affiliation(s)
- Mahiya Farooq
- Plant Virology and Molecular Pathology Laboratory, Division of Plant Pathology, Faculty of Horticulture (FOH), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, 190025, Jammu Kashmir, India
| | - Asha Nabi
- Plant Virology and Molecular Pathology Laboratory, Division of Plant Pathology, Faculty of Horticulture (FOH), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, 190025, Jammu Kashmir, India
| | - Sehla Khursheed
- Plant Virology and Molecular Pathology Laboratory, Division of Plant Pathology, Faculty of Horticulture (FOH), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, 190025, Jammu Kashmir, India
| | - Bilal A Padder
- Plant Virology and Molecular Pathology Laboratory, Division of Plant Pathology, Faculty of Horticulture (FOH), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, 190025, Jammu Kashmir, India
| | - T A Sofi
- Plant Virology and Molecular Pathology Laboratory, Division of Plant Pathology, Faculty of Horticulture (FOH), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, 190025, Jammu Kashmir, India
| | - Khalid Z Masoodi
- Division of Biotechnology, FOH, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, 190025, Jammu Kashmir, India
| | - Sumaira Hamid
- Plant Virology and Molecular Pathology Laboratory, Division of Plant Pathology, Faculty of Horticulture (FOH), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, 190025, Jammu Kashmir, India
| | - Mehraj D Shah
- Plant Virology and Molecular Pathology Laboratory, Division of Plant Pathology, Faculty of Horticulture (FOH), Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, 190025, Jammu Kashmir, India.
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Nissan S, Boelens J, Lagrou K, Roels D. Pyrenocheata unguis-hominis: A new cause of fungal keratitis in a contact lens wearer. Am J Ophthalmol Case Rep 2022; 28:101731. [PMCID: PMC9614820 DOI: 10.1016/j.ajoc.2022.101731] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/16/2022] Open
Abstract
Purpose Observations Conclusions
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Affiliation(s)
- Sima Nissan
- Department of Ophthalmology, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium,Corresponding author.
| | - Jerina Boelens
- Department of Clinical Biology, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
| | - Katrien Lagrou
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Herestraat 49, 3000, Leuven, Belgium,National Reference Centre for Mycosis, Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Dimitri Roels
- Department of Ophthalmology, Ghent University Hospital, Corneel Heymanslaan 10, 9000, Ghent, Belgium
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Pyrenochaeta fraxinina as colonizer of ash and sycamore petioles, its morphology, ecology, and phylogenetic connections. Mycol Prog 2022. [DOI: 10.1007/s11557-022-01827-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
AbstractPyrenochaeta fraxinina was first described in 1913 from the state of New York (USA) on petioles of Fraxinus sp. Since then, the species has not been reported from North America and reports from the other regions of the world are very sparse. The results of this study on P. fraxinina are based on the material collected in various regions of Poland from 2012 to 2019. The material comprised 2700 previous year’s leaf petioles of Fraxinus excelsior and 1970 petioles or leaf residues of eight other deciduous tree species. As a result, the occurrence of pycnidial conidiomata of P. fraxinina was confirmed on F. excelsior (3.4% of petioles), F. mandshurica (1.5%), F. pennsylvanica (3.2%), and Acer pseudoplatanus (2.0%). The morphology of the microstructures was described based on the fresh material and compared with the holotype of P. fraxinina. The optimal temperature for the growth of the fungus in vitro was estimated as 20 °C. The analyses based on ITS-LSU rDNA sequences and a protein coding sequence of TUB2 and RPB2 genes showed that P. fraxinina isolates form a well-supported clade in the phylogenetic trees. The species proved to be closely related to Nematostoma parasiticum (asexual morph Pyrenochaeta parasitica), a species occurring on Abies alba in connection with needle browning disease. Interactions between P. fraxinina and the ash dieback pathogen, Hymenoscyphus fraxineus, were analyzed in vivo on ash petioles and in vitro in dual cultures. Among 93 petioles of F. excelsior, for which P. fraxinina conidiomata were detected, 26 were also colonized by H. fraxineus. Mostly, these two fungi occurred separately, colonizing different sections of a petiole. For all dual cultures, both fungi, P. fraxinina and H. fraxineus, showed growth inhibition toward the counterpartner. The role of P. fraxinina as a saprotrophic competitor toward H. fraxineus in ash petioles is discussed.
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New Coelomycetous Fungi from Freshwater in Spain. JOURNAL OF FUNGI (BASEL, SWITZERLAND) 2021; 7:jof7050368. [PMID: 34066856 PMCID: PMC8151841 DOI: 10.3390/jof7050368] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/28/2021] [Accepted: 05/06/2021] [Indexed: 11/20/2022]
Abstract
Coelomycetous fungi are ubiquitous in soil, sewage, and sea- and freshwater environments. However, freshwater coelomycetous fungi have been very rarely reported in the literature. Knowledge of coelomycetous fungi in freshwater habitats in Spain is poor. The incubation of plant debris, from freshwater in various places in Spain into wet chambers, allowed us to detect and isolate in pure culture several pycnidia-producing fungi. Fungal strains were phenotypically characterized, and a phylogenetic study was carried out based on the analysis of concatenated nucleotide sequences of the D1–D2 domains of the 28S nrRNA gene (LSU), the internal transcribed spacer region (ITS) of the nrDNA, and fragments of the RNA polymerase II subunit 2 (rpb2) and beta tubulin (tub2) genes. As a result of these, we report the finding of two novel species of Neocucurbitaria, three of Neopyrenochaeta, and one of Pyrenochaetopsis. Based on the phylogenetic study, we also transferred Neocucurbitaria prunicola to the genus Allocucurbitaria. This work makes an important contribution to the knowledge of the mycobiota of plant debris in freshwater habitats.
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Li WJ, McKenzie EHC, Liu JK(J, Bhat DJ, Dai DQ, Camporesi E, Tian Q, Maharachchikumbura SSN, Luo ZL, Shang QJ, Zhang JF, Tangthirasunun N, Karunarathna SC, Xu JC, Hyde KD. Taxonomy and phylogeny of hyaline-spored coelomycetes. FUNGAL DIVERS 2020. [DOI: 10.1007/s13225-020-00440-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Gong Y, Chen Z, Ma Y, Jiang W, Hu Y, Shi Y. Cutaneous phaeohyphomycosis caused by Pyrenochaeta unguis-hominis in a diabetic patient: A case report. Australas J Dermatol 2019; 61:e221-e222. [PMID: 31724160 DOI: 10.1111/ajd.13177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Accepted: 09/01/2019] [Indexed: 11/29/2022]
Abstract
Phaeohyphomycosis, caused by opportunistic rare fungi, has increasingly been reported in diabetic and immunosuppressed patients. Pyrenochaeta unguis-hominis (P. unguis-hominis), a member of the dematiaceae group, has been identified to cause human nail infection. We report a rare case of cutaneous phaeohyphomycosis in a diabetic female caused by P. unguis-hominis.
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Affiliation(s)
- Yu Gong
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zeyu Chen
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yue'e Ma
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Weiwei Jiang
- Department of Dermatology, Shanghai Key Laboratory of Molecular Medical Mycology, Institute of Medical Mycology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Yifan Hu
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuling Shi
- Department of Dermatology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China
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Valenzuela-Lopez N, Cano-Lira JF, Stchigel AM, Guarro J. DNA sequencing to clarify the taxonomical conundrum of the clinical coelomycetes. Mycoses 2018; 61:708-717. [DOI: 10.1111/myc.12785] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Nicomedes Valenzuela-Lopez
- Mycology Unit; Medical School and IISPV; University Rovira i Virgili; Reus Spain
- Microbiology Unit; Medical Technology Department; Faculty of Health Science; University of Antofagasta; Antofagasta Chile
| | - José F. Cano-Lira
- Mycology Unit; Medical School and IISPV; University Rovira i Virgili; Reus Spain
| | - Alberto M. Stchigel
- Mycology Unit; Medical School and IISPV; University Rovira i Virgili; Reus Spain
| | - Josep Guarro
- Mycology Unit; Medical School and IISPV; University Rovira i Virgili; Reus Spain
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Sabri NSA, Zakaria Z, Mohamad SE, Jaafar AB, Hara H. Importance of Soil Temperature for the Growth of Temperate Crops under a Tropical Climate and Functional Role of Soil Microbial Diversity. Microbes Environ 2018; 33:144-150. [PMID: 29709895 PMCID: PMC6031386 DOI: 10.1264/jsme2.me17181] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/16/2018] [Indexed: 11/17/2022] Open
Abstract
A soil cooling system that prepares soil for temperate soil temperatures for the growth of temperate crops under a tropical climate is described herein. Temperate agriculture has been threatened by the negative impact of temperature increases caused by climate change. Soil temperature closely correlates with the growth of temperate crops, and affects plant processes and soil microbial diversity. The present study focuses on the effects of soil temperatures on lettuce growth and soil microbial diversity that maintains the growth of lettuce at low soil temperatures. A model temperate crop, loose leaf lettuce, was grown on eutrophic soil under soil cooling and a number of parameters, such as fresh weight, height, the number of leaves, and root length, were evaluated upon harvest. Under soil cooling, significant differences were observed in the average fresh weight (P<0.05) and positive development of the roots, shoots, and leaves of lettuce. Janthinobacterium (8.142%), Rhodoplanes (1.991%), Arthrospira (1.138%), Flavobacterium (0.857%), Sphingomonas (0.790%), Mycoplana (0.726%), and Pseudomonas (0.688%) were the dominant bacterial genera present in cooled soil. Key soil fungal communities, including Pseudaleuria (18.307%), Phoma (9.968%), Eocronartium (3.527%), Trichosporon (1.791%), and Pyrenochaeta (0.171%), were also recovered from cooled soil. The present results demonstrate that the growth of temperate crops is dependent on soil temperature, which subsequently affects the abundance and diversity of soil microbial communities that maintain the growth of temperate crops at low soil temperatures.
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Affiliation(s)
- Nurul Syazwani Ahmad Sabri
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia (UTM)Kuala LumpurMalaysia
| | - Zuriati Zakaria
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia (UTM)Kuala LumpurMalaysia
| | - Shaza Eva Mohamad
- Department of Environmental Engineering and Green Technology, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia (UTM)Kuala LumpurMalaysia
| | - A Bakar Jaafar
- Ocean Thermal Energy Centre, Universiti Teknologi Malaysia (UTM)Kuala LumpurMalaysia
| | - Hirofumi Hara
- Department of Chemical Process Engineering, Malaysia-Japan International Institute of Technology, Universiti Teknologi Malaysia (UTM)Kuala LumpurMalaysia
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