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Development of mitochondrial SSU rDNA-based oligonucleotide probes for specific detection of common airborne fungi
Authors:Zeng Qing-Yin  Wang Xiao-Ru  Blomquist Göran
Affiliation:1. National Institute for Working Life, SE-90713 Umeå, Sweden;2. Department of Molecular Biology, Umeå University, SE-90187, Umeå, Sweden;1. Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT, Utrecht, The Netherlands;2. Botanische Staatssammlung München, Menzinger Straße 67, D-80638, München, Germany;3. EMSL Analytical, Inc., 200 Route 130 North, Cinnaminson, NJ, 08077, United States;4. DTU Bioengineering, Technical University of Denmark, Søltofts Plads Building 221, DK-2800 Kgs., Lyngby, Denmark;5. Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa;6. Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands;1. Department of Animal Production, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia;2. Department of Theriogenology, Faculty of Veterinary Medicine, Zagazig University, Zagazig 44511, Egypt;3. Poultry and Fish Diseases Department, Faculty of Veterinary Medicine, Damanhour University, El Beheira 22511, Egypt;4. Department of Agricultural Microbiology, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt;5. Harry Butler Institute, Murdoch University, Murdoch, 6150, Western Australia, Australia;7. Department of Poultry, Faculty of Agriculture, Zagazig University, Zagazig 44511, Egypt;1. Westerdijk Fungal Biodiversity Institute, P.O. Box 85167, 3508 AD Utrecht, The Netherlands;2. Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa;3. State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China;4. Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa;5. Botanische Staatssammlung München, Menzinger Straße 67, D-80638 München, Germany;6. Martin-Luther-Universität, Institut für Biologie, Bereich Geobotanik und Botanischer Garten, Herbarium, Neuwerk 21, D-06099 Halle (Saale), Germany;7. A.M.B. Gruppo Micologico Forlivese “Antonio Cicognani”, Via Roma 18, Forlì, Italy;8. A.M.B. Circolo Micologico “Giovanni Carini”, C.P. 314, Brescia, Italy;9. Società per gli Studi Naturalistici della Romagna, C.P. 144, Bagnacavallo (RA), Italy;10. Senckenberg Museum of Natural History Görlitz, PF 300 154, 02806 Görlitz, Germany;11. Center of Excellence in Fungal Research, School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand;12. Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, PR China;13. AgriBio Centre for AgriBiosciences, Department of Economic Development, Jobs, Transport and Resources, 5 Ring Road, LaTrobe University, Bundoora, Victoria 3083, Australia;14. School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand;15. Microbe Interaction and Ecology Laboratory, Biodiversity and Biotechnological Resource Research Unit (BBR), BIOTEC, NSTDA 113 Thailand Science Park Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand;16. Department of Plant and Soil Science, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa;17. Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;18. Faculty of Natural and Agricultural Sciences, Department of Plant Sciences, University of the Free State, P.O. Box 339, Bloemfontein 9300, South Africa;19. Institute of Microbiology, P.O. Box 61, Beijing Forestry University, Beijing 100083, PR China;20. Centre for Crop Health, Institute for Agriculture and the Environment, University of Southern Queensland, Toowoomba 4350, Queensland, Australia;21. Department of Agriculture & Fisheries, Biosecurity Queensland, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia;22. Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CT Utrecht, The Netherlands;23. ARC – Plant Protection Research Institute, Biosystematics Division – Mycology, P. Bag X134, Queenswood 0121, South Africa;24. ARC – Plant Protection Research Institute, P. Bag X5017, Stellenbosch 7599, South Africa;1. CBS-KNAW Fungal Biodiversity Centre, Uppsalalaan 8, NL-3584 CT Utrecht, The Netherlands;2. Biodiversity (Mycology), Agriculture and Agri-Food Canada, Ottawa, ON K1A0C6, Canada;3. Department of Botany, University of Hawaii at Manoa, 3190 Maile Way, Honolulu, HI 96822, USA
Abstract:
In this study we sequenced partial mitochondrial small subunit rDNA from 32 fungal strains representing 31 species from 16 genera. Most of these species are common airborne fungi and pathogens that may cause various public health concerns. Sequence alignment showed several conserved and highly variable regions. The variable regions were deployed to design oligonucleotide probes for each fungal species. The specificity of the designed probes was first examined through homology search against GenBank database then further verified through hybridization experiments to 38 fungal strains. A total of 23 probes were verified as specific to 15 fungal species commonly detected in living and working environments. These new probes will have potential applications in clinical diagnosis and public health-related environmental monitoring.
Keywords:Fungi   Mitochondrial SSU rDNA   Probe   Specific detection
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