Using DNA Barcoding in Fungal Taxonomy

Abstract

Totally, 1.5 million fungal species estimated, of which less than 10 percent have been described to date. Recent advances in molecular biology as well as gene sequencing technologies facilitate the discovery and identification of new species in various groups of living organisms, especially fungi. Morphological methods do not have efficiency for the identification of fungal species, so, using new techniques based on DNA data has been considered in the rapid and accurate fungal species identification. DNA Barcoding is a new technique with several years’ backgrounds for detecting fungi and fungal like organisms. The Internal Transcribed Spacer in ribosomal RNA gene (ITS-rDNA) has been considered as a suitable barcode sequence. The efficacy of this region’s sequence data in most fungal groups has led to its use as a standard barcode by different mycologists. However, the ITS-rDNA region appears to be used as the primary barcode sequence for fungi of the genus or species group. The accurate species-specific identification is performed depending on the fungal group based on secondary barcodes. Due to the pleomorphic nature of fungi, the use of DNA barcoding is of importance. To date, hundreds of thousands of reference barcode sequences have been created for thousands of species of living organisms through DNA barcoding projects. The subsequent efforts of scientists are managing and automation of DNA barcoding in order to speed up the identification process.

Keywords

• DNA Barcoding
• Fungi
• Molecular Taxonomy
• Species Concept

Fungus Taksonomisinde DNA Barkodlamasının Kullanılması

Öz

Günümüzde toplam 1.5 milyon olduğu tahmin edilen fungus türünün %10’undan daha azı tanımlanmıştır. Moleküler biyolojideki son gelişmeler ve gen sıralama teknolojileri, çeşitli canlı organizma gruplarında, özellikle funguslarda yeni türlerin keşfedilmesini ve tanımlanmasını kolaylaştırmaktadır. Fungus türlerinin tanımlanmasında morfolojik yöntemler yeterli değildir, bu nedenle, hızlı ve doğru tanımlamada DNA verilerine dayalı yeni tekniklerin kullanılması ön plana çıkarılmıştır. DNA Barkodlama, fungus ve fungus benzeri mikroorganizmaları tespit etmek için kullanılan yıllık geçmişi olan yeni bir tekniktir. Ribozomal RNA genindeki ITS-rDNA uygun bir barkod dizisi olarak kabul edilmektedir. Bu bölge sekans verilerinin etkinliği, farklı mikologlar tarafından birçok fungusta standart bir barkod olarak kullanılmasına yol açmıştır. Bununla birlikte, ITS-rDNA bölgesinin fungus cins ve türlerinin tanılanmasında birincil barkod dizisi olarak kullanıldığı görülmekte, fungus gruplarındaki türe özgü kesin tanılama ise ikincil barkodlara dayalı olarak yapılmaktadır. Fungusların pleomorfik doğası nedeniyle, DNA barkodlamasının kullanılması çok önemlidir. Bugüne kadar, DNA barkodlama projeleri ile binlerce canlı organizma türü için yüz binlerce referans barkod dizisi oluşturulmuştur. Bilim adamlarının bundan sonraki çalışmaları tanımlama sürecini hızlandırmak için DNA barkodunun yönetimi ve otomasyonu yönündedir.

Anahtar Kelimeler

• Fungi
• Molecular Taxonomy
• Species Concept
• DNA Barcoding

References

1. Andersen, M. R., Salazaar, M. P., Schaap, P. J., van de Vondervoort, P. J. I., & Culley, P. (2011). Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme producing CBS 513.88. Genome Research, 21, 885–897.
2. Arver, B. A., Ward, T. J., Gale, L. R., Broz, K. L., Kistler, H. C., & Aoki, T. (2011). Novel Fusarium head blight pathogens from Nepal and Louisiana revealed by multi locus genealogical concordance. Fungal Genetics and Biology, 48, 1077–1152.
3. Badali, H., Bonifaz, A., Barrón-Tapia, T., Vázquez-González, D., Estrada-Aguilar, L., & Oliveira, N. M. (2010). Rhinocladiella aquaspersa proven agent of verrucous skin infection and a novel type of chromoblastomycosis. Medical Mycology, 48, 696–703.
4. Badali, H., Carvalho, V. O., Vicente, V., Attili-Angelis, D., Kwiatkowski, I. B., & Gerrits Van Den Ende, A. H. (2009). Cladophialophora saturnica sp. nov. a new opportunistic species of chaetothyriales revealed using molecular data. Medical Mycology, 47, 51–62.
5. Badali, H., Gueidan, C., Najafzadeh, M. J., Bonifaz, A., Gerrits van den Ende, A. H. G., & de Hoog, G. S. (2008). Biodiversity of the genus Cladophialophora. Studies in Mycology, 61, 175–191.
6. Badali, H., Prenafeta-Boldu, F. X., Guarro, J., Klaassen, C. H., Meis, J. F., & de Hoog, G. S. (2011). Cladophialophora psammophila, a novel species of Chaetothyriales with a potential use in the bioremediation of volatile aromatic hydrocarbons. Fungal Biology, 115, 1019–29.
7. Begerow, D., Nilsson, H., Unterseher, M., & Maier, W. (2010). Current state and perspectives of fungal DNA barcoding and rapid identification procedures. Applied Microbiology and Biotechnology, 87, 99–108.
8. Chase, M. W., Salamin, N., Wilkinson, M., Dunwell, J. M., Kesanakurthi, R. P., & Haidar, N. (2005). Land plants and DNA barcodes: short-term and long-term goals. Proceedings of the Royal Society of London, Series B, 360, 1889–1895.

9. Costa, F. O., & Carvalho, G. R. (2010). New insights into molecular evolution: prospects from the Barcode of Life Initiative (BOLI). Theory on Biosciences, 129, 149–157.
10. Crous, P. W., Verkley, G. J. M., Groenewald, J. Z., & Samson, R. A. (2009). Fungal Biodiversity. CBS Laboratory Manual Series 1. Centraal bureau voor Schimmel cultures: Utrecht. p. 269.
11. Desjardins, C., Champion, M., Holder, J., Muszewsha, A., Goldberg, J., & Baptista, A. J. (2011). Comparative genomic analysis of human fungal pathogens causing paracoccidioidomycosis. Plos Genetics, 7, e1002345.
12. Druzhinina, I. S., Kopchinskiy, A. G., Komoń, M., Bissett, J., Szakacs, G., & Kubicek, C. P. (2005). An oligonucleotide barcode for species identification in Trichoderma and Hypocrea. Fungal Genetics and Biology, 42, 813–828.
13. Elahi, E., & Ronaghi, M. (2004). Pyrosequencing: a tool for DNA sequencing analysis. Methods in Molecular Biology, 255, 211–219. Evans, K. M., Wortley, A. H., & Mann, D. G. (2007). An assessment of potential diatom ‘‘barcode’’ genes (cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in Sellaphora (Bacillariophyta). Protist, 158, 349–364.
14. Frézal, L., & Leblois, R. (2008). Four years of DNA barcoding: Current advances and prospects. Infection Genetics and Evolution, 8, 727 –736.
15. Gadd, G. M. (2008). Geomycology: biogeochemical transformations of rocks, minerals, metals and radionuclides by fungi, bio-weathering and bio-remediation. Mycological Research, 111, 3–49.
16. Hajibabaei, M., Janzen, D. H., Burns, J. M., Hallwachs, W., & Hebert, P. D. N. (2006). DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences USA, 103, 968–971.
17. Hawksworth, D. L. (2004). Fungal diversity and its implications for genetic resource collections. Studies in Mycology, 50, 9–18.
18. Hawksworth, D. L. (2011). A new dawn for the naming of fungi: impacts of decisions made in Melbourne in July 2011 on the future publication and regulation of fungal names. Myco Keys, 1, 7–20.
19. Hebert, P.D. N., Cywinska, A., Ball, S.L., & deWaard, J. R. (2003). Biological identifications through DNA barcodes. Proceedings of the Royal Society of London, Series B, 270, 313–321.
20. Kang, S., Mansfield, M. A., Park, B., Geiser, D. M., Ivors, K. L. (2010). The promise and pitfalls of sequence-based identification of plant-pathogenic fungi and oomycetes. Phytopathology, 100, 732–737.
21. Mostert, L., Groenewald, J. Z., Summerbell, R. C., Gams, W., & Crous, P. W. (2006). Taxonomy and pathology of Togninia (diaporthales) and its Phaeoacremonium anamorphs. Studies in Mycology, 54, 1–115.
22. Nancy, L. W. Binnicker, M. J. (2009). Fungal molecular diagnostics. Clinics in Chest Medicine, 30, 391–408.
23. Nilsson, R. H., Kristiansson, E., Ryberg, M., & Hallenberg, N. (2008). Intraspecific ITS variability in the kingdom fungi as expressed in the international sequence databases and its implications for molecular species identification. Evolution and Bioinformatics, 4, 193–201.
24. Rooney, A. P., & Ward, T. J. (2005). Evolution of a large ribosomal RNA multigene family in filamentous fungi: Birth and death of a concerted evolution paradigm. Proceedings of the National Academy of Sciences USA, 102, 14: 5084–5089.
25. Schoch, C. L., Seifert, K. A., Huhndorf, S., Robert, V., Spouge, J. L., & Levesque, C. A. (2012). Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences USA, 109, 6241–6246.
26. Shenoy, B. D., Jeewon, R., & Hyde, K. D. (2007). Impact of DNA sequence-data on the taxonomy of anamorphic fungi. Fungal Diversity, 26, 1–54.
27. Smith, M. A., Fisher, B. L., & Hebert, P. D. N. (2005). DNA barcoding for effective biodiversity assessment of a hyper diverse arthropod group: the ants of Madagascar. Proceedings of the Royal Society of London, Series B, 360, 1825–1834.
28. Taylor, J. W. (2006). Evolution of Human-Pathogenic Fungi: Phylogenies and Species. In J. Heitman, S. G. Filler, J. E. Edwards, & A. P. Mitchell (Eds.), Molecular Principles of Fungal Pathogenesis (pp. 113–132). Washington DC, ASM Press.
29. Taylor, J. W. (2011). One fungus one name: DNA and fungal nomenclature twenty years after PCR. IMA Fungus, 2, 113–120.
30. Taylor, J. W., Jacobson, D. J., Kroken, S., Kasuga, T., Geiser, D. M., & Hibbett, D. S. (2000). Phylogenetic species recognition and species concepts in fungi. Fungal Genetics and Biology, 31, 21–32.
31. Termorshuizen, A. J., & Arnolds, E. J. M. (1997). On the nomenclature of the European species of the Armillaria mellea group. Mycotaxon, 30, 101–106.
32. Xu, J. R., Peng, Y. L., Dickman, M. B., & Sharon, A. (2006). The dawn of fungal pathogen genomics. Annual Review of Phytopathology, 44, 337–66.