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FUNGAL SİSTEMATİKTEKİ MOLEKÜLER GELİŞMELER

MOLECULAR DEVELOPMENTS IN FUNGAL SYSTEMATICS

Journal Name:

  • Anadolu Tarım Bilimleri Dergisi

Publication Year:

  • 2008

Key Words:

Keywords (Original Language):

Author NameUniversity of AuthorFaculty of Author
Abstract (2. Language): 
Amazing developments in molecular biology have affected whole fields of biology positively in recent years. These developments have also showed their effects on fungal systematic and provided fast and reliable identifications. Before molecular studies, morphologic and biochemical techniques have been extensively used in researchs. But it was hard to obtain results, especially with the morphological examinations, and lost of time, experience have been required in these studies. The results of these studies have also been subjective, some times showing inconsistencies among the researchers. For these reasons, molecular techniques have started to used commonly with conventional techniques in fungal systematics. Some of these are, they are used in common recently, those based on PCR techniques and especially DNA sequences studies. In fungal systematics, it is both more reliable and less time consuming to work on DNA; the first molecule the changes have occured. DNA molecule has been preferred for taxonomic studies because there are species-specific (evolutionary chronometer) regions which reflects the evolution of the organisms. The most common regions used in fungal systematics are 18S rDNA and internal transcribed spacer (ITS) of rDNA. ITS being the noncoding region evolves faster and is useful for comparing the strains of a species or species in a genus. These developments in molecular biology have provided rapid methods for identification of plant pathogenic fungi causing quality and yield reduction of economically important crops.
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Abstract (Original Language): 
Son yıllarda moleküler biyolojide yaşanan baş döndürücü gelişmeler biyolojinin bütün alanlarını olumlu yönde etkilemiştir. Bu gelişmeler fungal sistematikte de etkisini göstererek hızlı ve güvenilir teşhislere olanak sağlamıştır. Moleküler çalışmalar yaygınlaşmadan önce morfolojiye ve biyokimyasal tekniklere dayalı araştırmalar yoğun olarak yapılmaktaydı. Ancak bu çalışmalarda özellikle morfolojik olarak yapılan gözlemlerle sonuçlara ulaşmak hem fazlasıyla deneyim hem de oldukça fazla zaman gerektirmekte, ayrıca sonuçlar zaman zaman araştırıcılara göre farlılıklar gösterebilmekteydi. Bu nedenlerle artık geleneksel yöntemlerin yanısıra moleküler yöntemler de fungal sistematikte sıkça kullanılmaya başlanmıştır. Bunlardan bazıları, giderek yaygın bir kullanım alanı bulan PCR temelli teknikler ve özellikle DNA dizileme çalışmalarıdır. Fungal sistematikte, değişikliğin ilk meydana geldiği moleküller olan DNA üzerinde çalışmalar yapmak, hem güvenilir hem de hızlı sonuçlar elde etmemizi sağlamaktadır. DNA molekülünde organizmaların evrimini yansıtabilecek türe özgü bölgeler (evrimsel kronometre) olduğu için taksonomik çalışmalarda tercih edilmektedir. Fungal sistematikte en çok tercih edilen bölge ribozomal DNA (rDNA) birimi içinde yer alan 18S rDNA'nın yanısıra Internal Transcribed Spacer (ITS)'dır. Kodlanmayan bölge olan ITS daha hızlı evrim geçiren bir bölge olup bir tür içindeki suşların yada bir cins içindeki fungal türlerin karşılaştırılması için kullanışlıdır. Moleküler yöntemlerdeki bu gelişmeler, özellikle ekonomik öneme sahip bitkilerde büyük hasara neden olan ve ürün kalitesini etkileyen hastalık etmeni fungusların kısa süre içinde teşhisinde ve bu doğrultuda önlemlerin alınmasında da faydalı olmuştur.
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REFERENCES

References: 

Abd-Elsalam, K.A., Aly, I.N., Mohmed, A., Abdel-Satar, M.A., Khalil,
M.S.
, Joseph, A., Verreet, J.A., 2003. PCR identification of Fusarium genus based on nuclear ribosomal-DNA sequence data. African Journal of Biotechnology. Vol. 2, pp. 82-85.
Abdel-Satar, M.A., Khalil, M.S., Mohmed I.N., Abd-Elsalam K.A., Verreet, J.A., 2003. Molecular
phylogeny of Fusarium species by AFLP fingerprint African Journal of Biotechnology. Vol. 2 (3), pp. 51-55 Appel, D.J., Gordon, T.R., 1995. Intraspecific variation within populations of Fusarium oxyporum based on RFLP analysis of the intergenic spacer region of the
rDNA. Experimental Mycology 19, 120-128.
Arora, D.K., Hirsch, P.R., Kerry, B.R. 1996. PCR based molecular discrimination of Verticillium chlamydosporium isolates. Mycological Research 100,
801-809.
Başıbüyük,
H.H.
, Bardakçı, F. Belshaw, R., Quicke, D.L.J., 2000. Phylogenetic Systematics: A Practical Guide to Theory and Practice. Önder Matbaa Sivas, 134p.
Blackwell, M., Vilgays, R., James, T.Y., Taylor, J.W., 2007. Fungi. Available From
http://tolweb.org/Fungi/2377/2007.07.13
Boysen, M., Bojra, M., del Moral, C., Salzar, O., Rubio, V., 1996. Identification at strain level of Rhizoctonia solani AG4 isolates by direct sequence of asymmetric PCR Product of the ITS regions. Current Genetics 29, 174¬181.
Bridge, P. D., Arora, D. K., Reddy, C. A., Elander, R. P.,
1998. Appliation of PCR in Mycology, Cab
International, New York, 357p. Bridge, P.D., Spooner, B.M., Roberts, P.J., 2005. The
Impact of Molecular Data in Fungal Systematics.
Advances in Botanical Research, 42, 33-67. Bruns, T. D., Fogel, R., Taylor, J. W., 1990. Amplification
and sequencing of DNA from fungal herbarium
specimens. Mycologia 82, 175-184. Bruns, T.D., Vilgays, T.J., Taylor, J.W., 1991. Fungal
molecular systematics. Annual Review of Ecology and
Systematics 22, 525-564. Bruns, T.D., Gardes, M., 1993. Molecular tools for the identification of ectomycorrhizal fungi-taxon-specific oligonucleotide probes for suilloid fungi. Molecular
Ecology 2, 233-242.
Bruns, T., 2007. Molecular Systematic Investigation of Rust Fungi Associated with Pinaceae. Available from http://www.sciencestorm.com/award/8918454.html
Castlebury, L.A., Carris, K.V., 2005. Phylogenetic analysis of Tilletia and allied genera in order Tilletiales
70
M. Ç. Kılıçoğlu, I. Özkoç
(Ustilaginomycetes; Exobasidiomycetidae) based on large submit nuclear rDNA sequences. Mycologia 97,
888-900.
Cubeta, M.A., Vilgayus, R.,
Gonzales
, D., 1996. Molecular analysis of ribosomal RNA genes in Rhizoctonia fungi. Kluwer Academic Press, Dordrecht, pp.81-86.
Dahlman, M., Danell, E., Spatafora, J.W., 2000. Molecular
systematics of Craterellus : cladistic analysis of nuclear LSU rDNA sequence data. Mycol. Res. 104 (4) 388¬394.
Di Bonita, R., Elliott, M.L., Desjardin, E.A., 1995. Detection of an arbuscular mycorrhizal fungus in roots of different plant species with the PCR. Applied and Environmental Microbiology 61, 2809-2810.
Dieffenbach, C.W., Lowe, T.M.J., Dveksler, G.S., 1993.
General concepts for PCR primer design. PCR Methods
and Applications 3, S30-S37. Dupuis, C.,
1984
. Willi Hennig's impact on taxonomic
thought. Annual Review of Ecolology and
Systematics15: 1-24. Edel, V., Steinberg, C., Avelance, I., Laguerre, G.,
Alabouvette, C., 1995. Comparison of three molecular
methods for the characterization of Fusarium oxyporum
strains. Phytopathology 85, 579-585.
Hibbett, S.A., Binder, M., Bischoff, J.F., Blackwell, M.,
Cannon, P.F., Eriksson, O.E., Huhndorf, S., James, T., Kirk, P.M., Lücking, R., Lumbsch H., Lutzoni, T., Matheny, F., Mclaughlin, P.B., Powell, D. J., Redhead, M.J., Schoch, S., Spatafora, C.L., Stalpers, J.W., Vilgalys, J.A., Aime, R., Aptroot, M.C., Bauer, A., Begerow, R., Benny, D., Castlebury, G.L., Crous, L.A.,
Dai, P.W., Gams, Y.C., Geiser, W., Griffith, D.M.,
Gueidan, G.W., Hawksworth, C., Hestmark, D.L., Hosaka, G., Humber, K., Hyde, R.A., Ironside, K.D.,
KLöljalg
, J.E., Kurtzman, U., Larsson, C.P., Lichtwardt, K.H., Longcore, R., Midlikowska, J., Miller, J., Moncalvo, A., Mozley-Standridge, J.M., Oberwinkler, S., Parmasto, F., Reeb, E., Rogers, V., Roux, J. D., Ryvarden, C., Sampaio, L., Schüssler, J. P., Sugiyama, A., Thorn, J., Tibell, R. G., Untereiner,
L., Walker, W.A., Wang, C., Weir, Z., Weiss, A., White, M.M., Winka, K., Yao, Y.J., Zhang, N., 2007.
A higher-level phylogenetic classification of the Fungi. Mycological Research. 111:509-547. Hyakumachi, M., Mushika, T., Ogiso, Y., Toda, T., Kageyama, K., Tsuge, T., 1998. Characterization of a new cultural type (LP) of Rhizoctonia solani AG2-2 isolated from warm-season turgrasses, and its genetic differentiation from other cultural types. Plant
Pathology 47.
JunZhi, Q., ZhiPeng,
H.
, Jieru, P., XueQin, X., YanPing, Z., ShaoSheng, Z., XiOng, G., 2004. RAPD and LSU rDNA sequences analyses of entomogenous fungus Aschersonia. Journal of Agricultural Biotechnology, Vol.12, pp, 578-582.
Kaminski, J., Dernoeden, P., Oneill, N.R., Whetzel, H.C. 2005. A PCR-based method for the detection of
Ophiosphaerella agrostis in creeping bentgrass. Plant
Disease. 89:980-985.
Karaca, G.H., Özkoç, I., Erper, I., 2002. Determination of the Anastomosis Groupings and Virulence of Rhizoctonia solani Kuhn Isolates Associated with Bean Plants Grown in Samsun/Turkey, Pakistan Journal of
Biological Sciences 5(4): 434-437.
Klassen, G.R., Buchko, J.,
1990
. Subrepeat structure of the intergenic region in the ribosomal DNA of the
oomycetous fungus Pythium ultimum. Current Genetic 17, 125-127.
Lee, S.B., Taylor, J.W., (1992). Phylogeny of five fungus¬like protoctistan Phytophthora species, inferred from the internal transcribed spacers of ribosomal DNA. Molecular Biology and evolution 9,636-653. Leonardi, M., Paolocci, F., Rubini, A., Simonini, G., Pacioni, G., 2005. Assessment of inter and intra-specific variability in the main species of Boletus edulis complex by ITS analysis. FEMS Microbiology Letters
243, 411-416
Lipscomb, D., 1998. Basics of cladistic Analysis. Available from
www.gwu.edu/~clade/faculty/lipscomb/Cladistics.pdf Liu, Z.L., Sinclair, J.B., 1993. Differentiation of intraspecific groups within anastomosis group I of Rhizoctonia solani species complex. Mycologia 85,
797-800.
Liu, Z.L., Domier, L.L., Sinclair, J.B., 1995. Polymorphism of genes coding for nuclear 18S rRNA indicates genetic distinctness of anastomosis group 10 from other groups in Rhizoctonia species complex. Applied and Environmental Microbiolgy 61, 2659-2664.
Madigan, M. T., Martinko, J. M., Parker. J., 2003. Brock
Biology of Microorganisms, tenth edition, Pirentice Hall, Pearson Educatin International.
Majer,D., Mithen, R., Lewis, B.G., Vos, P., Oliver, R.P.,
1996. The use of AFLP fingerprinting for the detection of genetic variation in fungi. Mycological Research
100, 1107-1111. Martınez-Culebras, P.V., Ramon, D., 2006. An ITS-RFLP
method to identify black Aspergillus isolates responsible for OTA contamination in grapes and wine. International Journal of Food Microbiology. Vol. 113,
pp. 147-153.
Maukhamedov, R., Hu, X., Nazar, R.N., Robb, J., 1994. Use
of polymerase chain reaction- amplified ribosomal intergenic sequences for the diagnosis of Verticillium tricorpus. Phytopathology 84, 256-259. Mazzola, M.,
Wong, O.T., Cook, R.J., 1996. Virulence of
Rhizoctonia oryzae and R. solani AG-8 on wheat and detection of R. oryzae in plant tissues by PCR.
Phytopatholgy 86, 354-360.
Moore-Landecker, E., 1996, Fundementals of the Fungi, Prentice Hall, Upper Saddle River, New Jersey. Sf 574. Morton, A., Tabrett, A.M., Carder, J.H., Barbara D.J., 1995. Sub-repeat sequences in the ribosomal RNA intergenic regions of Verticillium alboatrum and V. dahliae. Mycological Research 99, 256-266. Müler, M.V.G., Germani, J.C., Van Der Sand, S.T., 2005. The use of RAPD to characterize Bipolaris sorokiniana
isolates. Genet. Mol. Res. 4 (4): 642-652.
Nazar, R.N., Hu, X,
Schmidt
, J., Culham, D., Robb, J., 1991. Potential use of PCR amplified ribosomal intergenic sequences in the detection and differentiation of Verticillium wilt pathogen. Physiological and Molecular Plant Pathology 39, 1-11. Özkoç, I., Karaca, G.H., Erper, I., 2002. Pathogenicity of Rhizoctonia repens Bernard on different plants and its effect on the suppression of root-rot on cucumber
plants. Acta Horticulture, Vol 579, 463-467.
Quicke, D. L.J., 1993. Principles and Techniques of Contemporary Taxonomy. Blackie Academic & Professional, London, 311 pp. Reynolds, D.R., Taylor, J.W., 1992. The Fungal Holomorph: Mitotic, Meiotic and Pleomorphic Speciation in Fungal
71
Fungal sistematikteki moleküler gelişmeler
Systematics. Cab International. Newport Oregon. 375
pp.
Salazar, O., Julian, M.C., Rubia, V., 2000. Primers based on specific rDNA-ITS sequences for PCR detection of Rhizoctonia solani, R. solani AG 2 subgroups and ecological types, and binucleate Rhizoctonia. Mycol.
Res. 104, 281-285.
Samuels, G.J., 2004. Changes in taxonomy, occurrence of the sexual stage and ecology of Trichoderma spp.
Phytopathology 94, 138 Schilling, A.G., Moller, E.M., Geiger, H.H., 1996.
Polymerase chain reaction-based assays for species-specific detection Fusarium culmorum, F. graminearum ve F. avenaceum. Phytopathology 86,
515-522.
Sharon, M., Kuninaga, S., Hyakumachi, M., Sneh, B., 2006. The advancing identification and classification of Rhizoctonia spp. Using molecular and biotechnological methods compared with the classical anastomosis grouping. Mycoscience 47, 299-316.
Sneh, B., Burpee, L., Ogoshi, A., 1991. Identification of Rhizoctonia species, APS PRESS The American Phytopathological Society St. Paul, Minnesota, USA.
Sf 133.
Sneh, B., Jabaji -Hare, S., Neate, S., Dijst, G., 1996. Rhizoctonia species: Taxonomy, Molecular Biology, and Disease Control. Kluwer Academic Press, Dorcrecht, p. 578.,
Taylor, J. W., Jacobson, D.J., Kroken, S., Kasuga, T.,
Geiser, D. M., Hibbett, D. S., Fisher, M. C., 2000.
Phylogenetic species recognition and species concept in fungi. Fungal Genetic and Biology 31, 21-32.
Vilgalys, R., Gonzales, D., 1990. Ribosomal DNA
Restriction fragment lenght polymorphisms in Rhizoctonia solani. Phytopathology, 80, 151-158.
White, T. J., Bruns, T., Lee, S., Taylor. J., 1990.
Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. Academic Press, san Diego, pp. 315-322. Xu, J., Kerrigan, R.W., Sonnenberg, A.S., Callac, P., Horgen, P.A., Anderson, J.B., 1998. Mitochondrial DNA variation in natural populations of the mushroom Agaricus bisporus. Molecular Ecology 7, 19-33.
Zhang, N., Sung, G., Castlebury, L.A., Seifert, K.A.,
Rossman, A.Y., Rogers, J.D., Miller, N., Huhndorf, S.M., Schoch, C.L., Kohlmeyer, J., Volkmann-Kohlmeyer, B., 2007. An overview of Molecular Phylogeny of the Sordariomycetes. Mycologia. 98,
1076-1087.

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