PCR-RFLP analysis of Botryosphaeriaceae species isolated from the Aegean and Mediterranean vineyards

Yıl 2019, , 15 - 22, 29.06.2019

Davut Soner Akgül , Qamar Nawaz Awan Ali Erkılıç

https://doi.org/10.16955/bitkorb.454980

Cited By: 1

Öz

The classical identification of Botryosphaeriaceae fungi, causing dieback and local dead arms in many plant species, is very difficult and time-consuming. Some of the molecular tools, such as PCR using species-specific primed, RFLP (Restricted Fragment Length Polymorphism) or gene sequencing are necessary for the fast identification of species. This study aims to contribute for the fast identification of some fungal species belonging Botryosphaeriaceae family reported up to now in Turkey vineyards. DNA was extracted from the 25 isolates obtained from the Aegean and Mediterranean Regions, and 4 different species (Botryosphaeria dothidea, Diplodia seriata, Lasiodiplodia theobromae, and Neofusicoccum parvum) and β-tubulin (TUB2) and ITS region (specific for Botryosphaeriaceae genus) on genomic DNA was amplified by polymerase chain reactions. This region was digested by five different restriction endonuclease enzymes (AluI, BsaHI, MboI, RsaI, TaqI) and band profiles were analyzed on an agarose gel (2%). According to the results of the analysis, the region, amplified with genus-specific primers, was not suitable for RFLP analysis. On the other hand, to discriminate these species, it was revealed that the β-tubulin gene region should be digested at least two different restriction enzymes. The enzyme BsaHI generated two different band sizes for B. dothidea and D. seriata (250 and 700 bp for the first; 400 and 600 bp for the second one) digesting β-tubulin gene of these species but this enzyme could not generate any discriminative bands for L. theobromae and N. parvum. However the enzyme TaqI could not discriminate B. dothidea and D. seriata but digest β-tubulin gene of L. theobromae and N. parvum at two points and it generated three different bands (for L. theobromae: 200-400-800 bp and for N. parvum: 200-400-650 bp).

Anahtar Kelimeler

grapevine, Botryosphaeria dieback, restriction enzymes, BsaHI, TaqI

Ege ve Akdeniz Bölgesi bağlarından izole edilen Botryosphaeriaceae türlerinin PCR-RFLP analizi

Öz

Birçok bitki türünde lokal kuruma ve geriye ölümlere neden
olan Botryosphaeriaceae funguslarının klasik tanısı oldukça zor ve zaman
alıcıdır. Türlerin hızlı tanısı için türe özgü primerlerle PCR testi, RFLP
(Restricted Fragment Length Polymorphism) ya da gen sekanslama gibi bazı
moleküler yöntemlerin kullanılması gerekmektedir. Bu çalışma, Türkiye
bağlarında şimdiye kadar tespit edilmiş bazı Botryosphaeriaceae familyası fungus
türlerinin, PCR-RFLP yöntemi ile hızlı tanısına katkı sağlamayı amaçlamaktadır.
Ege ve Akdeniz Bölgesi bağlarından izole edilmiş 4 farklı türe ait (Botryosphaeria dothidea, Diplodia seriata, Lasiodiplodia theobromae ve
Neofusicoccum parvum) 25 izolatttan DNA ekstraksiyonları yapılmış, genomik
DNA üzerindeki β-tubulin (TUB2) ve ITS bölgesinden tasarlanmış
Botryosphaeriaceae cinslerine özgü bölgeler, polimeraz zincir reaksiyonlarıyla çoğaltılmıştır.
Bu bölgeler beş farklı restriksiyon endonükleaz enzimiyle (AluI, BsaHI, MboI, RsaI, TaqI) kesilmiş,
agaroz jeldeki (%2) bant profilleri incelenmiştir. Analizlerin sonuçlarına
göre; cinse özgü primerlerle çoğaltılan bölge RFLP analizi için uygun
olmamıştır. Ancak, β-tubulin bölgesinin bu türlerin ayrımı için en az iki
farklı restriksiyon enzimiyle kesilmesi gerektiği ortaya çıkmıştır. BsaHI enzimi B. dothidea ve D. seriata’nın
β-tubulin genini keserek, iki ayrı büyüklükte bant profili (B. dothidea: 250 ve 700 bp ve D. seriata: 400 ve 600 bp)
oluşturmuştur. Ancak bu enzim L.
theobromae ve N. parvum için
ayırt edici bant verememiştir. Buna karşın TaqI
enzimi de B. dothidea ve D. seriata‘yı ayırt edememiş ancak L. theobromae ve N. parvum’un β-tubulin genini 2 yerden keserek her bir tür için üç
ayrı bant (L. theobromae: 200-400-800
bp ve N. parvum: 200-400-650 bp)
meydana getirmiştir.

Anahtar Kelimeler

asma, Botryosphaeria geriye ölümü, kesim enzimleri, BsaHI, TaqI

Kaynakça

• Akgül D. S., Savaş N.G., Eskalen A., 2014. First report of wood canker caused by Botryosphaeria dothidea, Diplodia seriata, Neofusicoccum parvum, and Lasiodiplodia theobromae on grapevine in Turkey. Plant Disease, 98 (4): 568p.
• Alves A., Phillips A. J. L., Henriques I., Correia A., 2005. Evaluation of amplified ribosomal DNA restriction analysis as a method for the identification of Botryosphaeria species. FEMS Microbiology Letters, 245, 221-229.
• Amponsah N. T., Jones E. E., Ridgway H. J., Jaspers M. V., 2008. Production of Botryosphaeriaceae species conidia using grapevine green shoots. New Zealand Plant Protection, 61, 301-305.
• Chen S. F., Pavlic D., Roux J., Slippers B., Xie Y. J., Wingfield M. J., Zhou X. D., 2011. Characterization of Botryosphaeriaceae from plantation-grown Eucalyptus species in South China. Plant Pathology, 60, 739-751.
• Crous P. W., Slippers B., Wingfield M. J., Rheeder J., Marasas W. F. O., Phillips A. J. L., Alves A., Bur¬guess T., Barber P., Groenewald J.Z., 2006. Phylo¬genetic lineages in the Botryosphaeriaceae. Studies in Mycology, 55, 235–253.
• Farr D. F., Rossman A. Y., 2011. Fungal Databases, Systematic Mycology and Microbiology Laboratory, ARS, USDA. http:// nt.ars-grin.gov/fungaldatabases/fungushost/fungush¬ost.cfm (Erişim tarihi: 23.08.2018).
• Glass N. L., Donaldson G. C., 1995. Development of primer sets designed for use with the PCR to amplify conserved genes from the filamentous ascomycetes. Applied Environmental Microbiology, 61, 1323–1330.
• Hills D. M., Dixon M. T., 1991. Ribosomal DNA: molecular evolution and phylogenetic inference. Quarterly Reviews in Biology, 66, 411-453.Inderbitzin P., Bostock R. M., Trouillas F. P., Michailides T. J., 2010. A six locus phylogeny reveals high species diversity in Botryosphaeriaceae from California almond. Mycologia. 102, 1350-1368.
• Liu J. K., Phookamsak R., Doilom M., Wikee S., Li Y. M., 2012. Towards a natural classification of Botryosphaeriales. Fungal Diversity, 57, 149-210.
• Mahmodi F., Kadir J. B., Puteh A., Pourdad S. S., Nasehi A., Soleimani N., 2014. Genetic diversity and differentiation of Colletotrichum spp. isolates associated with leguminosae using multigene loci, RAPD and ISSR. Plant Pathology Journal, 30 (1), 10-24.
• Martin M. T., Cuesta M. J., Martin L., 2014. Development of SCAR primers for PCR assay to detect Diplodia seriata. International Scholarly Research Notices, http://dx.doi.org/10.1155/2014/824106 1-9.
• Mullis, K. B., Faloona F. A., 1987. Specific synthesis of DNA in vitro via a polymerase-catalysed chain reaction. Methods in Enzymology. 155, 335-350.Nejat N., Sijam, K., Abdullah S. N. A., Vadamalai G., Dickinson M., 2009. Molecular characterization of a phytoplasma associated with coconut yellow decline (CYD) in Malaysia. American Journal of Applied Sciences, 6 (7), 1331-1340.
• Pavlic D., Slippers B., Coutinho T. A., Wingfield M. J., 2007. Botryosphaeriaceae occurring on native Syzygium cordatum in South Africa and their potential threat to Eucalyptus. Plant Pathology, 56, 624-636.
• Pavlic D., Slippers B., Coutinho T. A., Wingfield M. J., 2009. Multiple gene genealogies and phenotypic data reveal cryptic species of the Botryosphaeriaceae: A case study on the Neofusicoccum parvum / N. ribis complex. Molecular Phylogenetics and Evolution, 51, 259-268.
• Ridgway H. J., Amponsah N. T., Brown D. S., Baskarathevan J., Jones E. E., Jaspers M. V., 2011. Detection of Botryosphaeriaceous species in environmental samples using a multi-species primer pair. Plant Pathology, 60, 1118-1127.
• Saiki R. K., Scharf S., Faloona F., Mullis K. B., Horn G. T., Erlich H. A., Arnheim N., 1985. Enzymatic amplification of B-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science, 239, 487-491.
• Slippers B., Wingfield M. J., 2007. Botryosphaeriaceae as endophytes and latent pathogens of woody plants: diversity, ecology and impact. Fungal Biology Reviews, 21, 90–106.
• Taylor A., Hardy G. E. J., Wood P., Burguess T., 2005. Identification and pathogenicity of Botryosphaeria species associated with grapevine decline in Western Australia. Australasian Plant Pathology, 34, 187–195.
• Urbez-Torres J. R., Phillips A. J. L, Gubler W. D., 2015. Botryosphaeria dieback. In: Compendium of Grape Diseases, Second Edition. Wilcox W. F., Gubler W. D., Uyemoto J. K., (Eds.), APS Press. St. Paul Minnesota, USA, 33-39.
• Urbez-Torres J. R., Castro-Medina F., Mohali S. R., Gubler W. D., 2016. Botryosphaeriaceae species associated with cankers and dieback symptoms of Acacia mangium and Pinus caribaea var. hondurensis in Venezuela. Plant Disease, 100, 2455-2464.
• Xu C., Zhang H., Chi F., Ji Z., Dong Q., Cao K., Zhou Z., 2016. Species-specific PCR-based assays for identification and detection of Botryosphaeriaceae species causing stem blight on blueberry in China. Journal of Integrative Agriculture, 15 (3), 573-579.