Türkiye'de Xiphinema index (Dorylaimida: Longidoridae)’in 28S Bölgesinin Moleküler Karakterizasyonu

Year 2024, , 117 - 123, 31.08.2024

Lerzan Öztürk , İbrahim Halil Elekcioğlu

https://doi.org/10.55507/gopzfd.1493529

Abstract

Xiphinema index (Dorylaimida: Longidoridae) virüs vektörü nematod türü olup dünya genelinde oldukça yaygındır. Bu çalışmada, Xiphinema index nematodunun DNA'sı ile, 28S bölgesini analiz etmek için D2A ve D3B primerleri kullanılarak Polimeraz Zincir Reaksiyonu (PCR) yapılmıştır. Elde edilen sekans verileri daha sonra diğer türlerle benzerliklerini belirlemek için BLAST analizine tabi tutulmuştur. Çalışmada X. index popülasyonu, Türkiye, Tekirdağ'daki bir incir plantasyonundan (Ficus carica L.) toplanmış, ve türün filogenetik analizini gerçekleştirmek için DNA'sı D2A ve D3B primerleri ile amplifiye edilmiştir. Nematodlar önce morfolojik olarak, daha sonra moleküler olarak tanımlanmıştır. Moleküler çalışmalarda D2A ve D3B primerleri kullanılmıştır. PCR sonrası amplifike yapılan nematod DNA’sı sekansa tabi tutulmuştur ve X. index’in 28S rRNA molekülünün D2-D3 bölgesinden gelen veriler BLAST (Basic Local Alignment Search Tool) kullanılarak GenBank dizi karşılaştırmasına tabi tutulmuştur.Yerel sekans PQ165044 aksesyon numarası ile GenBank’a kaydedilmiş ve diğer Xiphinema index türleri ile (% 98.26 – 99.81) benzerlik göstermiştir. Yerel X. index dizisi, 16 farklı X. index aksesyonu ve farklı Xihpinema türlerine ait 13 aksesyon ile yapılan Neighbor-joining ve Maximum likelihood analizlerinde yerel sekans, İspanya (HM921406, HM921400, HM921399, HM921398, HM921363, HM921349, HM921347 ve HM921364 ve Girit/Yunanistan sekanslarıyla aynı dalda kümelenmiştir.

Keywords

Kamalı nematod, 28S rRNA, Ficus carica L., Türkiye

Project Number

yok

Molecular Characterisation of 28S Region of Xiphinema index (Dorylaimida: Longidoridae) from Türkiye

Abstract

Xiphinema index (Dorylaimida: Longidoridae) is a virus vector nematode and is highly distributed worldwide. In this study, the DNA of the Xiphinema index nematode was subject to Polymerase chain reaction (PCR) using D2A and D3B primers to analyse the 28S region. The resulting sequence data were then subjected to a BLAST check in order to ascertain the similarity to other species. The X. index population in the study was recovered from a fig (Ficus carica L.) plantation in Tekirdağ, Türkiye. The DNA of specimens was amplified with D2A and D3B primers to perform phylogenetic analysis. At first, the nematodes were identified morphologically and then molecularly. D2A and D3B primers were used in the study. After PCR, amplified DNA was sequenced for molecular purposes, and data from the D2-D3 region of the 28S rRNA molecule of X. index were subjected to GenBank sequence comparison using BLAST (Basic Local Alignment Search Tool). The local sequence submitted to GenBank with accession number PQ165044 showed identity (98.26-99.81%) with several Xiphinema index hits. Local X. index sequence clustered close with Spanish (HM921406, HM921400, HM921399, HM921398, HM921363, HM921349, HM921347 and HM921364) and Crete/Greece (KJ802882) sequences in Neighbor-joining and Maximum likelihood analysis comparing the local sequence, 16 different X. index accessions and 13 accessions from various species.

Keywords

Dagger nematode, 28S rRNA, Ficus carica L., Türkiye

Supporting Institution

yok

Project Number

yok

References

• Andret-Link, P., C. Laporte, L. Valat, C. Ritzenthaler, G. Demangeat, E. Vigne, V. Laval, P. Pfeiffer, C. Stussi-Garaud, & Fuchs M. (2004). Grapevine fanleaf virus: Still a major threat to the grapevine industry. Journal of Plant Pathology, 86, 183-195.
• Basso, M.F., Fajardo, T.V.M., & Saldarelli, P. (2017). Grapevine virus diseases: economic impact and current advances in viral prospection and management. Rev. Bras. Frutic., 39, e-411.  https://doi.org/10.1590/0100-29452017411. 
• Bernardo, P., Charles-Dominique, T., Barakat, M., Ortet, P., Fernandez, E., Filloux, D., Hartnady, P., Rebelo, T. A., Cousins, S. R., Mesleard, F., Cohez, D., Yavercovski, N., Varsani, A., Harkins, G. W., Peterschmitt, M., Malmstrom, C. M., Martin, D. P., & Roumagnac, P. (2018). Geometagenomics illuminates the impact of agriculture on the distribution and prevalence of plant viruses at the ecosystem scale. The ISME journal, 12(1), 173–184. https://doi.org/10.1038/ismej.2017.155.
• Blaxter, M, De Ley P, Garey, J.R., Lui L.X., & Scheldeman, P., (1998). A molecular evolutionary framework for the phylum Nematoda. Nature, 392, 71–75. https://doi.org/10.1038/32160.
• Brown, D.J.F., & Boag, B. (1988). An examination of methods used to extract virus-vector nematodes (Nematoda: Longidoridae and Trichodoridae from soil samples. Nematol. Medit., 16, 93 – 99. 
• Brown, D.J.F. & Coiro, M.I. (1985). The reproductive capacity and longevity of Xiphinema index (Nematoda: Dorylaimida) from three populations on selected host plants. Rev. Nématol. 8, 171-173.
• Daramola, F. Y., Knoetze, R., Swart, A., & Malan, A. P. (2019). First report and molecular characterization of the dagger nematode, Xiphinema oxycaudatum (Nematoda, Dorylaimidae) from South Africa. Zookeys, 894, 1-17. doi: 10.3897/zookeys.894.35281.
• Decraemer, W., & Robbins, R. T. (2007). The who, what and where of Longidoridae and Trichodoridae. J Nematol., 39, 295–297. 
• De Klerk, C. A., & Loubser, J. T. (1988). Relationship between grapevine roots and soil-borne pests. In: The grapevine root and its environment. J.L. van Zyl, (ed.). South African Department of Agriculture and Water Supply, pp 88-105.
• Esmenjaud, D., & Bouquet, A. (2009). Selection and application of resistant germplasm for grapevine nematodes management. In: Integrated management of fruit crops and forest nematodes. A. Ciancio & K.G. Mukerji, (eds.). Springer Science+Business Media B.V., pp. 195-214. https://doi.org/10.1007/978-1-4020-9858-1_8.
• Fayaz, M., Moghadam, M. E., & Tehrani, F. A. A. (2022). Morphological and molecular characterisation of Xiphinema index populations in vineyards from Southwestern Iran. Russian Journal of Nematology, 30 (1), 11-17. doi: 10.24412/0869-6918-2022-1-11.-
• Hewitt, W. B., Raski D. J., & Goheen, A. C. (1958). Nematode vector of soil-borne Fanleaf Virus of Grapevines. Phytopathology, 48, 586-595.
• Hooper, D. J. (1961). A redescription of Longidorus elongatus (de Man, 1876) Thorne & Swanger, 1936 (Nematoda, Dorylaimidae) and descriptions of five new species of Longidorus from Great Britain. Nematologica, 6, 237-257.
• Hübschen, J, Kling L, Ipach, U., Zinkernagel, V., Brown D. J. F., & Neilson R. (2004a). Development and validation of species-specific primers that provide a molecular diagnostic for virus-vector longidorid nematodes and related species in German viticulture. European Journal of Plant Pathology, 110, 883-891. https://doi.org/10.1007/s10658-004-4841-x.
• Hübschen, J., Kling, L., Ipach, U., Zinkernagel, V., Bosselut N., Esmenjaud, D., Brown, D. J. F., Brown, D. J. F., & Neilson R. (2004b). Validation of the specificity and sensitivity of species-specific primers that provide a reliable molecular diagnostic for Xiphinema diversicaudatum, X. index and X. vuittenezi. European Journal of Plant Pathology, 110, 779-788. https://doi.org/10.1007/s10658-004-0995-9.
• Jawhar, J., Vovlas, N., & Digiaro, M. (2006). Occurrence of Xiphinema index in Lebanese vineyards. Journal of Plant Pathology, 88 (1), 117-119.
• Jenkins, W. R. (1964). Rapid centrifugal-flotation technique for separating nematodes from soil. Plant Dis. Rep., 48, 692.
• Kasapoğlu, Uludamar, E., Yıldız, Ş., İmren, M., Öcal, A., Elekçioğlu, İ. H. (2018). Occurrence of plant parasitic nematode species in important crops in the Southeast Anatolia Region of Turkey. Turkish Journal of Entomology, 42 (1), 63-74. doi: 10.16970/entoted.359616.
• Kepenekci, İ., Toktay, H., & Evlice, E. (2014). Plant parasitic and virus vector nematodes associated with vineyards in the Central Anatolia Region of Turkey. Pakistan Journal of Zoology, 46 (3), 866-870.
• Kumari, S., Decraemer, W., De Luca, F., & Tiefenbrunner, W. (2010).  Cytochrome c oxidase subunit 1 analysis of Xiphinema diversicaudatum, X. pachtaicum, X. simile and X. vuittenezi (Nematoda, Dorylaimida). European Journal of Plant Pathology, 127, 493–499. doi: 10.1007/s10658-010-9614-0
• Kumari, S., & Lišková, M. (2009). Molecular confirmation of Xiphinema italiae Meyl, 1953 (Nematoda: Longidoridae) from the Slovak Republic. Helminthologia, 46(2), pp. 131-134. doi:10.2478/s11687-009-0025-8
• Lafontaine, D. L., & Tollervey, D. (2001). Ribosomal RNA. Encyclopedia of Life Sciences. https://doi.org/10.1038/npg.els.0003832.
• Leopold, S. Borroto-Fernandez, E. Schartl, A., & Laimer, M. (2007). Identification of Xiphinema index in an Austrian vineyard. Vitis, 2007, 46, 49–50.
• Loof, P. A. A., & M. Luc, 1990. A revised polytomous key for the identification of species of the genus Xiphinema Cobb,1913 (Nematoda: Longidoridae) with exclusion of the X. americanum-group. Systematic Parasitology, 16, 36-66. https://doi.org/10.1007/BF00010531.
• Martelli, G. P., & Savino, V. (1990). Fanleaf degeneration. In: Pearson, R.C and Goheen, A. (eds.) Compendium of grape diseases, pp. 48-49. APS Press, St Paul, MN, USA.
• Mistanoğlu, İ., Kaşkavalcı, G., & Devran, Z. (2015). Identification of the economically important plant parasitic nematodes in vineyards areas of İzmir and Manisa provinces by morphological and molecular techniques. Turkish Journal of Entomology, 39 (3), 297-309. https://doi.org/10.16970/ted.65336.
• Nunn, G., B., (1992). Nematode molecular evolution: an investigation of evolutionary patterns among nematodes based upon DNA sequences. Ph.D. Dissertation, University of Nottingham, Nottingham, UK
• Öztürk, L., Avcı, G. G., & Elekcioğlu, İ. H., (2017). Incidence of viruses and vector nematodes in Thrace vineyards, Turkey. International Journal of Agriculture and Environmental Research, 3(6), 4078-4089.
• Powers, T. (2004). Nematode molecular diagnostics: from bands to barcodes. Annual Review of Phytopathology, 42:367-383. DOI: 10.1146/annurev.phyto.42.040803.140348.
• Seinhorst, J. W. (1959). A rapid method for the transfer of nematodes from fixative to anhydrous glycerin. Nematologica, 4(1), 67-69.
• Šırca, S., Stare, B. G., Pleško, I. M., Marn, M. V., Urek, G., & Javornik, B., (2007): Xiphinema rivesi from Slovania Transmit Tobacco Ringspot Virus and Tomato Ringspot Virus to Cucumber Bait Plants. Plant Disease, 91(6) pp. 770. DOI: 10.1094/PDIS-91-6-0770B.
• Subbotin, S. A., Ragsdale, E. J., Mullens, T., Roberts, P. A., Mundo-Ocampo, M., & Baldwin, J. G. (2008). A phylogenetic framework for root lesion nematodes of the genus Pratylenchus (Nematoda): Evidence from 18S and D2-D3 expansion segments of 28S ribosomal RNA genes and morphological characters. Mol Phylogenet Evol., 48, 491-505. doi: 10.1016/j.ympev.2008.04.028
• Taylor, C.E., & Raski, D.J., (1964). On the transmission of grape fanleaf by Xiphinema index. Nematologica, 10, 486-495
• Thorne, G., & Allen, M.W. (1950). Paratylenchus hamatus n.sp. and Xiphinema index n.sp, two nematodes associated with fig roots, with a note on Paratylenchus anceps Cobb. Proc. Helminth. Soc., 17, 27-35.
• Van Zyl, S., Vivier, M. A. & Walker, M. A. (2012). Xiphinema index and its relationship to grapevines: a review. South African Journal of Enology and Viticulture, 33, 21-32. doi: 10.21548/33-1-1302
• Wang, X., Bosselut, N., Castagnone, C., Voisin, R., Abad, P., & Esmenjaud, D. (2003). Multiplex polymerase chain reaction identification of single individuals of the Longidorid nematodes Xiphinema index, X. diversicaudatum, X. vuittenezi, and X. italiae using specific primers from ribosomal genes. Phytopathology, 93, 160–166. doi: 10.1094/PHYTO.2003.93.2.160.
• Vrain, T., Wakarchuk, D., Lévesque, C., & Hamilton, R. (1992). Intraspecific rDNA restriction fragment length polymorphism in the Xiphinema americanum group. Fundamental and Applied Nematology, 15, 563-573.
• Yıldız, Ş. & Elekcioğlu, İ. H. (2011). Şanlıurfa ilinde tarımsal ve doğal alanlarda nematod biyoçeşitliliği. Turkish Journal of Entomology, 35(2), 381-394. https://dergipark.org.tr/en/pub/entoted/issue/64049/969263