Molecular characterization based on coat protein gene of Beet soil-borne virus isolates obtained from the soils of sugar beet growing areas in Turkey

Öz

Sugar beet (Beta vulgaris L.) is widely grown in Turkey as a raw material for the sugar industry. The beet plant is infected by some soil-borne viruses, which are transmitted by the plasmodiophorid vector Polymyxa betae Keskin. Among the members of the genus Pomovirus in the family Virgaviridae, Beet soil-borne virus (BSBV) and Beet virus Q (BVQ) only infect sugar beet. In Turkey, BSBV was the first reported in 2003 and then was found to be very common (49.8%) in the sugar beet production areas. In the current study, 10 BSBV-infested soil samples were randomly selected according to their geographic origin, and the isolates derived from the soil samples by bait plant technique were molecularly analyzed. RT-PCR performed using BSBV-CP specific primers and sequence analysis revealed that the CP regions of all Turkish BSBV isolates consisted of 495 nucleotides and 164 amino acid (aa) residues. Interestingly, 9 BSBV isolates obtained from different locations had the same aa identity (100%) when those isolates were compared with each other. However, the isolate YZT-355S obtained from Yozgat province shared 98.17% aa identity with the corresponding sequences of other isolates, and had differences at the 92., 121. and 122. aa positions of the CP region when compared with other Turkish and previously identified BSBV isolates in the world. Besides this, phylogenetic analysis of 24 BSBV isolates (10 from this study and 14 retrieved from GenBank) showed that all isolates were clustered in four main groups, I, II, III and IV. Turkish isolates belonged to group I were divided into two subgroup (subgroup a, c) while the other Turkish isolates were clustered into group III and group IV.

Anahtar Kelimeler

• BSBV
• CP
• RNA-2
• RT-PCR
• Sequencing

Türkiye şeker pancarı üretim alanlarından elde edilen Beet soil-borne virus izolatlarının kılıf protein genine göre moleküler karakterizasyonu

Öz

Şeker pancarı (Beta vulgaris L.), Türkiye'de şeker endüstrisinin hammaddesi olup, yaygın olarak yetiştirilmektedir. Pancar bitkisi, plazmodiophorid vektör Polymyxa betae tarafından taşınan bazı toprak kaynaklı virüsler tarafından enfekte edilmektedir. Taksonomik olarak Virgaviridae familyası içinde yer alan ve Pomovirus cinsine ait Beet soil-borne virus (BSBV) ve Beet virus Q (BVQ) şeker pancarında enfeksiyon oluşturan toprak kökenli virüs türleridir. Bu virüslerden BSBV, Türkiye'de ilk olarak 2003 yılında kayıt edilmiş ve daha sonra şeker pancarı üretim alanlarında oldukça yaygın olduğu (% 49.8) belirlenmiştir. Bu çalışmada, BSBV ile bulaşık 10 toprak örneği coğrafik orjinlerine göre rastgele seçilmiş ve bu toprak örneklerinden tuzak bitki testi yöntemiyle elde edilen izolatlar, moleküler yönden analiz edilmiştir. BSBV kılıf protein (CP) genine spesifik primerler ile uygulanan RT-PCR yöntemi ve elde edilen DNA ürünlerinin baz dizi analizi sonrasında, tüm BSBV izolatlarının CP bölgelerinin 495 nükleotit ve 164 amino asit (aa) içerdiği tespit edilmiştir. İlginç bir şekilde, farklı lokasyonlardan elde edilen 9 BSBV izolatı birbirleriyle karşılaştırıldığında, bu izolatların aa düzeyinde % 100 benzer oldukları saptanmıştır. Bununla birlikte, Yozgat ilinden elde edilen YZT-355S izolatının, diğer izolatlarla aa benzerlik oranının % 98.17 olduğu ve 92., 121. ve 122. pozisyonlarda yer alan aa’lerin diğer Türkiye izotları ve daha önce tanımlanan BSBV dünya izolatlarından farklılık sergilediği tespit edilmiştir. Bunun yanı sıra, 24 BSBV izolatının (bu çalışmadan 10 ve GenBank'tan 14) filogenetik analizi, tüm izolatların I, II, III ve IV olmak üzere dört ana grupta toplandığını göstermiştir. Grup I'e ait Türkiye izolatları iki alt gruba (alt grup a ve c) ayrılırken, diğer Türkiye izolatları grup III ve grup IV içerisinde yer almışlardır.

Anahtar Kelimeler

• BSBV
• CP
• RNA-2
• RT-PCR
• Sekans analizi

Kaynakça

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