Tekirdağ ilinde bazı kabakgil virüslerinin araştırılması ve karpuz mozaik virüsü (watermelon mosaic virus, wmv)'nün moleküler karakterizasyonu
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Dosyalar
Tarih
2020
Yazarlar
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Yayıncı
Tekirdağ Namık Kemal Üniversitesi
Erişim Hakkı
info:eu-repo/semantics/openAccess
Özet
Bu çalışmada, Tekirdağ ili genelindeki kabakgil üretim alanlarında Watermelon mosaic virus (WMV), Papaya ringspot virus-Watermelon (PRSV-W) ve Zucchini yellow mosaic virus (ZYMV)'nin belirlenerek, virüs izolatlarının genotipik yakınlık düzeylerinin ortaya çıkarılması amaçlanmıştır. 2017 ve 2019 yıllarında yapılan arazi survey çalışmalarında viral enfeksiyon belirtileri gözlenen kabakgil bitkilerine ait yaprak örnekleri toplanarak DAS-ELISA ile ZYMV, PRSV-W ve WMV varlığı açısından test edilmesi sonucunda 180 adet bitki örneğinin %4,44 oranında WMV ile enfekteli olduğu belirlenmiştir. Toplanan bitki örneklerinden ELISA testleri sonucunda pozitif çıkan veya tipik virüs belirtisi gösteren 30 adet bitki örneği seçilerek WMV NIb-CP, PRSV-W ve ZYMV CP gen bölgesine spesifik oligonükleotitler ile Real-Time PCR ve RT-PCR kullanılarak test edilmiştir. Reverse Transcriptase PCR çalışmaları sonucunda 12 adet bitki örneğinde WMV'ye ait yaklaşık 408 bp boyutundaki bant oluşumu gözlenmiş, dizileme sonucunda 12 WMV izolatının NIb-CP genine ait 342 ve 348 nükleotidin filogenetik analiz çalışmaları yapılmıştır. Bu çalışma kapsamında elde edilen WMV izolatlarının Gen Bank'asına kayıtlı bazı WMV izolatları ile benzerlikleri açısından kıyaslamalar yapılmıştır. Bu çalışmada elde edilen 342 nükleotid uzunluğunda WMV NIb-CP geni kodlayan kısmın sekans analizleri sonucunda TR-Tn2 (MT448602), TR-Tn5 (MT448603), TR-Tn8 (MT448604), TR-Tn9 (MT448605), TR-Tn10 (MT448606), TR-Tn18 (MT448607), TR-Tu75 (MT448612) ve TR-Tu80 (MT448613) izolatları İtalya (EU660590), Fransa (NC_006262 ve JF273459), Türkiye (EU660579), Şili (EU660582), Pakistan (AB218280) izolatları ile %99.7-95 arasında benzerlik göstermiş ve Moleküler Grup 1'de yer almıştır. TR-Tf50 (MT448610), TR-Ta63 (MT448608), TR-Ta64 (MT448609) ve TR-Ts71 (MT448611) izolatlarının WMV NIb-CP kodlayan 348 nükleotid kısmının analizi sonucunda Güney Kore (AB369278), Çin (EF127832 ve DQ399708), Güney Kore (MN854651) ve Japonya (AB353119) izolatları ile %98,2-92.2 arasında değişen oranlarda benzerlik göstermişler ve WMV Moleküler Grup 3'te yer almışlardır.
In this study, determination of Watermelon mosaic virus (WMV), Papaya ringspot virus-Watermelon (PRSV-W) and Zucchini yellow mosaic virus (ZYMV) were aimed in cucurbit growing areas in Tekirdağ province. Additionally, comparison of virus isolates in order to reveal genetic identities were also aimed. Leaf samples of cucurbits plants with viral infection symptoms were collected during surveys in 2017 and 2019, and tested by ELISA to determine ZYMV, WMV and PRSV-W, and of tested 180 plant samples only 4,44% were found infected by WMV 30 of collected 180 plant samples that found positive or with typical viral infection symptoms were tested using CP gene region for ZYMV and PRSV-W, and NIb-CP gene region for WMV specific primers by Real time PCR and RT PCR, respectively. 12 of 30 selected plant samples showed about 408 nucleotides bands in agarose gel of WMV using RT-PCR. Sequence analysis revealed 342 and 348 nucletides of 12 isolates of WMV from Tekirdağ. Sequences were registered and deposited in GenBank and used for phylogenetic analysis and compared to WMV isolates available in GenBank. Sequence analysis of WMV NIb-CP gene coding 342 nucleotides obtained in this study, 8 of 12 isolates determined in this study namely TR-Tn2 (MT448602), TR-Tn5 (MT448603), TR-Tn8 (MT448604), TR-Tn9 (MT448605), TR-Tn10 (MT448606), TR-Tn18 (MT448607), TR-Tu75 (MT448612) and TR-Tu80 (MT448613) showed 99.7-95% identity with isolates from Italy (EU660590), France (NC_006262 and JF273459), Turkey (EU660579), Chile (EU660582) and Pakistan (AB218280) and grouped in WMV molecular Group 1. 4 of 12 isolates sequence analysis of WMV NIb-CP gene coding 348 nucleotides, determined in this study namely TR-Tf50 (MT448610), TR-Ta63 (MT448608), TR-Ta64 (MT448609) and TR-Ts71 (MT448611) showed 98,2-92.2% identity with isolates from South Korea (AB369278), China (EF127832 and DQ399708), South Korea (MN854651) and Japan (AB353119), and grouped in WMV Molecular Group 3.
In this study, determination of Watermelon mosaic virus (WMV), Papaya ringspot virus-Watermelon (PRSV-W) and Zucchini yellow mosaic virus (ZYMV) were aimed in cucurbit growing areas in Tekirdağ province. Additionally, comparison of virus isolates in order to reveal genetic identities were also aimed. Leaf samples of cucurbits plants with viral infection symptoms were collected during surveys in 2017 and 2019, and tested by ELISA to determine ZYMV, WMV and PRSV-W, and of tested 180 plant samples only 4,44% were found infected by WMV 30 of collected 180 plant samples that found positive or with typical viral infection symptoms were tested using CP gene region for ZYMV and PRSV-W, and NIb-CP gene region for WMV specific primers by Real time PCR and RT PCR, respectively. 12 of 30 selected plant samples showed about 408 nucleotides bands in agarose gel of WMV using RT-PCR. Sequence analysis revealed 342 and 348 nucletides of 12 isolates of WMV from Tekirdağ. Sequences were registered and deposited in GenBank and used for phylogenetic analysis and compared to WMV isolates available in GenBank. Sequence analysis of WMV NIb-CP gene coding 342 nucleotides obtained in this study, 8 of 12 isolates determined in this study namely TR-Tn2 (MT448602), TR-Tn5 (MT448603), TR-Tn8 (MT448604), TR-Tn9 (MT448605), TR-Tn10 (MT448606), TR-Tn18 (MT448607), TR-Tu75 (MT448612) and TR-Tu80 (MT448613) showed 99.7-95% identity with isolates from Italy (EU660590), France (NC_006262 and JF273459), Turkey (EU660579), Chile (EU660582) and Pakistan (AB218280) and grouped in WMV molecular Group 1. 4 of 12 isolates sequence analysis of WMV NIb-CP gene coding 348 nucleotides, determined in this study namely TR-Tf50 (MT448610), TR-Ta63 (MT448608), TR-Ta64 (MT448609) and TR-Ts71 (MT448611) showed 98,2-92.2% identity with isolates from South Korea (AB369278), China (EF127832 and DQ399708), South Korea (MN854651) and Japan (AB353119), and grouped in WMV Molecular Group 3.
Açıklama
Anahtar Kelimeler
Biyoteknoloji, Biotechnology, Genetik, Genetics, Ziraat, Agriculture, Dizi analizi, Sequence analysis, Kabak sarı mozaik virüsü, Zucchini yellow mosaic virus, PCR, ; RNA virüsleri, RNA viruses
