Research towards elucidation of the complete genome of grapevine deformation virus (GDefV) isolates in Turkey
Küçük Resim Yok
Tarih
2022
Yazarlar
Dergi Başlığı
Dergi ISSN
Cilt Başlığı
Yayıncı
Niğde Ömer Halisdemir Üniversitesi
Erişim Hakkı
info:eu-repo/semantics/openAccess
Özet
Bu araştırmada, Nevşehir ve Niğde bağlarında Grapevine deformasyon virüsünün (GDefV) yaygınlığının belirlenmesi ve virüs izolatlarının tüm genom varyasyonunun araştırılması amaçlanmıştır. Nevşehir ve Niğde bağlarından, Haziran-Temmuz 2020'de, toplam 150 adet simptomatik asma örneği toplanmıştır. Test edilen asma örnekleri arasında GDefV genel enfeksiyon oranı %14 olarak belirlenirken, enfeksiyon oranı Niğde'de %18 ve Nevşehir'de %12 olmuştur. Daha önce illumina sekanslama teknolojisi ile sekanslanmış iki asma verisi (örnek 105 ve 107), GDefV'nin tam RNA1 ve RNA2 genomlarını sağlamak için biyoinformatik araçlar olan CLC Genomic Workbench 11 ve Geneious Prime yazılımı ile araştırılmıştır. 105 ve 107 GDefV izolatı RNA2 tam dizileri, sırasıyla referans izolatı GDefV ile %91 ve %90 benzerliği paylaşırken birbiriyle %96 benzerlik göstermiştir. Örnek 105 ve 107 RNA2 sonuç dizilerinde Nepovirüs alt grup A poliproteini, Nepovirüs kılıf proteini domainleri olan N-terminal domain, merkezi domain ve C-terminal domain belirlenerek GDefV RNA2 sonuç dizileri doğrulanmıştır. Elde edilen bilgiler, hem virüs genomik bilgisine hem de asmayı enfekte eden viral ajanlar literatürüne daha fazla GDefV izolatının tam genom bilgisinin eklenmesine katkıda bulunmuştur.
In this research, the main objective consists of determination the prevalence of Grapevine deformation virus (GDefV) in Nevşehir and Niğde vineyards, and elucidation of the genomic variation of the virus isolates. Totally 150 symptomatic grapevine samples was collected from Nevşehir and Niğde vineyards in June-July 2020. The overal GDefV infection rate was 14% among the tested grapevine samples, and the infection rate was 18% in Niğde and 12% in Nevşehir. Two grapevine samples (sample 105 and 107) sequenced previously with illumina sequencing technology were investigated for providing the complete RNA1 and RNA2 genomes of the GDefV by bioinformatics tools CLC Genomic Workbench 11 and Geneious Prime software. The 105 and 107 GDefV isolate RNA2 complete sequences were identical 96% to each other while sharing the identity of 91% and 90% with the reference isolate GDefV, respectively. We provided Nepovirus subgroup A polyprotein, Nepovirus coat protein N-terminal domain, central domain and C-terminal domain in sample 105 and 107 RNA2 consensus sequences validating the GDefV consensus sequences. This information is the exclusive in that, it contributes both to virus genomic information and to the addition of more GDefV isolates complete genome information to the literature of viral agents infecting vine.
In this research, the main objective consists of determination the prevalence of Grapevine deformation virus (GDefV) in Nevşehir and Niğde vineyards, and elucidation of the genomic variation of the virus isolates. Totally 150 symptomatic grapevine samples was collected from Nevşehir and Niğde vineyards in June-July 2020. The overal GDefV infection rate was 14% among the tested grapevine samples, and the infection rate was 18% in Niğde and 12% in Nevşehir. Two grapevine samples (sample 105 and 107) sequenced previously with illumina sequencing technology were investigated for providing the complete RNA1 and RNA2 genomes of the GDefV by bioinformatics tools CLC Genomic Workbench 11 and Geneious Prime software. The 105 and 107 GDefV isolate RNA2 complete sequences were identical 96% to each other while sharing the identity of 91% and 90% with the reference isolate GDefV, respectively. We provided Nepovirus subgroup A polyprotein, Nepovirus coat protein N-terminal domain, central domain and C-terminal domain in sample 105 and 107 RNA2 consensus sequences validating the GDefV consensus sequences. This information is the exclusive in that, it contributes both to virus genomic information and to the addition of more GDefV isolates complete genome information to the literature of viral agents infecting vine.
Açıklama
Fen Bilimleri Enstitüsü, Tarım Bilimleri ve Teknolojileri Ana Bilim Dalı
Anahtar Kelimeler
Ziraat, Agriculture
