Association of satellite RNA with Grapevine fanleaf virus in its geographical origin and sequence characteristics

Afsaneh Delpasand Khabbazi ,Nemat Sokhandan Bashir ,Shaheen Nourinejhad Zarghani

doi:10.15832/ankutbd.549511

Abstract

The region between The Caspian Sea and Black Sea has been hypothesized as the origin of grapevine. Likewise, an extensive study on Grapevine fanleaf virus (GFLV) from this region suggests this region as a possible origin of the virus. However, as yet there is no information as to whether or not the virus variants from this region accompanied with the virus satellite RNA (satRNA) and if so, how diverse theses satRNAs can be. To answer these questions, Grapevine fanleaf virus isolates were collected from different vineyards in the northwest region of Iran for the occurrence of the satellite RNA. A total of 421 samples including Vitis vinifera , Chenopodium quinoa , Chenopodium amaranticolor , Cynodon dactylis , Medicago sativa were initially screened against GFLV by RT-PCR with the coat protein primers (Cp433, Cp912). When the GFLV-infected plants (36 samples) were screened by RT-PCR with the newly designed satRNA primers Gf750 and Gr750, three samples appeared to possess the satRNA. The satellite cDNA fragments were cloned and sequenced and when the resulting data were compared with sequences of previously-reported satRNA of GFLV and Arabis mosaic virus (ArMV), 70–98% and 69–71% similarities were found, respectively. Phylogenetic studies revealed distinctness of the satRNAs from Iran. This may suggest coevolution of the satRNA with the helper virus because GFLV isolates from this region also form a distinct branch. Among previously reported corresponding satRNA sequences to those from Slovenia and South Central Europe were the closest. This study also reports C. amaranticolor as the natural host for GFLV, which was previously reported only as an experimental host.

Highlights

Grapevine fanleaf virus (GFLV) is responsible for one of the important diseases of grapevine (Vitis vinifera L.), fan leaf, worldwide and causes economic losses (Martelli & Boudon-Padieu 2006)
GFLV satellite RNA (satRNA) was initially reported in GFLV isolate F13 which caused severe symptoms on Chenopodium quinoa (Pinck et al 1988)
Reported GFLV satRNA sequences were retrieved from GenBank (Sequences which reported by Fuchs et al 1989; Liu et al 1990; Gottula et al 2013; Cepin et al 2016; Chiumenti et al 2016) and incorporated in the design of new primers (Table 1) by the use of Primer 3 software (Primer3web version 4.1.0, http://primer3.ut.ee/)

Summary

Introduction

Grapevine fanleaf virus (GFLV) is responsible for one of the important diseases of grapevine (Vitis vinifera L.), fan leaf, worldwide and causes economic losses (Martelli & Boudon-Padieu 2006). This virus has two genomic RNA molecules each coding for a viral polyprotein (Andret-Link et al 2004; Sokhandan Bashir et al 2009). Some GFLV isolates have an extra RNA molecule known as satellite RNA (satRNA). GFLV satRNA was initially reported in GFLV isolate F13 which caused severe symptoms on Chenopodium quinoa (Pinck et al 1988). SatRNA was detected in other nepoviruses such as Arabis mosaic virus and Tomato black ring virus (Cepin et al 2016)

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