Frequency of occurrence and genetic variability of Grapevine fanleaf virus satellite RNA

Abstract

Little is known about the natural occurrence and genetic variability of nepovirus large satellite RNA (satRNA). This study screened 71 Grapevine fanleaf virus (GFLV) isolates mainly from Slovenia, but also from other countries in Europe and the USA, for the presence of satRNA, using a newly developed RT-PCR assay. GFLV satRNA (satGFLV) was detected in 72% of naturally GFLV-infected grapevines analysed, which is the highest frequency of occurrence of sat-GFLV reported to date. From 39 naturally GFLV-infected grapevines, 122 satGFLV clones were sequenced and compared to publicly available sequences of satGFLVs and the closely related satRNAs from Arabis mosaic virus (satArMVs). Phylogenetic analyses of these satRNAs revealed that their evolution was driven by substitutions, insertions, deletions, recombinations and reassortments between closely related helper viruses. Phylogenetic relationships of the satGFLVs and satArMVs show their separate and subsequent common evolution. Furthermore, the satGFLVs varied in size and showed higher variability at the amino acid level than at the nucleotide level, just as the 2AHP gene of their helper virus. This study shows that satGFLVs are also similar to their helper virus with respect to their quasispecies nature and their transmission route through anthropogenic exchange of propagation material.

Metagenomic‐based impact study of transgenic grapevine rootstock on its associated virome and soil bacteriome

“…Similarly, 31 full‐length sequences of GFLV satRNA were obtained (GenBank accessions ‐). While all sequences clustered together (clade I, Figure S3a) compared to the known satellite diversity (Čepin et al ., ; Gottula et al ., ), no effect of the GM plants on the satRNA diversity and selection was observed, as confirmed by the absence of genetic structure between GM and WT populations (Figure S4a, F ST = −0.013; P = 0.645). As for GFLV RNA2, 44 complete sequences (GenBank accessions ‐) were assembled, alongside a total of 75 partial sequences spanning the 1515 bp of the cp .…”

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

“…Initially, previously-published (Fuchs et al 1989;Cepin et al 2016) primer pairs, Gsat191f/Gsat1005r and Fp3/Rp, were used for detection of GFLV satRNA in RT-PCR before designing new primers. Previously 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/).…”

“…GFLV satRNA was initially reported in GFLV isolate F13 which caused severe symptoms on Chenopodium quinoa (Pinck et al 1988). Later on, satRNA was also detected in other nepoviruses such as Arabis mosaic virus and Tomato black ring virus (Cepin et al 2016).…”

“…Some GFLV isolates have an extra RNA molecule known as satellite RNA (satRNA). SatRNAs are thought to be originated from similar helper viruses through mutation events such as deletion, insertion, recombination or reassortment (Cepin et al 2016). GFLV satRNA was initially reported in GFLV isolate F13 which caused severe symptoms on Chenopodium quinoa (Pinck et al 1988).…”

“…The large satRNAs usually encode nonstructural proteins. They all encode a protein which is necessary for the replication of satRNA associated with nepoviruses (Hu et al 2009;Cepin et al 2016). In contrast, the small satRNAs are highly structural and have internal base pairing.…”