Genetic variability of Polish tomato black ring virus isolates and their satellite RNAs

Abstract

Tomato black ring virus (TBRV), a member of the Nepovirus genus, is a serious plant pathogen distributed worldwide. It causes significant damage to several economically important crops, such as artichoke or strawberry. The TBRV bipartite genome consists of two polyadenylated single‐stranded positive‐sense RNA molecules, which may be accompanied by subviral particles such as defective interfering RNAs (DI RNAs) and satellite RNAs (satRNAs). In this study, we obtained the complete genome sequence of six TBRV isolates originating from different hosts and determined the presence of eight TBRV satRNAs. Subsequently, genetic variability, recombination, phylogenetic and selection pressure analyses were performed. The results revealed that the TBRV population is genetically diverse. The occurrence of potential recombination events, evidence of positive selection pressure acting on particular codons and the diversification of satRNAs within the TBRV population indicated that the virus mutates and can rapidly adapt to new environmental conditions or hosts. The presented data shed some light on TBRV evolutionary dynamics and epidemiology.

Historical and recent tomato black ring virus and beet ringspot virus isolate genomes reveal interspecies recombination and plant health regulation inconsistencies

“…In previous studies to ours (Hemmer et al, 1987; Zarzyńska‐Nowak et al, 2020), satellite RNAs were found to be commonly associated with the genomes of TBRV and BRSV. The study by Zarzyńska‐Nowak et al (2020) working on TBRV isolated in Poland identified satellite RNAs in 8 of 10 isolates from a range of different plant species, finding them to be associated rather commonly.…”

Genetic variability and evolutionary dynamics of tomato black ring virus population

“…The genome structure consists of two linear single‐stranded positive‐sense RNAs: RNA1 and RNA2. Both RNAs show some flexibility in size (depending on particular isolates), with approximately 7,400 and 4,500 nucleotides (nt) for RNA1 and RNA2, respectively (Zarzyńska‐Nowak et al, 2020). The TBRV genome contains two open reading frames (ORFs, one per RNA strand) surrounded by 5′ and 3′ untranslated regions (UTRs) with the small VPg protein attached at the 5′ end and a poly(A) tail at the 3′ end of the RNA molecules.…”

“…Previous research indicated that ORF1 (RNA1) encodes mostly nonstructural peptides responsible for virus replication and genome expression, whereas ORF2 (RNA2) encodes structural proteins involved in virion formation and movement (Digiaro et al, 2015). For some of the TBRV isolates, the presence of additional, subgenomic particles like satellite RNAs (satRNA) or defective RNAs (D RNA) has been observed (Budzyńska et al, 2020; Hasiów‐Jaroszewska et al, 2012, 2018; Rymelska et al, 2013; Zarzyńska‐Nowak et al, 2020). These particles are relatively short, noninfectious and their replication, encapsidation, and spread depend on the helper virus.…”

“…The presence of satRNAs has also been confirmed for some of the TBRV isolates. TBRV satRNAs consisted of 1,374 nt and did not show sequence similarity with the helper virus genome (Zarzyńska‐Nowak et al, 2020). The effect of satRNAs on TBRV replication and accumulation has not been established yet.…”

“…Similarly, Lithuanian isolates tend to cluster into two groups and the level of genetic diversity among them ranges from 78.2% to 97.6% (Šneideris & Staniulis, 2014). The latest study performed by Zarzyńska‐Nowak et al (2020) included the full genomes of nine Polish isolates as well as sequence of TBRV‐Mirs isolate available in GenBank (Digiaro et al, 2015). The analyses showed that nucleotide sequence identity of ORF1 and ORF2 ranged from 87.5% to 100% and from 89.4% to 99.9%, respectively.…”