Genetic variability and evolutionary dynamics of tomato black ring virus population

Abstract

Tomato black ring virus (TBRV) is an important pathogen infecting a wide range of plant species worldwide. Phylogenetic studies of TBRV have already been conducted, although limited by the use of short genomic regions or a reduced amount of isolates.In the present study, we carried out an exhaustive phylogenetic and population genetic analysis based on the coat protein gene (CP) sequence of 57 TBRV isolates originating from different host plants and European geographic regions (47 isolates from Poland, 8 from Lithuania, one from the UK, and one from Hungary). Moreover, the selective pressure acting on particular codons and coevolution of amino acid residues in the CP were analysed. The results clearly showed that the TBRV population is being shaped by recombination and both positive and purifying selection. The analyses revealed that the placement of TBRV isolates in the phylogenetic trees was nonrandom, with isolates clustering according to host plant families and geographic origin.

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

“…More evidence for recombination was found within RNA1 than in RNA2 and multiple events (seven from the eight isolates of TBRV/BRSV) were more common than single events. This mirrors the findings of Budzyńska et al (2021) who found that intraspecies recombination was common in TBRV and suggested it is likely to be a major mechanism shaping TBRV populations. In contrast with the two earlier studies, we also found interspecies recombination.…”

“…As previously noted for TBRV by Zarzyńska‐Nowak et al (2020) and Budzyńska et al (2021) and in our analysis using RDP4, considerable intraspecies recombination was identified within the genomes of both TBRV and BRSV. For TBRV, there was intraspecies recombination within 6 of 15 isolates for RNA1 and 5 of 15 isolates for RNA2.…”

“…Due to the high frequency of recombination present, instead of full virus genomes, the two fragments of RNA2 unaffected by recombination (P1 region, nucleotides [nt] 1–477 of the CP and the P2 region, nt 478–1533 of the CP gene) described previously (Budzyńska et al, 2021) were used for phylogenetic analysis. The evolutionary history was inferred by using the maximum‐likelihood method based on the Jukes–Cantor model (Jukes & Cantor, 1969).…”

“…Phylogenetic analysis of the CP sequences of 12 TBRV isolates from Lithuania indicated isolates that were more similar to isolates from Poland than to isolates from the UK (Šneideris & Staniulis, 2014). More recently, phylogenetic analysis of nonrecombinant regions of the CP gene of TBRV isolates clustered sequences based on the geographical locations of the original isolation hosts, although only isolates from four countries were available for analysis (Budzyńska et al, 2021).…”

Forty-year-old beet ringspot virus isolate: tests for potato true seed transmission, genome sequencing, recombination analysis and phylogenetic placement

“…Because recombination occurs commonly in complete TBRV and BRSV genomic sequences, two non-recombinant portions of its RNA2 CP gene (P1 nts 1 to 477, and P2 nts 478 to 1533) were used in recent phylogenetic comparisons involving these two viruses (Budzyńska et al 2021;Fowkes et al 2022). The P1 and P2 nt sequence portions of isolate IF were compared with those of the same 15 TBRV or BRSV isolates included previously in the comparison of Fowkes et al (2022).…”