Insight into Population Structure and Evolutionary Analysis of the Emerging Tomato Brown Rugose Fruit Virus

Abstract

A total of 112 symptomatic tomatoes (Solanum lycopersicum L.) and 83 symptomatic pepper (Capsicum spp.) samples were collected in Ankara, Eskişehir, Bartın, and Zonguldak provinces of Turkey during 2020–2021. Six tomatoes and one pepper sample (3.6%) tested positive for tomato brown rugose fruit virus (ToBRFV, genus Tobamovirus) infection by DAS-ELISA and RT-PCR. ToBRFV-positive tomato and pepper plants were removed from greenhouses as soon as possible, and the greenhouses and tools were disinfected completely. Phylogenetic analysis on the complete CP sequences suggested the clustering of 178 GenBank isolates and 7 novel isolates into three groups. A study using DnaSP software showed very low genetic variation among current global ToBRFV isolates. All four ORFs of the virus genome were under strong negative evolutionary constraints, with a ω value range of 0.0869–0.2066. However, three neutrality tests indicated that most populations of the newly identified ToBRFV are currently expanding by assigning statistically significant negative values to them. The very low FST values (0.25 or less) obtained by all comparisons of the isolates from Europe, the Middle East, China, and America concluded that there is no clear genetic separation among currently known isolates from different geographic origins. The divergence time of ToBRFV was estimated to be in the middle of the course of the evolution of 11 tested tobamoviruses. The time to the most recent common ancestors (TMRCAs) of ToBRFV were calculated to be 0.8 and 1.87 with the genetically closest members of Tobamovirus. The results of this study could improve our understanding on the population structure of the emerging ToBRFV.

Molecular Analysis of the Global Population of Potato Virus S Redefines Its Phylogeny, and Has Crop Biosecurity Implications

“…When genetic variation results in functional gain, the high frequency of mutation, recombination, and reassortment that occurs in viral genomes encourages generation of novel forms that quickly spread across the viral population [ 24 ]. Therefore, to control viral pathogens effectively, it is important to understand virus population structure and assess its diversity [ 25 , 26 ].…”

Genetic diversity and population structure of tomato brown rugose fruit virus (ToBRFV) variants from Antalya province, Turkey

“…Similarly, very low genetic variation has been reported in TMGMV, one of the important species of tobamoviruses (Karanfil et al, 2023). Furthermore, studies to reveal the genetic diversity and population structure of ToBRFV are very limited (Çelik et al, 2022;Abrahamian et al, 2022). In addition, many of the sequenced ToBRFV genomes were obtained from the Netherlands (van de Vossenberg et al, 2020).…”