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

• Published in: Plants (Basel) Vol. 11; no. 23; p. 3279
• Main Authors: Çelik, Ali, Coşkan, Sevgi, Morca, Ali Ferhan, Santosa, Adyatma Irawan, Koolivand, Davoud
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 28-11-2022; MDPI
• Subjects: Analysis; Capsicum; Clustering; Crops; Diagnosis; Diseases and pests; Disinfectants; Divergence; divergence time; Environmental aspects; Epidemics; Evolution; evolutionary constraints; Fruits; Genetic aspects; Genetic diversity; genetic variation; Genomes; Greenhouses; Infections; Mutation; Peppers; phylogenetic analysis; Phylogenetics; Phylogeny; Physiological aspects; Plant diseases; Plant virus diseases; Plant viruses; Population; Population structure; Proteins; Quarantine; Seeds; Solanum lycopersicum; Statistical analysis; Tobamovirus; Tomatoes; Virus diseases of plants; Viruses; Netherlands; Iran; China; Germany; Turkey; divergence time; genetic variation; phylogenetic analysis; evolutionary constraints
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants11233279

A total of 112 symptomatic tomatoes (
L.) and 83 symptomatic pepper (
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
) 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
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
. The results of this study could improve our understanding on the population structure of the emerging ToBRFV.