Population structure and genetic diversity of tobacco mild green mosaic virus variants in Western Anatolia of Turkey

Abstract

Tobamoviruses have been pioneers in understanding the population genetic structure, host-vector interactions, and evolutionary processes of viruses. To better understand the population genetic structure and molecular evolutionary relationships of tobacco mild green mosaic virus (TMGMV), a significant species of tobamoviruses, extensive analyses were performed using bioinformatics tools in this study. 300 samples were collected from plants exhibiting viruses and virus-like symptoms from Turkey's largest tobacco cultivation areas during the plant vegetation period between 2019 and 2020. Samples were tested using conventional molecular techniques for tobamoviruses, including ToBRFV, TMV, TMGMV, ToMV, and ToMMV species. Single and double tobamovirus infections were determined in 258 of 300 samples. Single infections were 225 (75%), 10 (3.33%), and 1 (0.33%) for TMGMV, TMV, and ToMV, respectively. Double infections were 21 (7.0%) and 1 (0.33%) for TMGMV + TMV and TMV + ToMV, respectively. TMGMV-infected samples from each region were chosen, and their complete genomes were revealed. Detailed analyses were carried out from Turkey, with global variants available in GenBank. Molecular evolutionary analyses revealed three main lineages (Clades I, II, and III) at the p126, p183, MP, and complete genome levels and two main lineages at the CP gene (Clades I and II). Variants from Turkey were distributed in two different branches in other phylogenetic trees, except for the CP gene. High haplotype diversity and low nucleotide diversity were determined in each gene region, indicating consistent genetic stability. In addition, purifying selection pressures were determined in specific gene regions. With AMOVA (analysis of molecular variance), it was determined that the source of genetic variation came from within the main lineages, including various hosts and geographies. The differences in lineages were confirmed by independent test statistics. While neutrality tests revealed population expansions in the CP and MP genes, other p183 and p126 genes revealed bottlenecks or balancing selection. The fact that TMGMV was more common than TMV in Turkey strongly supported the phenomenon called “mutational melting” or “Müller latch,” which presumably causes TMV to disappear from its niche.