Mapeamento do sinal temporal ao longo de sequências de DNA-A do tomato severe rugose virus

Abstract

The genus Begomovirus (family Geminiviridae) constitutes one of the most diverse groups of plant viruses. They are known for their wide host range among dicotyledonous plants and are transmitted through a complex of cryptic species of whiteflies referred to as Bemisia tabaci. Populations of begomoviruses evolve rapidly through mechanisms of mutation, recombination, and pseudorecombination. The tomato severe rugose virus (ToSRV) causes significant damage to Brazilian tomato crops, especially in the central and southern regions of the country. Given the importance of ToSRV, this work aimed to analyze the temporal structure across their DNA-A sequences available from Genbank, obtained from viral isolates collected between 2000 and 2018. Additionally, the study aimed to quantify the impact of recombination events on the calibration of the molecular clock. To achieve this, a meticulous data curation process was carried out to obtain information on viral isolates such as collection location, host, and sampling date. Temporal signal evaluation analyses were conducted based on two primary datasets: the first including all DNA-A sequences, even duplicated ones, and the second maintaining only one representative isolate of each viral haplotype. Furthermore, multiple sequence alignments were also subjected to an automated refinement step. The alignments were sliced into sliding windows of 100, 200, and 300 nucleotides (nt) in length, with steps of 10, 20, and 30 nt, respectively. Root-to-tip linear regression analyses between the genetic distances and sampling dates of viral isolates were conducted using the TreeTime program. Overall, little temporal signal was observed throughout the DNA-A sequences of ToSRV, except for two segments within the coding regions of the central portion of the CP protein and the C-terminal portion of the Rep protein. It was concluded that subjecting the alignments to a preliminary refinement step improves the quality of results and that maintaining only one representative of each haplotype set invariably led to the same results as those alignments with duplicated sequences. Additionally, it was also observed that the occurrence of recombination events affects not only the intensity of the temporal signal but also the distribution pattern of R2 values calculated from root-to-tip linear regression analyses across DNA-A sequences of ToSRV.