Complete Genome Sequence of Turnip yellows polerovirus from Iraq: Insight into the Factors Affecting the Genetic Variability of TuYV Populations

Abstract

Turnip yellows virus (TuYV), is one of the most important viruses belonging to the Polerovirus genus. Incidence, genetic variability, and population structure of TuYV have not yet been studied in mid-Eurasia Iraq. Different brassica fields in Babylon, Basrah, Najaf, and Qadisiyeh provinces of Iraq were surveyed for TuYV infection. A total of 149 symptomatic leaf samples were checked for TuYV infection using reverse transcription polymerase chain reaction (RT-PCR). Furthermore, total RNA from three symptomatic rapeseed (Brassica napus) leaf samples from Basrah-Iraq was used for RNA-Seq. The diversity and population structure of TuYV and the evolutionary forces that shape these populations have been considered. High prevalence infections (52.34%) of TuYV were detected in surveyed fields. An Iraqi isolate was fully sequenced and showed the highest identity 92.68% to a Swedish isolate. Full genome sequences indicated two main phylogroups, however, using ORF0, TuYV isolates clustered in four clades. Clade I was further divided into two subclades (IA and IB), where the Iraqi isolate fell into IB. The recent distribution of TuYV populations in GI and GIII can be inferred from high haplotype diversity and low genetic differentiation. The Fst and Nm values indicate that the gene flow was low, thus the opportunity for divergence in populations via genetic drift is enhanced. By selective pressure, it was found that amino acid substitutions also contribute to TuYV evolution. This is the first evidence of the TuYV full genome sequence in mid-Eurasian Iraq and highlights the importance of recombination and selection pressure in the evolution of TuYV. Analysis of these variations is necessary for making advances in control strategies of viral diseases to prevent their spread.

Keywords

• full genome
• Iraq
• molecular analysis
• Turnip yellows virus