GENETIC DIVERSITY, PHYLOGENETIC RELATIONSHIPS AND RECOMBINATION SIGNAL IN THE COAT PROTEIN GENE OF CITRUS TRISTEZA VIRUS ISOLATES FROM PAKISTAN

Abstract

Citrus tristeza virus (CTV Closterovirus genus, Closteroviridae) is a virus that is one of the most economic diseases of citrus worldwide. In this study, the coat protein (CP) gene of ten Pakistani CTV field isolates (Haripur, Fatehjang, Islamabad ×2, Nowshera, Sawabi, Faislabad, Sargodha and Khanpur) was retrieved from GenBank and analysed alongside a comparative reference panel comprising two additional CTV CP sequences, five CTV ORF1a genotype-marker fragments (genotypes B3 and D1–D4). Five citrus host EST cDNA sequences and representative sequences of three other citrus infecting viruses (Citrus leaf blotch virus, Citrus bright spot virus and Citrus leprosis virus N) for a total of 31 raw GenBank records. Sequences were aligned with MAFFT trimmed to a 456 nucleotide informative block using BMGE and the resulting alignment was used to build a max likelihood tree with PhyML. A recombination detection algorithm based on a genetic algorithm (GARD) suggested a single recombination breakpoint at position 259 of the alignment with a low AICc score of 1197.25 compared to a single tree model and 696 candidate topologies screened. It meaning the different parts of the analysed sequence have evolved differently. The pairwise identity between the ten Pakistani isolates was observed between 90.8% to 99.8% and there was no indication of a single tight monophyletic cluster in the ML tree suggesting co circulation of divergent CTV genotypes in Pakistan.