Publications - Faculty - Recently Submitted Faculty Publications 2009
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Brlansky - Journal of Virology
Complete Sequence and Comparative Genome Analysis Reveal a Novel Citrus Tristeza Virus Genotype: Genetic Divergence and Evidence for Natural Recombination
Avijit Roy and R. H. Brlansky
Abstract -Sequence variation of an Indian Citrus tristeza virus (CTV) isolate B165 was compared to the three well known CTV genotypes namely T36, T30 and VT. The genome of the predominant component of CTV-B165 was 19247 nt in length with 12 open reading frames (ORFs) and was structurally identical to the other CTV isolates. All the completely sequenced CTV isolates were 2-55 nt longer than the CTV-B165 except the VT isolate. In comparison to the other fully sequenced CTV isolates, CTV-B165 had nucleotide identity of 72-86% in ORF1 and 92-99% in ORFs 2 to 11. The predicted RNA secondary structure by MFOLD in CTV-B165 showed a discrete folding in comparison to the other CTV isolates in the 5´-UTR. Sequence data of independent overlapping clones from the CTV-B165 genome showed highly divergent sequences of the overlapping region of 5´-UTR and ORF1a, the inter-domain region of ORF1a and the partial regions of ORF2. Phylogenetic analysis of informative five domains of ORF1a, ORF1b and ORF2 revealed that CTV-B165 isolate distinctly segregates from the existing three genotypes in the dendrograms and was supported by high bootstrap values and robust tree topology. The PHYLPRO graphical analysis of the above mentioned three regions showed strong to weak recombination signals with significant correlation values. Collectively, the statistical data and recombination analysis suggest that the observed CTV-B165 genotype variation is an outcome of inter genotype recombination that might be evolved from VT and T30 genotypic ancestral isolates.
