Nucleotide heterogeneity at the terminal ends of the genomes of two California Citrus tristeza virus strains and their complete genome sequence analysis

Authors: CHEN, ANGEL - University Of California; WATANABE, SHIZU - University Of California; Yokomi, Raymond - Ray; NG, JAMES - University Of California

Submitted to: Virology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/13/2018
Publication Date: 9/15/2018
Citation: Chen, A.Y., Watanabe, S., Yokomi, R.K., Ng, J.C. 2018. Nucleotide heterogeneity at the terminal ends of the genomes of two California Citrus tristeza virus strains and their complete genome sequence analysis. Virology Journal. 15(1):141. https://doi.org/10.1186/s12985-018-1041-4.
DOI: https://doi.org/10.1186/s12985-018-1041-4

Interpretive Summary: Development of innovative methods to control difficult agricultural problems can contribute significantly to sustainable agriculture. One method, using recombinant technology, converts a citrus virus to express and confer specific control elements against other citrus pests. To this end, research was conducted to identify gene sequences of Citrus tristeza virus (CTV) that will be used to design methods to incorporate genes into infectious clones of CTV that provide therapies against specific pests. The infectious cloned virus can then be used to inoculate existing citrus to help protect them against that pest. This strategy is compatible with other pest management strategies providing growers with another weapon to enhance a sustainable and environmentally-friendly pest management strategy against specific pests.

Technical Abstract: Terminal, non-translated regions of RNA viruses serve diverse functions and exhibit various levels of nucleotide (nt) heterogeneity. This study characterized termini diversity of two California Citrus tristeza virus (CTV) genotypes, T36-CA and T30-CA. The terminal nts were identified by sequencing cDNA clones of + and – strands of viral double-stranded (ds)RNAs generated by 5' and 3' rapid amplification of cDNA ends. Cloned cDNAs corresponding to the complete genome sequences of both virus strains were generated using reverse transcription-polymerase chain reactions, sequenced, and subjected to phylogenetic analysis. Among the predominant terminal nts identified, some were identical to consensus sequences in GenBank, while others were unique. Remarkably, one of the predominant 5' nt variants of T36-CA contained the consensus nts “AATTTCAAA” in which a highly conserved cytidylate, seen in all other full-length T36 sequences, was absent. As expected, unique variants with additional nt(s) incorporated upstream of the 5' terminal consensus nts of T36-CA and T30-CA also were identified. In contrast to the extreme 5' terminal nts, those at the extreme 3' termini of T36-CA and T30-CA were more conserved compared to the reference sequences, although variants also were found. Notably, an additional thymidylate at the extreme 3' end was identified in many T36-CA sequences. Finally, based on pairwise comparisons and phylogenetic analysis with multiple reference sequences, the complete sequences of both viruses were found to be highly conserved with those of the respective genotypes. In summary, the extreme terminal nts in the T36-CA and T30-CA genomes were identified, revealing new insights on heterogeneity of these CTV genomic regions.