Unusual Sequence Relationships Between Two Isolates of Citrus Tristeza Virus

Abstract

The complete, 19226 nt sequence of the RNA genome from VT, a seedling yellows strain of citrus tristeza virus (CTV), was determined and found to have a genome organization identical with that of the previously determined CTV-T36 isolate, except that ORF 1 of CTV-VT was 70 nt shorter due to two widely separated 18 nt deletions. Sequence comparison of CTV-VT and CTV-T36 revealed approximately 89% identity throughout the ten 3' ORFs, but only 60-70% identitythroughout ORF 1. The 5' nontranslated regions were only 60% identical whereas the 3' nontranslated regions were 97% identical. The transition between regions of similarity and deviation was gradual, suggesting that the sequence similarities and differences compared to CTV-T36 were unlikely to have arisen from a recent recombination event between a close T36 relative and a distantly related CTV isolate. This is the first attempt to compare in detail the variation between the genomes of two strains of a member of the closterovirus group. The observed deviation between the large RNA genomes of the two CTV strains is greater than that among different viruses of most other groups, raising the question of how to define the taxonomy of these viruses.

Comparison of multiple viral population characterization methods on a candidate cross-protection Citrus tristeza virus (CTV) source

“…The establishment of a threshold regarding the presence/absence of a genotype remains vexing as reads from the Illumina data mapped back to every one of the reference genomes, but PCR results only confirm the presence of 4 different genotypes. This may be explained by the fact that some regions of the genome are conserved amongst strains (Mawassi et al, 1996) and that mapping of small fragments can occur with all of these regions. The BLAST results from the contigs obtained from the immuno-capture enriched template with de novo assembly also confirmed the presence of RB and VT, in addition to the HA16-5 genotype, and a contig similar to the CT14A strain which is most closely related to the B165 genotype.…”

“…The 3" half of the 19.3kb RNA genome (Albiach-Marti et al, 2010;Bar-Joseph, Marcus, and Lee, 1989) is generally conserved amongst sources, whereas the 5" half is much more divergent (Mawassi et al, 1996). The virus is classified into a number of genotypes based on sequence diversity.…”

“…The virus is classified into a number of genotypes based on sequence diversity. The acknowledged genotypes of CTV are continually being expanded, and thus far include T36, T30, T3, VT, B165, HA16-5, T68 and RB (Albiach-Marti et al, 2000;Harper, Dawson, and Pearson, 2010;Harper, 2013;Karasev et al, 1995;Mawassi et al, 1996;Melzer et al, 2010;. The CTV population of a single host may contain many different genotypes as the longevity of citrus plants allows for repeated infections of various CTV sources through aphid transmission (Rubio et al, 2001).…”

A cDNA clone from a defective RNA of citrus tristeza virus is infective in the presence of the helper virus.

“…75-85 nm, is encapsidated by p27, a diverged coat protein (CPd) (Febres et al, 1996). The CTV particles contain a single component positive-stranded genomic RNA, of 19 296 nt for the T-36 strain from Florida and of 19 226 nt for the Israeli strain VT (Mawassi et al, 1996). The genomes of these strains showed considerable Author for correspondence : Moshe Bar-Joseph.…”

“…The CTV particles contain a single component positive-stranded genomic RNA, of 19 296 nt for the T-36 strain from Florida and of 19 226 nt for the Israeli strain VT (Mawassi et al, 1996). The genomes of these strains showed considerable Author for correspondence : Moshe Bar-Joseph.Fax j972 3 9604180. e-mail vpmbj!volcani.agri.gov.il sequence deviation within the 5h half, but were found to have similar organization and to encompass 12 ORFs, which potentially code for at least 17 protein products, including the replication associated proteins, a homologue of the HSP70 proteins and the two coat proteins Mawassi et al, 1996). In addition to the genomic and subgenomic RNAs plants infected with CTV contain multiple species of defective RNAs (D-RNAs).…”