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Table 2 Nucleotide variations at the extreme termini in the genome of CTV with the T30-CA genotype

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

  1. aThe extreme 5′ end sequences of three nt variants were identified by sequencing cloned DNA corresponding to the 5′ end of the T30-CA genome. The consensus (black colored) nts located at the 5′ ends of other T30 sequences (GenBank accession nos. KC517489, KC517490, KC517491 and AF260651) were identified in the population of T30-CA in addition to nt variants with an extra nt (“C”, in red). The number of clones for each nt variant sequenced are as indicated
  2. bThe 5′ end nts of the T30-CA genome was determined by sequencing the (+)-DNA generated by 5′ RLM-RACE using the (+)-strand of dsRNA as a genetic template for reverse transcription (RT) and PCR amplification
  3. cThe 5′ end nts of the T30-CA genome was determined by sequencing the (−)-DNA generated by 3′ RACE using the (−)-strand of dsRNA as a genetic template for reverse transcription (RT) and PCR amplification
  4. dThe extreme 3′ end sequences of three nt variants were identified by sequencing cloned (+)-DNA (generated by 3′ RACE) corresponding to the 3′ end of the T30-CA genome. The conserved consensus nts and the variant nts are indicated in black and red, respectively. The number of clones for each nt variant sequenced are as indicated