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Table 1 Nucleotide variations at the extreme termini in the genome of CTV with the T36-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 seven nt variants were identified by sequencing cloned DNA corresponding to the 5′ end of the T36-CA genome. In comparison with the T36 consensus genomic 5′ end nt sequences (black colored), the nt variants of T36-CA were found to contain extra/variant nt (s) (red colored nts). Group 1 nt variants (variants 1 to 3) (unshaded box) have consensus 5′ nt sequence “AATTTCTCAA” identical to that of T36 isolate FS674 (GenBank accession no. KC517485) and FS703 (GenBank accession no. KC517487). Group 2 nt variants (variants 4 to 7) (shaded box) have consensus 5′ nt sequence “AATTTCAAA” similar to that (“AATTTCACAA”) of the T36 sequences (GenBank accession nos. EU937521 and AY170468), except that it does not contain a “C” at position 8. The number of clones for each nt variant sequenced are as indicated
  2. bThe 5′ end nts of the T36-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 T36-CA genome was determined 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 4 nt variants were identified by sequencing cloned (+)-DNA (generated by 3′ RACE) corresponding to the 3′ end of the T36-CA genome. The T36 consensus genomic 3′ end nts (black colored) and the T36-CA nt variants (red colored) are as shown. The number of clones for each nt variant sequenced are as indicated