Fig. 1From: Nucleotide heterogeneity at the terminal ends of the genomes of two California Citrus tristeza virus strains and their complete genome sequence analysiscDNA fragments corresponding to the genome of CTV with the T36-CA or the T30-CA genotype. a The genome organization of CTV. The numbered boxes (1a, 1b and 2 to 11) represent open reading frames (ORFs) and the proteins they encode (as indicated above or below the ORFs). RdRp, RNA-dependent RNA polymerase; CPm, minor coat protein; CP, major coat protein; and proteins named according to their predicted molecular weight, as indicated by the number (s) after the letter “p”. b To obtain the cDNA of the T36-CA genomic (g) RNA, the first strand cDNA (arrow with dotted line) was generated by reverse transcription (RT) using denatured T36-CA dsRNA and a reverse primer, CTV30-AC. The T36-CA 5′ fragment, corresponding to nucleotide (nt) position 1 to 8391, was PCR-amplified using primers CTV34-AC and CTV39-AC. The T36-CA 3′ fragment, corresponding to nt position 7800 to 19,292, was amplified using primers CTV38-AC and CTV35-AC. c The first strand cDNA of T30-CA (arrow with dotted line) was generated by the same method as described for T36-CA, using a reverse primer, CTV30-AC. Primers CTV32-AC and CTV37-AC were used to amplify the T30-CA 5′ fragment corresponding to nt position 1 to 8430, while primers CTV36-AC and CTV33-AC were used to amplify the T30-CA 3′ fragment (nt position 7584 to 19,259). Nucleotide sequences and other details of the primers (represented by solid arrows) used for generating the cDNA fragments are shown in Additional file 1: Table S1Back to article page