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ARS Home » Pacific West Area » Parlier, California » San Joaquin Valley Agricultural Sciences Center » Crop Diseases, Pests and Genetics Research » Research » Publications at this Location » Publication #316394
Title: Nucleotide heterogeneity at the genomic 5’- and 3’-termini of California (CA) isolates of Citrus tristeza virus (CTV)

Author
item CHEN, ANGEL - University Of California
item WATANABE, SHIZU - University Of California
item Yokomi, Raymond - Ray
item NG, JAMES - University Of California

Submitted to: Phytopathology
Publication Type: Abstract Only
Publication Acceptance Date: 6/14/2015
Publication Date: 11/5/2015
Citation: Chen, A.Y., Watanabe, S., Yokomi, R.K., Ng, J.C. 2015. Nucleotide heterogeneity at the genomic 5’- and 3’-termini of California (CA) isolates of Citrus tristeza virus (CTV). Phytopathology. 105:S4.27.

Interpretive Summary:

Technical Abstract: Nucleotide (nt) sequences in the genomic ends of sense (+)-RNA viruses serve essential biological functions and are important considerations in the construction of infectious clones. Two isolates of Citrus tristeza virus (CTV) from California (CA) having a T30- and a T36-genotype were inoculated in Mexican lime and Madam Vinous, respectively. The termini of viral double-stranded (ds) RNAs were amplified by Rapid Amplification of cDNA-PCR and sequenced. Compared with the 5’-end nts in the most related sequence (GenBank KC517491), most of the T30-CA sequences had an extra A or G upstream of the first nt in the (+)-RNA and an extra C downstream of the last nt in the antisense (-)-RNA. The 3’ end sequences of T30-CA were mostly conserved, with a small number having one or two heterogeneous nts at the extreme ends. The 5’ end sequences of T36-CA were heterogeneous compared to that of a Florida (FL) T36 isolate (GenBank AY170468). More than 15 variations of nts were seen at the extreme 5’ end of the T36-CA sequences, most of which had an extra A upstream of the first nt in the (+)-RNA and an extra C downstream of the last nt in the (-)-RNA. Nucleotide heterogeneity was also observed in the 3’ end sequences of T36-CA - 45% of the 5’ end sequences in the (-)-RNA were identical to those of T36-FL, while 47.6% of the 3’ end sequences in the (+)-RNA had an extra T downstream of the last nt. These results were consistent with published reports of nt variations in CTV isolates from different hosts and locations.