Prevalence of severe Citrus tristeza virus infection in Khasi mandarin throughout the north-eastern states of India: an evidence study based on coat protein gene analysis

Abstract

Citrus tristeza virus (CTV) infected plant samples from the North Eastern states of India namely Arunachal Pradesh (AR1), Assam (AS1), Nagaland (NL1), Meghalaya (M1), Sikkim (SK1) and Tripura (TR1) were examined through double antibody sandwich enzyme linked immunosorbent assay and reverse transcriptase polymerase chain reaction using coat protein (CP) gene specific primers, yielding amplicon of 672 base pair for all the isolates. The sequence analysis revealed nucleotide (nt) and amino acid (aa) sequence similarity with other exotic CTV isolates. AR1 and AS1 shared similarity with T3 isolate (Florida) at 98–99% and 95–99% for nt-aa respectively, whereas, M1 showed 99% similarity with stem pitting isolate B165 (Bangalore). SK1 and NL1 were 95–97% and 97–99% similar with Hawaiian isolate HA at nt-aa level. TR1 showed 97% homology with seedling yellowing Israeli isolate VT. The CP gene sequence based phylogenetic analysis grouped present isolates into four clades with reference severe isolates (i.e. VT, B165, HA and T3), indicating their probable evolution. TR1 and NL1 are the putative recombinant isolates and ASI and SK1 were the major and minor parents respectively. This might be due to the conserved nature of CP gene. Moreover, the CP gene sequences of present isolates showing nucleotide identity to the VT, T3 and B165 isolates also suggest the prevalence of severe CTV isolates in Khasi mandarin growing areas comes under North East (NE) region of India.