Evidence of Recombinant Citrus tristeza virus Isolate Occurring in Acid Lime cv. Pant Lemon Orchard in Uttarakhand Terai Region of Northern Himalaya in India

Abstract

The present study for the first time describes biological and molecular characterization of Citrus tristeza virus (CTV) occurring in the Terai area of Uttarakhand State in Northern Himalaya region of India. Direct antigen coated-ELISA and reverse transcriptase-polymerase chain reaction (RT-PCR) detected the CTV infection in Acid lime cv. Pant lemon (Citrus aurantifolia) orchards of Pantnagar with an estimated disease incidence of 16.6-20.5 %. To know the biological and genetic properties, an isolate, CTV Pant 4 was characterized. Isolate Pant 4 could be graft transmitted to Kinnow, Nagpur and Darjeeling mandarins, Mosambi sweet orange, Kagzi lime, Sweet lime, Sour orange but not to Rough lemon. The sequence analyses of the 5 0 ORF1a (3038 nucleotides) of LPro domain and 3 0 end (2058 nt) covering ORF7-ORF10 regions of the CTV genome revealed that Pant 4 was closely related to the previously reported Indian CTV isolate, Kpg3 from Northeastern Himalaya region with 97 and 98 % sequence identity, respectively. Whereas, it differed from the previously reported CTV isolate B165 from Southern India with 79 and 92 % identity, respectively for 5 0 ORF1a and 3 0 end regions. Recombination and SplitsTree decomposition analyses indicated that CTV isolate Pant 4 was a recombinant isolate originating from Kpg3 as a major and B165 as a minor donor.

Citrus tristeza Virus Variants and their Distribution in Mandarin Orchards in Northeastern Himalayan Hill Region of India

“…Evidence for recombination events in the origin of many divergent CTV isolates has been documented earlier in India (Sharma et al, 2011, Biswas et al, 2012Singh et al, 2013). The present study determined that isolates 37 and K38 are recombinant isolates.…”

“…CTV is present wherever the citrus is grown naturally or commercially in India (Ahlawat, 1997;Biswas, 2008;Biswas et al, 2014). CTV causes leaf yellowing, growth cessation, chlorosis, plant stunting with poor fruit yield and quality, and ultimately tree decline in India (Chakroborty et al, 1992;Biswas, 2008;Sharma et al, 2011;Singh et al, 2013;Biswas et al, 2014). Northeastern Himalayan region of India is known to produce mandarin, called Darjeeling mandarin (C. reticulata) commercially.…”

Codon Usage Bias Analysis of Citrus tristeza virus: Higher Codon Adaptation to Citrus reticulata Host

“…CTV shows diverse disease syndromes in different citrus species, indicating the occurrence of highly diversified CTV populations in India [7,8]. Extensive genetic diversity in CTV from different citrus-growing regions of India was reported [7,8,9,10,11,12]. At the international level, six distinct CTV genotypes (VT, T36, T30, T3, RB, and T68) and one recombinant entity (HA16-5) were recognized based on phylogenetic analysis of several complete CTV genomes [13,14,15,16].…”

Analyses of 3' half genome of citrus tristeza virus reveal existence of distinct virus genotypes in citrus growing regions of India

“…Of them VT genotype has been described as biologically severe, T30 as mild and T36 as intermediate CTV strain [3]. It has also been suggested that homologous and nonhomologous recombination are major factors in the evolution CTV variants in India and other countries [5,18,20,23,30].…”