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Intra-farm diversity and evidence of genetic recombination of Citrus tristeza virus in Delhi region of India

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Abstract

Infection of Citrus tristeza virus (CTV) in different citrus orchards of New Delhi was detected by direct antigen coated-ELISA and RT-PCR. Sweet orange (Citrus sinensis) orchards were found to be susceptible to CTV with estimated disease incidence up to 39%. Kagzi kalan (C. lemon), Pumello (C. paradisi) and Kinnow mandarin (C. reticulata) orchards did not show CTV infection. Three CTV isolates, D1, D7 and D15 randomly selected from infected sweet orange orchards were considered for biological and molecular characterization. In the host range study, all the Delhi isolates infected Darjeeling mandarin (C. reticulata), Kagzi lime (C. aurantifolia), sour orange (C. aurantium) and sweet orange but not Kinnow mandarin. A fragment of 5′ORF1a and complete coat protein (CP) gene of these three isolates were cloned, sequenced and compared with other Indian and international CTV isolates. Delhi isolates shared 85–92% sequence identity for 5′ORF1a fragment and 89–91% for CP gene among them. Phylogenetic analysis segregated three Delhi isolates into three genogroups for each of 5′ORF1a fragment and CP gene, however phylogenetic relationships for both the genomic regions was incongruent. Recombination detecting program RDP3 detected CTV isolate D7 as recombinant, indicating genetic variability in CTV isolates might be the outcome of recombination events between divergent CTV sequences. An attempt was made in present study to characterize CTV isolates biologically and at genetic level, and to determine genetic diversity at farm level and study the recombination of CTV isolates in Delhi region.

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Abbreviations

cDNA:

Complimentary deoxyribo nucleic acid

CP:

Coat protein

CTV:

Citrus tristeza virus

ELISA:

Enzyme-linked immunosorbent assay

kb:

Kilo base

NCBI:

National centre for biotechnology information

nt:

Nucleotide

ORF:

Open reading frame

RT-PCR:

Reverse transcription-polymerase chain reaction

UPGMA:

Unweighted pair group method with arithmetic mean

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Acknowledgements

First author is grateful to ICAR for financial assistantship as JRF. This work was financially supported through externally funded Research Project of Department of Biotechnology, Govt. of India (Project code 24:33). Authors are grateful to Director, IARI; Dr. R.K. Jain, Head, Division of Plant Pathology; Dr. V.G. Malathi, In-charge, ACPV, IARI for providing financial and laboratory facilities. First author is also grateful to Dr. T.R. Sharma and Dr. S.C. Dubey, IARI for their valuable suggestions during this research work.

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Authors and Affiliations

  1. Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi, 110012, India

    Susheel Kumar Sharma, Avijit Tarafdar, Dilruba Khatun, Kumari Sumita & Kajal Kumar Biswas

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  1. Susheel Kumar Sharma
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  2. Avijit Tarafdar
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  3. Dilruba Khatun
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  4. Kumari Sumita
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  5. Kajal Kumar Biswas
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Correspondence to Kajal Kumar Biswas.

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Fig. 3

UPGMA phylogenetic tree analysis in RDP3; For non-recombinant (385–234 nt) (a) and recombinant part (235–384 nt) (b) in 5 ORF1a; non-recombinant (154–449 nt) (c) and recombinant part (450–153 nt) (d) in CP sequences. Parental sequences are in bold and recombinant in underline. (PDF 27 kb)

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Sharma, S.K., Tarafdar, A., Khatun, D. et al. Intra-farm diversity and evidence of genetic recombination of Citrus tristeza virus in Delhi region of India. J. Plant Biochem. Biotechnol. 21, 38–43 (2012). https://doi.org/10.1007/s13562-011-0071-4

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