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ARS Home » Pacific West Area » Riverside, California » National Clonal Germplasm Repository for Citrus » Research » Publications at this Location » Publication #276584
Title: Distribution, genetic diversity and recombination analysis of Citrus tristeza virus of India

Author
item BISWAS, KAJAL - Indian Agricultural Research Institute
item TARAFDAR, AVIJIT - Indian Agricultural Research Institute
item KUMARI, SUMITA - Indian Agricultural Research Institute
item Lee, Richard

Submitted to: Virus Genes
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2012
Publication Date: 5/5/2012
Citation: Biswas, K.K., Tarafdar, A., Kumari, S., Lee, R.F. 2012. Distribution, genetic diversity and recombination analysis of Citrus tristeza virus of India. Virus Genes. DOI: 10.1007/s11262-012-0748-3.

Interpretive Summary: A total of 66 isolates of Citrus tristeza virus (CTV) were collected from the four major citrus production regions of India: Vidarbha (Central region), Bangalore (South), Darjeeling Hills (Northeast), and Delhi (North). A region near the 5’ Open Reading Frame 1a (5’ORF1a) and the coat protein (CP) gene near the 3’ end of the CTV genome were sequenced. The sequences were compared to the sequences of the six genotypes commonly recognized presently based on the GenBank information and previous publications. Phylogenetic analyses of the 5’ORF1a regions revealed eight clades with most Indian isolates in the VT (severe stem pitting CTV)clade; two clades are comprised of only Indian CTV isolates. The phylogenetic analyses of the CP gene revealed seven clades with two clades being comprised of only Indian isolates. Analyses of the Indian isolates by programs designed to detect recombination events provided evidence of recombination occurring with the Indian CTV isolates. CTV probably originated in Southern Asian along with the origin of many species of citrus, and our results indicate great genetic diversity occurring in Indian isolates of CTV.

Technical Abstract: Citrus tristeza virus (CTV) isolates representing all the citrus growing geographical zones of India were analyzed for sequence of the 5'ORF1a fragments of the partial LProI domain and for the coat protein (CP) gene. The sequences were compared with previously reported Indian and CTV genotypes from GenBank. The Indian isolates had 80-99% sequence identity for the 5'ORF1a and 89-99% identity for the CP genes. In phylogenetic analysis, all the Indian and previously reported isolates segregated into eight clades or groups for the 5'ORF1a region. Indian CTV isolates were clustered in all the clades of which four groups D13, K5, BAN-1 and B165 consisted of only Indian isolates. Phylogenetic analysis of the CP gene resulted in seven clades with Indian CTV isolates clustered in six of the groups, of which groups I and VI consisted of only Indian isolates. The phylogenetic clustering of the Indian CTV isolates did not reflect to the geographical origin of CTV isolates with the CTV isolates occurring in all the citrus growing areas in India. Diversities in CTV isolates within samples collected from individual citrus farms were identified. Because incongruent phylogenetic relationships were observed for both the genomic regions, 5'ORF1a and CP gene, recombination analysis, performed using program RDP3, detected potential recombination events among the CTV isolates which involved exchange of sequences between divergent CTV variants. The SplitsTree analysis showed evidence of phylogenetic conflicts in evolutionary relationships among CTV isolates.