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Detection and frequency of recombination in tomato-infecting begomoviruses of South and Southeast Asia.

Prasanna HC, Rai M - Virol. J. (2007)

Bottom Line: Distribution of recombination hotspots was found to be reliant on the relatedness of the genomic region involved in the exchange.Overall the frequency of phylogenetic violations and number of recombination events decreased with increasing parental sequence diversity.These findings provide valuable new information for understanding the diversity and evolution of tomato-infecting begomoviruses in Asia.

View Article: PubMed Central - HTML - PubMed

Affiliation: Indian Institute of Vegetable Research, P B 5002, P 0-B H U, Varanasi, Uttar Pradesh, 221005, India. prasanahc@yahoo.com

ABSTRACT

Background: Tomato-infecting begomoviruses are widely distributed across the world and cause diseases of high economic impact on wide range of agriculturally important crops. Though recombination plays a pivotal role in diversification and evolution of these viruses, it is currently unknown whether there are differences in the number and quality of recombination events amongst different tomato-infecting begomovirus species. To examine this we sought to characterize the recombination events, estimate the frequency of recombination, and map recombination hotspots in tomato-infecting begomoviruses of South and Southeast Asia.

Results: Different methods used for recombination breakpoint analysis provided strong evidence for presence of recombination events in majority of the sequences analyzed. However, there was a clear evidence for absence or low Recombination events in viruses reported from North India. In addition, we provide evidence for non-random distribution of recombination events with the highest frequency of recombination being mapped in the portion of the N-terminal portion of Rep.

Conclusion: The variable recombination observed in these viruses signified that all begomoviruses are not equally prone to recombination. Distribution of recombination hotspots was found to be reliant on the relatedness of the genomic region involved in the exchange. Overall the frequency of phylogenetic violations and number of recombination events decreased with increasing parental sequence diversity. These findings provide valuable new information for understanding the diversity and evolution of tomato-infecting begomoviruses in Asia.

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Neighbor-Net generated for the tomato-infecting begomoviruses of South and Southeast Asia. Evidence for reticulate evolution is reported on pairwise Hamming distances using only parsimonious sites. Networked relationships among the viral species with boxes, instead of bifurcating evolutionary tree indicate to the presence of recombination.
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Figure 1: Neighbor-Net generated for the tomato-infecting begomoviruses of South and Southeast Asia. Evidence for reticulate evolution is reported on pairwise Hamming distances using only parsimonious sites. Networked relationships among the viral species with boxes, instead of bifurcating evolutionary tree indicate to the presence of recombination.

Mentions: The neighbor-net analysis revealed clear evidence of phylogenetic conflicts within the analysed sequences (Fig. 1). Notably, every sequence represented within the tree was implicated as a potential recipient of horizontally acquired sequences at some time in its evolutionary past. Unsurprisingly, the PHI test strongly supported the presence of recombination in these sequences (p < 0.0001).


Detection and frequency of recombination in tomato-infecting begomoviruses of South and Southeast Asia.

Prasanna HC, Rai M - Virol. J. (2007)

Neighbor-Net generated for the tomato-infecting begomoviruses of South and Southeast Asia. Evidence for reticulate evolution is reported on pairwise Hamming distances using only parsimonious sites. Networked relationships among the viral species with boxes, instead of bifurcating evolutionary tree indicate to the presence of recombination.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2170441&req=5

Figure 1: Neighbor-Net generated for the tomato-infecting begomoviruses of South and Southeast Asia. Evidence for reticulate evolution is reported on pairwise Hamming distances using only parsimonious sites. Networked relationships among the viral species with boxes, instead of bifurcating evolutionary tree indicate to the presence of recombination.
Mentions: The neighbor-net analysis revealed clear evidence of phylogenetic conflicts within the analysed sequences (Fig. 1). Notably, every sequence represented within the tree was implicated as a potential recipient of horizontally acquired sequences at some time in its evolutionary past. Unsurprisingly, the PHI test strongly supported the presence of recombination in these sequences (p < 0.0001).

Bottom Line: Distribution of recombination hotspots was found to be reliant on the relatedness of the genomic region involved in the exchange.Overall the frequency of phylogenetic violations and number of recombination events decreased with increasing parental sequence diversity.These findings provide valuable new information for understanding the diversity and evolution of tomato-infecting begomoviruses in Asia.

View Article: PubMed Central - HTML - PubMed

Affiliation: Indian Institute of Vegetable Research, P B 5002, P 0-B H U, Varanasi, Uttar Pradesh, 221005, India. prasanahc@yahoo.com

ABSTRACT

Background: Tomato-infecting begomoviruses are widely distributed across the world and cause diseases of high economic impact on wide range of agriculturally important crops. Though recombination plays a pivotal role in diversification and evolution of these viruses, it is currently unknown whether there are differences in the number and quality of recombination events amongst different tomato-infecting begomovirus species. To examine this we sought to characterize the recombination events, estimate the frequency of recombination, and map recombination hotspots in tomato-infecting begomoviruses of South and Southeast Asia.

Results: Different methods used for recombination breakpoint analysis provided strong evidence for presence of recombination events in majority of the sequences analyzed. However, there was a clear evidence for absence or low Recombination events in viruses reported from North India. In addition, we provide evidence for non-random distribution of recombination events with the highest frequency of recombination being mapped in the portion of the N-terminal portion of Rep.

Conclusion: The variable recombination observed in these viruses signified that all begomoviruses are not equally prone to recombination. Distribution of recombination hotspots was found to be reliant on the relatedness of the genomic region involved in the exchange. Overall the frequency of phylogenetic violations and number of recombination events decreased with increasing parental sequence diversity. These findings provide valuable new information for understanding the diversity and evolution of tomato-infecting begomoviruses in Asia.

Show MeSH
Related in: MedlinePlus