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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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Related in: MedlinePlus

(A) Relationship between the number of phylogeny violations and fragment diversity. Jukes-Cantor distance was calculated for each pairwise comparison used in TreeOrder Scan analysis and corresponding violations were counted and plotted. (B) Relationship between the number of recombination events and fragment diversity. The fragments involved in the exchange with identified parental sequences were used and the number of recombination events detected were counted and plotted.
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Figure 4: (A) Relationship between the number of phylogeny violations and fragment diversity. Jukes-Cantor distance was calculated for each pairwise comparison used in TreeOrder Scan analysis and corresponding violations were counted and plotted. (B) Relationship between the number of recombination events and fragment diversity. The fragments involved in the exchange with identified parental sequences were used and the number of recombination events detected were counted and plotted.

Mentions: We examined phylogeny violations and number of recombination events in our data set from the perspective of parental sequence relatedness. We noted that in general phylogeny violations clustered around the genetic distance 0.30. The observed frequency of phylogeny violations were inversely correlated (r = -0.36 p < 0.05) to the pairwise distances of the fragments involved in exchange (Fig. 4A). In addition, the number of recombination events was also inversely correlated (r = -0.35 p < 0.05) to the diversity between the exchanged fragments (Fig. 4B), we used only identified parental sequences to estimate the genetic distance between horizontally transferred fragments and the sequences that they replaced. Overall the frequency of phylogenetic violations and number of recombination events decreased with increasing parental sequence diversity. In a study with artificial and natural geminivirus recombinants Martin and co-workers [38] demonstrated that the degree of similarity between a horizontally inherited sequence and the sequence it replaces is an important determining factor of recombinant fitness. Rather than the non-random distribution of break points observed here being due to higher recombination rates in some genome regions than others [39], the distribution seems to have been created by natural selection only allowing the survival of recombinants with high fitness. In the more diverse genome regions where recombination events are not detected it is possible that these regions would not function properly when transferred into foreign genetic backgrounds.


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

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

(A) Relationship between the number of phylogeny violations and fragment diversity. Jukes-Cantor distance was calculated for each pairwise comparison used in TreeOrder Scan analysis and corresponding violations were counted and plotted. (B) Relationship between the number of recombination events and fragment diversity. The fragments involved in the exchange with identified parental sequences were used and the number of recombination events detected were counted and plotted.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: (A) Relationship between the number of phylogeny violations and fragment diversity. Jukes-Cantor distance was calculated for each pairwise comparison used in TreeOrder Scan analysis and corresponding violations were counted and plotted. (B) Relationship between the number of recombination events and fragment diversity. The fragments involved in the exchange with identified parental sequences were used and the number of recombination events detected were counted and plotted.
Mentions: We examined phylogeny violations and number of recombination events in our data set from the perspective of parental sequence relatedness. We noted that in general phylogeny violations clustered around the genetic distance 0.30. The observed frequency of phylogeny violations were inversely correlated (r = -0.36 p < 0.05) to the pairwise distances of the fragments involved in exchange (Fig. 4A). In addition, the number of recombination events was also inversely correlated (r = -0.35 p < 0.05) to the diversity between the exchanged fragments (Fig. 4B), we used only identified parental sequences to estimate the genetic distance between horizontally transferred fragments and the sequences that they replaced. Overall the frequency of phylogenetic violations and number of recombination events decreased with increasing parental sequence diversity. In a study with artificial and natural geminivirus recombinants Martin and co-workers [38] demonstrated that the degree of similarity between a horizontally inherited sequence and the sequence it replaces is an important determining factor of recombinant fitness. Rather than the non-random distribution of break points observed here being due to higher recombination rates in some genome regions than others [39], the distribution seems to have been created by natural selection only allowing the survival of recombinants with high fitness. In the more diverse genome regions where recombination events are not detected it is possible that these regions would not function properly when transferred into foreign genetic backgrounds.

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