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

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.

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.

Figure 2

TreeOrder Scan of tomato-infecting begomoviruses sequences. Changes in tree order(Y axis) resulting from changes in phylogenetic relationships at 70% bootstrap level are shown for sequential 300 bases sequence fragments at 100 base fragment intervals (X axis). Sequences are assigned to groups based on geographical locations and groups are color coded as indicated by labels. The genome map drawn to scale has been superimposed to indicate the positions of genes in DNA A sequences. Positions were drawn relative to the ToLCGV-[Var] strain.

Figure 3

Phylogenetic compatibility matrix of tomato-infecting begomovirus sequences, exhibiting frequencies of phylogeny violations for each pairwise comparison of sequence fragments. For this analysis sequence fragments of 300 bases and 100 base intervals were used. Phylogeny violations above the threshold bootstrap value of 70% are shown. Frequencies are color coded to indicate number of phylogeny violations per sequence. The genome map drawn to scale has been superimposed to indicate the positions of genes in DNA A sequences. Positions were drawn relative to the ToLCGV-[Var] strain.

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.