Abstract
Experimental investigations into virus recombination can provide valuable insights into the biochemical mechanisms and the evolutionary value of this fundamental biological process. Here, we describe an experimental scheme for studying recombination that should be applicable to any recombinogenic viruses amenable to the production of synthetic infectious genomes. Our approach is based on differences in fitness that generally exist between synthetic chimaeric genomes and the wild-type viruses from which they are constructed. In mixed infections of defective reciprocal chimaeras, selection strongly favours recombinant progeny genomes that recover a portion of wild-type fitness. Characterizing these evolved progeny viruses can highlight both important genetic fitness determinants and the contribution that recombination makes to the evolution of their natural relatives. Moreover, these experiments supply precise information about the frequency and distribution of recombination breakpoints, which can shed light on the mechanistic processes underlying recombination. We demonstrate the value of this approach using the small single-stranded DNA geminivirus, maize streak virus (MSV). Our results show that adaptive recombination in this virus is extremely efficient and can yield complex progeny genomes comprising up to 18 recombination breakpoints. The patterns of recombination that we observe strongly imply that the mechanistic processes underlying rolling circle replication are the prime determinants of recombination breakpoint distributions found in MSV genomes sampled from nature.
Highlights
It has long been recognized that recombination is important for its role in unlinking deleterious mutations from those that may be neutral or beneficial (Felsenstein, 1974; Keightley & Otto, 2006), allowing populations at least partial escape from the negative fitness effects of accumulating slightly deleterious mutations (Chao, 1990; Muller, 1964)
We agroinoculated approximately 400 maize streak virus (MSV)-resistant maize plants with mixed MatMPCPVW and VWMPCPMat inocula, and identified 30 that unambiguously developed symptoms ranging from extremely mild to moderately severe
Our results show that even though recombination often resulted in surprisingly complex mosaic sequences, comprising up to nine alternating sections of parental DNA sequences in one case, the progeny genomes contained an average of 91.7 % of the polymorphisms expected in the target solution
Summary
It has long been recognized that recombination is important for its role in unlinking deleterious mutations from those that may be neutral or beneficial (Felsenstein, 1974; Keightley & Otto, 2006), allowing populations at least partial escape from the negative fitness effects of accumulating slightly deleterious mutations (Chao, 1990; Muller, 1964). While natural recombination between distantly related genomes has only rarely been shown to occur in doublestranded DNA and RNA viruses (Suzuki et al, 1998; Varsani et al, 2006), it is apparently quite common amongst most reverse-transcribing (Chenault & Melcher, 1994; Katz & Skalka, 1990; Sharp et al, 1995), positivesense single-stranded RNA (Chare & Holmes, 2006; Heath et al, 2006) and single-stranded DNA (ssDNA) (Heath et al, 2004; Padidam et al, 1999; Shackelton et al, 2007; Worobey, 2000) viruses Such inter-species recombination features prominently in the evolution of ssDNA geminiviruses
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