Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses

Abstract

The combinatorial nature of genetic recombination can potentially provide organisms with immediate access to many more positions in sequence space than can be reached by mutation alone. Recombination features particularly prominently in the evolution of a diverse range of viruses. Despite rapid progress having been made in the characterization of discrete recombination events for many species, little is currently known about either gross patterns of recombination across related virus families or the underlying processes that determine genome-wide recombination breakpoint distributions observable in nature. It has been hypothesized that the networks of coevolved molecular interactions that define the epistatic architectures of virus genomes might be damaged by recombination and therefore that selection strongly influences observable recombination patterns. For recombinants to thrive in nature, it is probably important that the portions of their genomes that they have inherited from different parents work well together. Here we describe a comparative analysis of recombination breakpoint distributions within the genomes of diverse single-stranded DNA (ssDNA) virus families. We show that whereas nonrandom breakpoint distributions in ssDNA virus genomes are partially attributable to mechanistic aspects of the recombination process, there is also a significant tendency for recombination breakpoints to fall either outside or on the peripheries of genes. In particular, we found significantly fewer recombination breakpoints within structural protein genes than within other gene types. Collectively, these results imply that natural selection acting against viruses expressing recombinant proteins is a major determinant of nonrandom recombination breakpoint distributions observable in most ssDNA virus families.

Characterization of a New World Monopartite Begomovirus Causing Leaf Curl Disease of Tomato in Ecuador and Peru Reveals a New Direction in Geminivirus Evolution

“…Low levels of diversity and purifying selection in the V1 and C1 genes reflect the conserved functions of the CP and Rep proteins, whereas the higher level of diversity and positive selection in the C4 gene indicate a role in the evolution of ToLDeV. The majority of the genetic diversity in the ToLDeV genome was found in the LIR, C4, and C1 genes, which is a well-known recombinational hot spot in the genomes of bipartite and monopartite begomoviruses (73)(74)(75). Evidence for recombination in this region of the ToLDeV genome came from the Simplot analysis (Fig.…”

Synonymous site variation due to recombination explains higher genetic variability in begomovirus populations infecting non-cultivated hosts

“…Recombination is the most intensively studied population genetic process in begomoviruses, and has been considered more significant than mutation by many researchers (Lefeuvre et al, 2007a(Lefeuvre et al, , 2009Martin et al, 2005Martin et al, , 2011Monci et al, 2002;Padidam et al, 1999;Pita et al, 2001). It appears to heavily contribute to begomovirus genetic diversity, increasing the evolutionary potential and local adaptation of strains (Berrie et al, 2001;Graham et al, 2010;Harrison & Robinson, 1999;Monci et al, 2002;Padidam et al, 1999).…”

Replicative intermediates of maize streak virus found during leaf development

“…However, the recent demonstration that recombination patterns are broadly conserved amongst ssDNA virus families -from prokaryote-infecting microviruses through to vertebrateinfecting circoviruses (Lefeuvre et al, 2009) -suggests that the degrees of replicational multitasking found in geminiviruses might also exist in these other families.…”