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Journal of Virology, March 2009, p. 2697-2707, Vol. 83, No. 6
0022-538X/09/$08.00+0     doi:10.1128/JVI.02152-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Widely Conserved Recombination Patterns among Single-Stranded DNA Viruses {triangledown} ,{dagger}

P. Lefeuvre,1 J.-M. Lett,1 A. Varsani,2,3 and D. P. Martin4*

CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, Ligne Paradis, 97410 Saint Pierre, La Réunion, France,1 Electron Microscope Unit, University of Cape Town, Private Bag, Rondebosch 7701, South Africa,2 School of Biological Science, University of Canterbury, Private Bag 4800, Christchurch, New Zealand,3 Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa4

Received 13 October 2008/ Accepted 23 December 2008

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.

* Corresponding author. Mailing address: Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa. Phone: 27-21-406 6366. Fax: 27-21-698 1528. E-mail: Darrin.Martin{at}uct.ac.za

{triangledown} Published ahead of print on 30 December 2008.

{dagger} Supplemental material for this article may be found at http://jvi.asm.org/.

Journal of Virology, March 2009, p. 2697-2707, Vol. 83, No. 6
0022-538X/09/$08.00+0     doi:10.1128/JVI.02152-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



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