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Begomovirus ‘melting pot’ in the south-west Indian Ocean islands: molecular diversity and evolution through recombination

¹ CIRAD, UMR 53 PVBMT CIRAD-Université de la Réunion, Pôle de Protection des Plantes, 7 Chemin de l'IRAT, 97410 Saint Pierre, La Réunion, France
² Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory 7925, South Africa
³ Electron Microscopy Unit, University of Cape Town, Rondebosch 7701, South Africa
⁴ Museum National d'Histoire Naturelle, Dept RDDM, USM 501, CNRS UMR 5166, Evolution des Régulations Endocriniennes, 57 rue Cuvier, CP 32, 75005 Paris, France

Correspondence
J.-M. Lett
lett{at}cirad.fr

During the last few decades, many virus species have emerged, often forming dynamic complexes within which viruses share common hosts and rampantly exchange genetic material through recombination. Begomovirus species complexes are common and represent serious agricultural threats. Characterization of species complex diversity has substantially contributed to our understanding of both begomovirus evolution, and the ecological and epidemiological processes involved in the emergence of new viral pathogens. To date, the only extensively studied emergent African begomovirus species complex is that responsible for cassava mosaic disease. Here we present a study of another emerging begomovirus species complex which is associated with serious disease outbreaks in bean, tobacco and tomato on the south-west Indian Ocean (SWIO) islands off the coast of Africa. On the basis of 14 new complete DNA-A sequences, we describe seven new island monopartite begomovirus species, suggesting the presence of an extraordinary diversity of begomovirus in the SWIO islands. Phylogenetic analyses of these sequences reveal a close relationship between monopartite and bipartite African begomoviruses, supporting the hypothesis that either bipartite African begomoviruses have captured B components from other bipartite viruses, or there have been multiple B-component losses amongst SWIO virus progenitors. Moreover, we present evidence that detectable recombination events amongst African, Mediterranean and SWIO begomoviruses, while substantially contributing to their diversity, have not occurred randomly throughout their genomes. We provide the first statistical support for three recombination hot-spots (V1/C3 interface, C1 centre and the entire IR) and two recombination cold-spots (the V2 and the third quarter of V1) in the genomes of begomoviruses.

Supplementary material is available with the online version of this paper.

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