A Complex of Begomoviruses Affecting Tomato Crops in Nicaragua

Rojas, A. 2004. A complex of Begomoviruses affecting tomato crops in Nicaragua. Doctor’s dissertation ISSN 1401-6249, ISBN 91-576-6772-1 Diseases caused by begomoviruses (family Geminiviridae, genus Begomovirus) constitute a serious constraint to vegetable production in Nicaragua as they are associated with large economical losses. This thesis was done in an effort to identify and characterize the begomoviruses responsible for the tomato diseases and to understand their relationships. The cropping system used by small-holding farmers comprises essentially five crops: maize and bean as consumption crops, and tomato, pepper and cucurbits as cash crops. These crops are grown in the three different growing seasons all the year around. Except maize, all the other crops are hosts for begomoviruses and whiteflies. In this study, begomovirus sequences detected with universal and virus specific primers were cloned, sequenced and used for phylogenetic analysis. The plants from which the viruses were detected were tomato, pepper, cucurbits and Euphorbia heterophylla. The sequence comparisons revealed high identity with other already described begomovirus species, including Euphorbia mosaic virus (EuMV), Squash yellow mild mottle virus (SYMMoV) Tomato severe leaf curl virus (ToSLCV), Tomato leaf curl Sinaloa virus (ToLCSinV) and Pepper golden mosaic virus (PepGMV). One viral sequence from tomato showed only low identity to previously sequenced begomoviruses (84%) and represents a new tentative species designated as Tomato leaf curl Las Playitas virus (ToLCLPV). The complete nucleotide (nt) sequences of the DNA-A and DNA-B components were determined for ToLCSinV, and the complete nt sequence was determined for the DNA-A component of two isolates of ToSLCV. The genome organization of ToLCSinV and ToSLCV was identical to the bipartite genomes of other begomoviruses described from the Americas. A phylogenetic analysis of DNA-A showed that the indigenous begomoviruses of the New World can be divided into three major clades and an intermediate group, and that ToLCSinV and ToSLCV belong to different clades. Computer-based predictions indicated that recombination with another begomovirus had taken place within AV1 of ToSLCV dividing this species into two strains. Mixed infection with different strains of the same virus, and mixed infections with up to three begomovirus species were detected in tomato plants. Three begomoviruses were detected in both tomato and pepper in the field. Detection of predicted recombinant viral isolates is consistent with other findings of this study which indicate that begomoviruses commonly occur as mixed infections in the field, and that intraspecific sequence variability within an infected plant may be as high as between different plants. These conditions provide a high risk for evolution of new virus strains and species via recombination. Acquisition and transmission of ToLCSinV and ToSLCV by their whitefly vector, Bemisia tabaci, required only 10 min on tomato plants. Longer acquisition and inoculation access periods tended to increase the virus transmission rates. Whiteflies transmitted the viruses for seven days without new virus acquisition.