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Evidence of a Naturally Occurring Recombinant Between Tomato yellow leaf curl virus and Tomato yellow leaf curl Sardinia virus in Spain

Tomato yellow leaf curl virus (TYLCV, formerly TYLCV-Is) and Tomato yellow leaf curl Sardinia virus (TYLCSV, formerly TYLCV-Sar) are geminivirus species of the genus Begomovirus that cause the disease known as tomato yellow leaf curl. In Spain, TYLCV and TYLCSV have coexisted in field and greenhouse tomato (Lycopersicon esculentum) crops since 1996 (2). TYLCV is also the causal agent of the leaf crumple disease of common bean (Phaseolus vulgaris) (1), a species that TYLCSV is unable to infect (2). Analysis of field samples from common bean plants affected by leaf crumple disease collected in Almería (southeastern Spain) during 1999 showed that, unexpectedly, several samples hybridized with TYLCV- and TYLCSV-specific probes prepared to the intergenic region (IR) as previously described (1). Polymerase chain reactions (PCR) performed with total nucleic acids extracted from one of these samples (ES421/99) using primer pairs specific to the IR of TYLCV (MA-30/MA-31) or TYLCSV (MA-14/MA-15) (1) gave no amplification product. However, the combination of MA-30 (5′ end of TYLCV IR) and MA-15 (3′ end of TYLCSV IR) produced a PCR DNA product of the expected size (351 bp). Direct DNA sequencing of this product (GenBank Accession No. AF401478) indicated the presence of a chimeric IR in ES421/99. Comparison of the obtained sequence with those available for isolates reported from Spain showed that the 5′ side (149 nt) from the stem-loop structure conserved in the IR of all geminiviruses was 99% identical to the corresponding region of TYLCV (GenBank Accession No. AF071228) and only 62% identical to TYLCSV (GenBank Accession No. Z25751). In contrast, the 3′ side (124 nt) from the stem-loop was 98% identical to the corresponding region of TYLCSV and only 57% identical to TYLCV. The 33-nt region involved in the stem-loop was 100% identical to TYLCV and showed one nucleotide change in the loop with respect to TYLCSV. Therefore, this DNA sequence data showed evidence of the occurrence in ES421/99 of a natural recombination between TYLCV and TYLCSV. The biological and epidemiological consequences of the presence of this new interspecific recombinant have yet to be determined.

References: (1) J. Navas-Castillo et al. Plant Dis. 83:29, 1999. (2) S. Sánchez-Campos et al. Phytopathology 89:1038, 1999.