Natural occurrence of begomovirus recombinants associated with tomato yellow leaf curl disease co-existing with parental viruses in tomato crops and weeds in Tunisia

Abstract

Tomato yellow leaf curl virus disease (TYLCVD) is the main limiting factor for tomato production in the Mediterranean Basin, and particularly in Tunisia where climatic and crop production conditions, as well as the occurrence of many weeds, provide suitable conditions for the presence and spread of TYLCVD all year round. In Tunisia, epidemics in tomato-growing regions have been associated with two begomoviruses: Tomato yellow leaf curl virus (TYLCV) and Tomato yellow leaf curl Sardinia virus (TYLCSV) but the presence of recombinants between them has never been investigated. A large-scale survey was conducted on leaves sampled from late-season tomato crops exhibiting severe curling symptoms, from beans, and from nine nearby weed species in the South and Sahel regions of Tunisia to investigate: (i) the natural occurrence of the TYLCV and TYLCSV species; (ii) the presence of the two recombinant types, RecA and RecB, derived from these species. Identification of TYLCV and TYLCSV was based on a multiplex PCR with primers generating a typical pattern on gels (750 bp and 366 bp fragments, respectively). Recombinants were identified by simplex PCR, which amplified the intergenic region, the most common recombination site described for begomoviruses, and sequencing. The occurrence of TYLCSV and TYLCV was confirmed in both Tunisian regions. Their co-existence was shown on tomato and in new weed species. This is the first time that recombinants between TYLCV and TYLCSV species showing 93% to 95% nucleotide identity with tomato yellow leaf curl recombinant viruses, are reported in Tunisia in tomato and black nightshade