Detection via high-throughput sequencing of a rare host jump event of a bipartite weed-infecting begomovirus to tomato

We report herein the complete genomic characterization of a novel Cleome leaf crumple virus - CleLCrV (= Begomovirus cleomecrispi) isolate involved in a rare host jump event from a Cleomaceae weed to tomato. This isolate was originally detected in high-throughput sequencing (HTS) analysis of tomato samples in Brazil and displayed a typical bipartite organization with the DNA-A component comprising six open reading frames (ORFs), including AC5, and the DNA-B component displaying two ORFs. Sanger sequencing of both components confirmed the HTS results. Recombination analyses indicated putative recombination signals in the DNA-A component, encompassing the AV1/AC5 ORFs of the monopartite tomato mottle leaf curl virus. Phylogenetic analysis of the entire DNA-A component clustered the novel isolate with CleLCrV isolates from the original weed host (Cleome affinis). However, specific genomic differences were detected in the iteron and in the structural helix 4 motif of this isolate. Our study supports previous observations that host jump events of begomoviruses from weeds to tomatoes are naturally taking place in Neotropical areas. However, it is noteworthy that only one out of 107 samples tested positive for CleLCrV, implying that detection of these events is feasible due to the superior analytical power of HTS.