Contribution of plant–bacteria interactions to horizontal gene transfer in plants

Horizontal gene transfer (HGT) is recognized as a major driver of adaptive evolution in prokaryotes. However, HGT seems impossible in eukaryotes, particularly as recipients; therefore, debate rages regarding whether HGT takes place in eukaryotes, in addition to its potential mechanism or frequency. Bacterial symbionts, whether mutualistic, commensalistic or parasitic, have been considered potential donors for eukaryotes. In this study, we used a bacterial–plant interaction system to systematically investigate HGT in plants. In total, 373 HGT events were identified based on a pipeline procedure, and 90 HGTs were confirmed as true events, with 27.27%–86.5% sequence similarities. We propose that both ancient transfer and recent specific transfer (e.g. Agrobacteria) occurred in the course of plant evolution. The most enriched functional categories of the HGTs were metabolism processes of amino acids, cofactors and vitamins, and carbohydrates, and genetic information processing. Donor bacterial genera were significantly enriched in plant-associated bacterial groups, which indicated that plant–bacterial interaction facilitates HGT in plants. No clade- or species-specific HGTs were detected, and all occurred anciently during the origin of angiosperm plants. In addition, we identified 309 ‘one-species’ HGT events, and as expected, all the events could be accounted for as sequence errors or inaccurate annotations.