Interkingdom horizontal gene transfer in plants: a perspective on methodological limitations and evolutionary...

Over the past decade, numerous studies have suggested that plant genomes have been substantially influenced by interkingdom horizontal gene transfer (iHGT). Although the prevalence of this process in eukaryotes-particularly in multicellular organisms-remains an active area of discussion, many reported plant iHGT candidates have not always been examined in light of alternative evolutionary explanations. This raises the possibility that the contribution of iHGT to plant genome evolution may be less pervasive than currently proposed. In this perspective article, we revisit the evidence commonly used to support iHGT in plants and consider plausible alternative scenarios that could generate similar phylogenetic patterns. We also outline key limitations of the methods currently used to detect iHGT and suggest directions for improving future analyses. Our goal is to encourage careful evaluation of the criteria applied to infer iHGT and to promote a balanced view of its potential impact on plant genome evolution.