Reassessing Interkingdom Horizontal Gene Transfer Suggests Limited Influence on Plant Genomes

Horizontal gene transfer (HGT) is a well-established mechanism of genetic innovation in bacteria, but its impact on eukaryotes-and particularly on plants-remains debated. In recent years, numerous studies have reported hundreds of putative nuclear genes in plants with origins in other kingdoms, often interpreted as adaptive acquisitions. Most of these claims rely on phylogenetic reconstructions, which are highly sensitive to taxon sampling and can shift as new homologs are identified. To reassess this evidence, we systematically collected published reports of interkingdom HGT in plants and reconstructed phylogenetic trees using up-to-date genomic data from public databases. Candidate topologies were first evaluated with an automated tool and then manually curated. Our reanalysis shows that only 29.3% of previously reported cases remain consistent with an interkingdom HGT scenario. Many candidates are more parsimoniously explained by alternative processes such as gene loss or incomplete taxon sampling. These findings highlight the dynamic nature of phylogenetic inference and caution against treating HGT as the default explanation for anomalous phylogenies in plant genomes.