Reassessing Interkingdom Horizontal Gene Transfer Suggests Limited Influence on Plant Genomes

Area of Science:

• Genomics
• Evolutionary Biology
• Plant Science

Background:

• Horizontal gene transfer (HGT) is a known driver of bacterial evolution.
• Its role in eukaryotic genomes, especially plants, is under active investigation.
• Numerous studies have proposed interkingdom HGT events in plants, suggesting adaptive gene acquisition.

Purpose of the Study:

• To systematically re-evaluate reported cases of interkingdom HGT in plant nuclear genomes.
• To determine the validity of previously identified HGT events using current genomic data and phylogenetic methods.
• To identify alternative explanations for anomalous gene phylogenies in plants.

Main Methods:

• Systematic literature review to collect reported instances of plant interkingdom HGT.
• Phylogenetic tree reconstruction using comprehensive, up-to-date genomic data from public repositories.
• Automated and manual curation of phylogenetic topologies to assess HGT candidates.

Main Results:

• Only 29.3% of previously reported interkingdom HGT cases in plants were supported by reanalysis.
• Many candidate HGT events are better explained by factors like incomplete taxon sampling or gene loss.
• Phylogenetic reconstructions are sensitive to data and methodology, requiring careful interpretation.

Conclusions:

• The prevalence of interkingdom HGT in plants is likely overestimated.
• Alternative evolutionary mechanisms provide more parsimonious explanations for many observed gene phylogenies.
• Caution is advised against defaulting to HGT as the primary explanation for unusual gene origins in plant genomes.