Lateral gene transfer leaves lasting traces in Rhizaria

Eukaryotic lineages acquire numerous prokaryotic genes via lateral gene transfer (LGT). However, LGT in eukaryotes holds many unknowns, especially its frequency, its long-term impact, and the importance of eukaryote-to-eukaryote LGT. LGT, and genome evolution in general, has not been rigorously studied in Rhizaria, which is a large and diverse eukaryotic clade whose members are mostly free-living, single-celled phagotrophs. We here explore LGT across Rhizaria since their origin until modern-day representatives, using a systematic, phylogenetic approach. On average, 30% of the genes present in current-day rhizarian genomes have originated through LGT at some point during the history of Rhizaria, which emerged about one billion years ago. We show that while LGTs are outnumbered by gene duplications, transferred genes themselves duplicate frequently, thereby amplifying their impact on the recipient lineage. Strikingly, eukaryote-derived LGTs were more prevalent than prokaryotic ones, and carry distinct signatures. Altogether, we here quantitatively and qualitatively reveal how LGT affected an entire eukaryotic phylum, thereby further demystifying LGT in eukaryotes.