Lateral gene transfer leaves lasting traces in Rhizaria

Lateral gene transfer (LGT) is a fundamental process that has contributed to the genetic makeup of various eukaryotic lineages. Yet our comprehension of its prevalence and significance across the eukaryotic domain remains incomplete, particularly when it comes to eukaryote-to-eukaryote transfers. The Rhizaria forms an expansive, ancient, and morphologically diverse clade of mostly free-living, single-celled phagotrophs, whose genetic diversity reflects their adaptability and evolutionary success across a range of habitats. Here, we undertake a comprehensive investigation of LGT within Rhizaria, tracing its role from the clade's emergence to the present day, employing advanced phylogenetic analyses and machine learning techniques. Contrary to previous assertions that LGT in eukaryotes is rare, our findings suggest that at least 8% of genes in contemporary rhizarian genomes were acquired through LGT at various points during their billion-year history. Our analysis reveals that although gene duplications exceed the number of LGT events, the duplicated genes that were originally acquired through LGT have a visible effect on the evolutionary trajectory of the recipient organisms. Our results also indicate that LGTs originating from other eukaryotes are more common than those from prokaryotes and exhibit unique patterns. By offering both quantitative and qualitative insights into the role of LGT in shaping the evolution of a major eukaryotic lineage, this work further demystifies lateral gene transfer in eukaryotes.