Horizontal gene transfer is widespread in diverse eukaryotes

Horizontal gene transfer (HGT) is the transfer of genetic material between distantly related organisms. Although HGT is a pervasive mechanism of genetic exchange among prokaryotes, gene transfer events involving eukaryotes are generally considered rare and restricted to a small number of lineages. Here we report genome-wide identification of HGT regions (HGTs) in 10 eukaryotes, including human, mouse, cow, lizard, frog, zebrafish, fruit fly, nematode, Arabidopsis and yeast. By comparing their genomes with thousands of eukaryote, bacteria and virus genomes, we found between 10 and 237 non-redundant HGTs per eukaryote species. Third-generation sequencing across most of the 10 analyzed genomes, combined with targeted PCR in Arabidopsis thaliana, was applied to validate the result HGTs and exclude contamination. Genes impacted by HGTs are enriched in transmembrane transport. Some HGTs have duplicated extensively within the host genome, affecting hundreds, even thousands of genes. Our findings reveal that HGT is ubiquitous in all diverse eukaryotes analyzed here, and it is a non-negligible, previously underappreciated contributor to genome evolution for eukaryotes.