Horizontal Gene Transfer

Eukaryotes

"Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic "domains". Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes".

Analysis of DNA sequences suggests that horizontal gene transfer has also occurred within eukaryotes from the chloroplast and mitochondrial genomes to the nuclear genome. As stated in the endosymbiotic theory, chloroplasts and mitochondria probably originated as bacterial endosymbionts of a progenitor to the eukaryotic cell.
Horizontal transfer of genes from bacteria to some fungi, especially the yeast Saccharomyces cerevisiae, has been well documented.
There is also recent evidence that the adzuki bean beetle has somehow acquired genetic material from its (non-beneficial) endosymbiont Wolbachia. New examples have recently been reported demonstrating that Wolbachia bacteria represent an important potential source of genetic material in arthropods and filarial nematodes.
There is also evidence for horizontal transfer of mitochondrial genes to parasites of the Rafflesiaceae plant family from their hosts (also plants), from chloroplasts of a not-yet-identified plant to the mitochondria of the bean Phaseolus, and from a heterokont alga to its predator, the sea slug Elysia chlorotica.
Striga hermonthica, a eudicot, has undergone a horizontal gene transfer from Sorghum (Sorghum bicolor) to its nuclear genome. The gene is of unknown functionality.
Researchers at the University of Arizona have found that the genome of pea aphids (Acyrthosiphon pisum) contains multiple genes that were horizontally transferred from fungi. Plants, fungi, and microorganisms can synthesize carotenoids, but torulene made by pea aphids is the only carotenoid known to be synthesized by an organism in the animal kingdom.
It was recently suggested that the malaria causing pathogen Plasmodium vivax has horizontally acquired from humans genetic material that might help facilitate its long stay in the body.
A 2012 paper proposes a novel bacteriophage-mediated mechanism of horizontal gene transfer between prokaryotes and eukaryotes. The authors show the widespread presence of nuclear localization signals in bacteriophage terminal proteins (TP), which prime DNA replication and become covalently linked to the viral genome. Taking into account the known role of virus and bacteriophages in HGT in bacteria, the authors propose that TP-containing genomes could be a vehicle of inter-kingdom genetic information transference all throughout evolution.