Chapter 28 Horizontal Gene Transfer in Eukaryotic Parasites: A Case Study of Entamoeba histolytica and Trichomonas vaginalis U. Cecilia Alsmark, Thomas Sicheritz-Ponten, Peter G. Foster, Robert P. Hirt, and T. Martin Embley Abstract Over the past few years it has become apparent that horizontal gene transfer (HGT) has played an impor- tant role in the evolution of pathogenic prokaryotes. What is less clear is the exact role that HGT has played in shaping the metabolism of eukaryotic organisms. The main problems are the reliable inference of HGT on a genomic scale as well as the functional assignment of genes in these poorly studied organ- isms. We have screened the completed genomes of the protists Entamoeba histolytica and Trichomonas vaginalis for cases of HGT from prokaryotes. Using a fast primary screen followed by a conservative phy- logenetic approach, we found 68 and 153 recent cases of HGT in the respective organisms. The majority of transferred genes that fall into functional categories code for enzymes involved in metabolism. We found a broad range of prokaryotic lineages represented among the donors, but organisms that share similar environmental niches with E. histolytica and T. vaginalis, such as the gut and the vaginal mucosa, dominate. Key words: Entamoeba histolytica, Trichomonas vaginalis, genome-wide analysis, phylogeny, metabolic genes, donor lineages, sampling. 1. Introduction HGT plays a significant role in prokaryotic genome evolution, contributing up to ∼20% of the content of a given genome (1). HGT thus provides an efficient means of gaining new phenotypes, such as resistance to antibiotics and new physiolog- ical and metabolic capabilities, permitting or facilitating adapta- tion to new ecological niches (2–4). More recently, data from microbial eukaryotes suggest that HGT also plays a role in Maria B. Gogarten et al. (eds.), Horizontal Gene Transfer: Genomes in Flux, vol. 532 C  Humana Press, a part of Springer Science+Business Media, LLC 2009 DOI 10.1007/978-1-60327-853-9 28 Springerprotocols.com 489