Chapter 27 Horizontal Gene Transfer Between Microbial Eukaryotes Jan O. Andersson Abstract Comparative genomics have identified two loosely defined classes of genes: widely distributed core genes that encode proteins for central functions in the cell and accessory genes that are patchily distributed across lineages and encode taxa-specific functions. Studies of microbial eukaryotes show that both cate- gories undergo horizontal gene transfer (HGT) from prokaryotes, but also between eukaryotic organ- isms. Intra-domain gene transfers of most core genes seem to be relatively infrequent and therefore comparatively easy to detect using phylogenetic methods. In contrast, phylogenies of accessory genes often have complex topologies with little or no resemblance of organismal relationships typically with eukaryotes and prokaryotes intermingled, making detailed evolutionary histories difficult to interpret. Nevertheless, this suggests significant rates of gene transfer between and among the three domains of life for many of these genes, affecting a considerably diversity of eukaryotic microbes, although the current depth of taxonomic sampling usually is insufficient to pin down individual transfer events. The occurrence of intra-domain transfer among microbial eukaryotes has important implications for studies of organismal phylogeny as well as eukaryote genome evolution in general. Key words: Accessory genes, core genes, gene loss, genome evolution, inter-domain HGT, intra- domain HGT, patchily distributed genes, phylogeny, protists. 1. Introduction Due to the shortage of comparative genomic data covering the eukaryotic diversity, the knowledge about HGT in eukary- otic genome evolution is currently rather limited, in contrast to the situation for prokaryotes where this evolutionary mech- anism have been intensively studied (1, 2). However, large- scale phylogenetic analyses on genomic data (phylogenomics) have shown that several distantly related microbial eukary- otes have acquired mostly metabolic genes from prokaryotes 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 27 Springerprotocols.com 473