Horizontal gene transfer (HGT) is the movement of genetic material between different species and is considered to be one of the major driving forces of prokaryotic evolution [1
]. Until recently, it was believed that this phenomenon was largely restricted to the prokaryotic domain. In eukaryotes, gene duplication has classically been viewed as the major source of genetic novelty [5
]; this paradigm of eukaryotic evolution is based on genome studies of model organisms such as multicellular plants, animals, and fungi. In the last decade, rapid accumulation of genome data from unicellular eukaryotes, protists, has allowed researchers to reassess the role of HGT in eukaryotic evolution. The results of comparative analyses of genomes of anaerobic parasitic protists provided a major breakthrough in our understanding of the impact of interdomain HGT in eukaryotes. For example, 96 potential cases of prokaryote-to-eukaryote HGT were identified in the genome of an intestinal parasite of humans and animals Entamoeba histolytica
], 84 in the fish parasite Spironucleus salmonicida
], 152 in a sexually transmitted human pathogen Trichomonas vaginalis
], 24 in Cryptosporidium parvum
], and 148 in anaerobic rumen ciliates [11
]. These numbers comprise up to 4% of genes in the extremely reduced genomes of these anaerobic protists. It is believed that the acquisition of bacterial genes by these eukaryotes accelerated their adaptation to anaerobic environments and the transition to a parasitic life style. Several recent reports indicate that HGT also plays a role in the genome evolution of free-living protists. Analysis of the complete genome sequence of the soil amoeba Dictyostelium discoideum
led to the identification of 18 genes derived from prokaryotes [12
]. Several cases of HGT have been reported for dinoflagellate and chlorarachniophyte algae [13
]. The fact that complete genome sequences are available now for a limited number of free living protists explains a significant disproportion in the study of HGT in different groups of protists. However, public databases also contain Expressed Sequence Tag (EST) libraries for over 50 species of free living unicellular eukaryotes [17
] that can also be used to assess the impact of HGT on genome evolution in protists.
Here we analyze EST and complete genome data to study HGT in chromalveolate protists. Chromalveolates comprise the six eukaryotic lineages, cryptophytes, haptophytes, stramenopiles, ciliates, apicomplexans, and dinoflagellates and have adapted to a wide variety of environments. They are characterized by a tremendous diversity of forms and modes of nutrition including heterotrophy, parasitism, phototrophy, and mixotrophy. According to the chromalveolate hypothesis, the common ancestor of the six constituent lineages was a free living photosynthetic organism that derived its plastid via
a red algal secondary endosymbiosis [19
]. Within-chromalveolate taxon relationships and the monophyly of this group are controversial [20
]. Nuclear gene phylogenies support the monophyly of stramenopiles, ciliates, apicomplexans, and dinoflagellates and monophyly of cryptophytes and haptophytes [21
]. However, relationships between the two clades still remain unresolved.
Gene movement from the endosymbiont to the host nucleus is a specific instance of HGT that is referred to as endosymbiotic gene transfer (EGT). The impact of EGT on the evolution of chromalveolate genomes has been intensively studied in the last decade [23
] and will not be considered here. We limited our research to gene transfers from non-organellar sources. To identify genes acquired by chromalveolates through HGT at different time points in their evolutionary history, we performed a broad scale phylogenetic analysis of the EST data generated for a free living phototrophic dinoflagellate alga Karenia brevis
that is renowned as an agent of toxic algal blooms that annually cause massive fish and marine mammal mortality in the Gulf of Mexico [28
]. Detailed analyses of the identified genes presented in this paper suggest that recurring inter- and intradomain gene movement should be considered as an important source of genetic novelty in chromalveolates.