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Cryptomonads are aquatic unicellular eukaryotes that inhabit both marine and freshwater environments. Most cryptomonads are photosynthetic (and are thus referred to as cryptophytes) and possess plastids that are very diverse in pigmentation (Figure 1). In addition to being important from an ecological perspective, the cryptophytes are of pivotal significance in terms of our understanding of endosymbiosis and the evolution of plastids. This is because cryptophytes acquired photosynthesis by the process of secondary (i.e., eukaryote-eukaryote) endosymbiosis, having engulfed and assimilated a red algal endosymbiont at some time during their evolutionary past (Archibald and Keeling 2002; Bhattacharya et al. 2003; Gould et al. 2008). As a result, cryptophytes are extremely complex from a genetic and cell biological perspective, having a four-membrane-bound plastid and four distinct DNA-containing cellular compartments, the plastid, mitochondrion, host nucleus and endosymbiont nucleus, the latter being referred to as the nucleomorph. The cryptophyte nucleomorph genome is highly reduced in structure and coding capacity, and is the focus of ongoing research aimed at understanding the pattern and process of secondary endosymbiosis (Gilson and McFadden 2002; Archibald 2007).