Contents -- List of contributors -- Introduction -- Part I -- 1 Current perspectives on high-level groupings of protists -- Part II: Evolutionary genomics of eukaryotic microbes -- 2 Comparative genomics of Plasmodium species -- 3 The genomes of dinoflagellates -- 4 Ciliate genome evolution -- 5 Molecular evolution of Foraminifera -- 6 Photosynthetic organelles and endosymbiosis -- 7 Genome evolution of anaerobic protists: metabolic adaptation via gene acquisition -- 8 Horizontal and intracellular gene transfer in the Apicomplexa: The scope and functional consequences -- Part III: Analyses of complete genomes -- 9 The nuts and bolts of sequencing protist genomes -- 10 Comparative genomics of the trypanosomatids -- 11 The genome of Entamoeba histolytica -- 12 Genome reduction in Microsporidia -- 13 Nucleomorphs: remnant nuclear genomes -- 14 Genomic insights into diatom evolution and metabolism -- 15 The Dictyostelium genome - a blueprint for a multicellular protist -- Index -- A -- B -- C -- D -- E -- F -- G -- H -- I -- J -- K -- L -- M -- N -- O -- P -- Q -- R -- S -- T -- U -- V -- W -- X -- Y -- Z.