A schematic of a Chlamydomonas cell (from transmission electron micrographs) showing the anterior flagella rooted in basal bodies, with intraflagellar transport (IFT) particle arrays between the axoneme and flagellar membrane, the basal cup-shaped chloroplast, central nucleus and other organelles. An expanded cross section of the flagellar axoneme, as redrawn from (48), shows the nine outer doublets and the central pair (9+2) microtubules; axoneme substructures are color-coded and labeled (see inset).

Linkage group I depicted as a long horizontal rod, with genetically mapped scaffolds shown as open rectangles below (the scaffold number is under each scaffold, and arrows indicate the orientation of the scaffold where it is known; other scaffolds were placed in their most likely orientation on the basis of genetic map distances. The scale of each map is determined by molecular lengths of the mapped scaffolds. Short and long red ticks are drawn on scaffolds every 0.2 Mb and 1.0 Mb, respectively. We assumed small 50 kb gaps between scaffolds. Genetic distances between markers (centimorgans), where they are known, are shown by two-headed arrows above the scaffold, with the gene symbol and any synonyms in parentheses shown at the top. Genomic regions are labeled below the scaffolds: 5S, rDNA, mito (insertion of mitochondrial DNA). Chlamydomonas genes with homologs in other organisms/lineages (“Cuts” as defined in the text and Fig. 5) are shown as tracks of vertical bars: light red, genes shared between Chlamydomonas and humans, but not occurring in nonciliated organisms; dark red, genes in CiliaCut; light green, genes shared between Chlamydomonas and Arabidopsis, but not in nonphotosynthetic organisms; dark green, genes in GreenCut; magenta, predicted tRNAs, including those that represent SINE sequences; dark blue, small nucleolar RNAs (snoRNAs).

Summary of genomic comparisons to photosynthetic and ciliated organisms. (A) GreenCut: The GreenCut comprises 349 Chlamydomonas proteins with homologs in representatives of the green lineage of the Plantae (Chlamydomonas, Physcomitrella, and Ostreococcus tauri and O. lucimarinus), but not in nonphotosynthetic organisms. Genes encoding proteins of unknown function that were not previously annotated were given names on the basis of their occurrence in various cuts. CGL refers to conserved only in the green lineage. The GreenCut protein families, which also include members from the red alga Cyanidioschyzon within the Plantae, were assigned to the PlantCut (blue plus green rectangles). CPL refers to conserved in the Plantae. GreenCut proteins also present in at least one diatom (Thalassiosira and Phaeodactylum) were assigned to the DiatomCut (yellow plus green rectangle). CGLD refers to conserved in the green lineage and diatoms. Proteins present in all of the eukaryotic plastid-containing organisms in this analysis were assigned to the PlastidCut (green rectangle). CPLD refers to conserved in the Plantae and diatoms. The criteria used for the groupings associated with the GreenCut are given in the lower table. (B) CiliaCut: The CiliaCut contains 195 Chlamydomonas proteins with homologs in human and species of Phytophthora, but not in nonciliated organisms. This group was subdivided on the basis of whether or not a homolog was present in Caenorhabditis, which has only nonmotile sensory cilia. The 133 CiliaCut proteins without homologs in Caenorhabditis were designated the MotileCut (orange rectangle). Unnamed proteins in this group were named MOT (motility). Proteins with homologs in Caenorhabditis are associated with nonmotile cilia (white and yellow areas). Proteins in this group that were not already named were named SSA. The CentricCut (yellow plus light orange box) is made up of 69 CiliaCut homologs present in the centric diatom Thalassiosira. These proteins can be divided into those also in the MotileCut (38 proteins; light orange box) or those not present in the MotileCut (31 proteins; yellow box).

Evolutionary relationships of 20 species with sequenced genomes (54, 55) used for the comparative analyses in this study include cyanobacteria and nonphotosynthetic eubacteria, Archaea and eukaryotes from the oomycetes, diatoms, rhodophytes, plants, amoebae and opisthokonts. Endosymbiosis of a cyanobacterium by a eukaryotic protist gave rise to the green (green branches) and red (red branches) plant lineages, respectively. The presence of motile or nonmotile flagella is indicated at the right of the cladogram.

(A) Scatter plot of best BLASTP hit score of Chlamydomonas proteins to Arabidopsis proteins versus best BLASTP hit score of Chlamydomonas proteins to human proteins. Functional or genomic groupings are colored [see inset key in (A)]: Chlamydomonas flagellar proteome (42) high confidence set (chlamyFPhc); CiliaCut; Arabidopsis stroma plastid proteome (stromaPP); Arabidopsis thylakoid plastid proteome (thylakoidPP); eyespot proteome; GreenCut; remaining proteins are gray. (B) Chlamydomonas protein paralogs were grouped into families together with their homologs from human and Arabidopsis. The outer circle represents the proteins in Chlamydomonas, 7476 (out of 15,143 total), that fall into 6968 families. Another 7937 proteins cannot be placed in families. Counts of families (and the numbers of proteins from each species in them) with proteins from Chlamydomonas and human only, Chlamydomonas and Arabidopsis only, and Chlamydomonas and human and Arabidopsis, are shown in the inner circles and the overlap between the two inner circles, respectively. Cre, Chlamydomonas; Hsa, human; Ath, Arabidopsis.