Research Article

The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions

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Science  12 Oct 2007:
Vol. 318, Issue 5848, pp. 245-250
DOI: 10.1126/science.1143609
  • Fig. 1.

    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 sub-structures are color-coded and labeled (see inset).

  • Fig. 2.

    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.

  • Fig. 3.

    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).

  • Fig. 4.

    (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.

  • Fig. 5.

    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).

  • Table 1.

    Comparison of Chlamydomonas genome statistics to those of selected sequenced genomes. nd, Not determined. [Source for all but Chlamydomonas (1)]

    ChlamydomonasOstreococcus tauriCyanidioschyzonArabidopsis Human
    Assembly length (Mb) 121 12.6 16.5 140.1 2,851
    Coverage 13× 6.7× 11× nd ∼8×
    Chromosomes 17 20 20 5 23
    G+C (%) 64 58 55 36 41
    G+C (%) coding sequence 68 59 57 44 52
    Gene number 15,143 8,166 5,331 26,341 ∼23,000
    Genes with EST support (%) 63 36 86 60 nd
    Gene density (per kb) 0.125 0.648 0.323 0.190 ∼0.0008
    Average bp per gene 4312 nd 1553 2232 27,000
    Average bp per transcript 1580 1257 1552 nd nd
    Average number of amino acids per polypeptide 444 387 518 413 491
    Average number of exons per gene 8.33 1.57 1.005 5.2 8.8
    Average exon length 190 750 1540 251 282*
    Genes with introns (%) 92 39 0.5 79 85
    Mean length of intron 373 103 248 164 3,365
    Coding sequence (%) 16.7 81.6 44.9 33.0 ∼1
    Number of rDNA units (28S/18S/5.8S + 5S) 3 + 3 4 + 4 3 + 3 12 + 700 5 + nd
    Number tRNAs 259§ nd 30 589 497
    Selenocysteine (Sec) tRNAs 1 nd nd 0 1
    • * National Center for Biotechnology Information (NIH) NCBI 36 from Ensembl build 38.

    • [Source (56)].

    • Three regions contain 5S rDNA exclusively, and three regions contain 28S-18S-5.8S rDNAs exclusively.

    • § 65 tRNAs that were included in SINE elements were removed from the tRNA-scanSE predictions.

Additional Files


  • The Chlamydomonas Genome Reveals the Evolution of Key Animal and Plant Functions
    Sabeeha S. Merchant, Simon E. Prochnik, Olivier Vallon, Elizabeth H. Harris, Steven J. Karpowicz, George B. Witman, Astrid Terry, Asaf Salamov, Lillian K. Fritz-Laylin, Laurence Mar�chal-Drouard, Wallace F. Marshall, Liang-Hu Qu, David R. Nelson, Anton A. Sanderfoot, Martin H. Spalding, Vladimir V. Kapitonov, Qinghu Ren, Patrick Ferris, Erika Lindquist, Harris Shapiro, Susan M. Lucas, Jane Grimwood, Jeremy Schmutz, Chlamydomonas Annotation Team, JGI Annotation Team, Igor V. Grigoriev, Daniel S. Rokhsar, Arthur R. Grossman

    Supporting Online Material

    This supplement contains:
    Materials and Methods
    SOM Text
    Figs. S1 to S25
    Tables S1 to S14
    References

    This file is in Adobe Acrobat PDF format.

    Other Supporting Online Material for this manuscript includes the following:
    (available at www.sciencemag.org/cgi/content/full/318/5848/245/DC1)
    Table SA. Details of genes in GreenCut
    Table SB. Details of genes in CiliaCut

    Supporting Tables S1 and S2. Data tables, in Microsoft Excel format. Files are packaged as a compressed archive, in *.zip format; users should download the compressed file to their machine and decompress the file on their local hard drive, using the instructions below.

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