Figure 1.
Unrooted Consensus Phylogeny of Major Eukaryotic Lineages
Representative genera are shown for which whole genome sequence data are either in progress (marked with asterisks *) or available. The ciliates, dinoflagellates, and apicomplexans constitute the alveolates (lighter yellow box). Branch lengths do not correspond to phylogenetic distances. Adapted from the more detailed consensus in [197].
Figure 2.
Relationship between MIC and MAC Chromosomes
The top horizontal bar shows a small portion of one of the five pairs of MIC chromosomes. MAC-destined sequences are shown in alternating shades of gray. MIC-specific IESs (internally eliminated sequences) are shown as blue rectangles, and sites of the 15-bp Cbs are shown as red bars (not to scale). Below the top bar are shown macronuclear chromosomes derived from the above region of the MIC by deletion of IESs, site-specific cleavage at Cbs sites, and amplification. Telomeres are added to the newly generated ends (green bars). Most of the MAC chromosomes are amplified to approximately 45 copies (only three shown). Through the process of phenotypic assortment, initially heterozygous loci generally become homozygous in each lineage within approximately 100 vegetative fissions. Polymorphisms located on the same MAC chromosome tend to co-assort.
Table 1.
Important Genome Statistics
Figure 3.
(A) Scaffold sizes versus MAC chromosome size. Blue diamonds represent scaffolds capped by telomeres on both ends. Red squares and green triangles represent incomplete scaffolds capped by telomeres at one or neither end, respectively.
(B) Size distribution of scaffolds capped by telomeres on both ends.
Figure 4.
Depth of Coverage versus Scaffold Size
Black diamonds indicate all scaffolds; red diamonds, scaffolds capped with telomeres on both ends.
Table 2.
Characteristics of Ab Initio Predicted Genes
Figure 5.
(A) Effective number of codons (ENc; a measure of overall codon bias) for each predicted ORF is plotted versus GC3 (the fraction of codons that are synonymous at the third codon position that have either a guanine or a cytosine at that position). The upper limit of expected bias based on GC3 alone is represented by the black curve; most T. thermophila ORFs cluster below the curve [red dots as in (B)].
(B) Principal component analysis of relative synonymous codon usage in T. thermophila. The 232 genes in the tail of the comma-shaped distribution (those with the most biased codon usage) are colored red.
(C) Principal component analysis of relative synonymous codon usage in P. falciparum.
Table 3.
Gene Families
Table 4.
Numbers of Protein-Coding Genes in Various Eukaryotes
Figure 6.
Orthologs Shared among T. thermophila and Selected Eukaryotic Genomes
Venn diagram showing orthologs shared among human, the yeast S. cerevisiae, the apicomplexan P. falciparum, and T. thermophila. Lineage-specific gene duplications in each of the organisms were identified and treated as one single gene (or super-ortholog). Pairwise mutual best-hits by BLASTP were then identified as putative orthologs.
Table 5.
Distribution of Selected Protein Kinase Classes in T. thermophila and Other Classified Kinomes
Table 6.
Comparison of the Numbers of Membrane Transporters in T. thermophila and Other Eukaryotes by Family and Predicted Substrate
Table 7.
Protease Complements in T. thermophila and Other Model Organisms
Table 8.
Numbers of Loci Encoding Selected Types of Cytoskeletal Genes in T. thermophila and H. sapiens
Figure 7.
Tubulin Gene Diversity in T. thermophila
The figure shows a neighbor-joining tree built from a clustalX alignment. Species abbreviations: Hs, H. sapiens; Dm, D. melaogaster; Sc, S. cerevisiae; Tt, T. thermophila; Pt, P. tetraurelia; Cr, C. reinhardtii; Tb, T. brucei; Ec, E. coli; Xl, Xenopus laevis. A prokaryotic tubulin ortholog, Escherichia coli FtsZ, was used as the outgroup.