Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote

Abstract

The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.

Origin and Distribution of Calvin Cycle Fructose and Sedoheptulose Bisphosphatases in Plantae and Complex Algae: A Single Secondary Origin of Complex Red Plastids and Subsequent Propagation via Tertiary Endosymbioses

“…2). Therefore, these non-orthologous genes provide no evidence for a cryptic plastid in ciliates, which is in agreement with the recent analysis of the complete genome of Tetrahymena thermophila (Eisen et al 2006). On the contrary, they likely fulfill a nonphotosynthetic function, as proposed for their kinetoplastid and ascomycete counterparts.…”

A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids

“…In particular, the data now supporting the photosynthetic ancestor of apicomplexans and dinoflagellates lead us to infer that the ancestor of the apicomplexan Cryptosporidium had a plastid despite the absence of plastid ultrastructure or genes for plastid-targeted proteins. A similar case can be made for ciliates and various nonphotosynthetic heterokonts (in particular oomycetes) where whole genomes again confirm the absence of a plastid (37,38), although claims of relict plastid endosymbiont genes have been made (38,39). Overall, the apicomplexans, dinoflagellates, and their close relatives are a hotspot for loss of plastids and photosynthesis and further research on this group will likely give us important clues about plastid and photosynthesis loss in other algal lineages.…”

Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species

“…To be able to observe different expansion patterns, these z-score profiles were hierarchically clustered. We removed the gene families that were only expanded in the outgroups and the gene families only expanded in one or both of the ciliates because their massive duplication events (28,29) reduce the expansion signal of the other chromalveolates. This analysis yielded 119 gene families (see Methods) (Fig.…”