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

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

Early Intervention in Low-Birth-Weight Premature Infants: Results Through Age 5 Years From the Infant Health and Development Program

Objective.—To evaluate the persistence of effects on health and development at age 5 years of the Infant Health and Development Program, an early childhood intervention that was provided to low-birth-weight (LBW) premature infants from neonatal discharge through age 3 years.Design.—Randomized, controlled, multicenter trial, stratified by two LBW groups: lighter (≤2000 g) and heavier (2001 to 2500 g).Setting.—Eight socioeconomically heterogeneous clinical sites.Participants.—Of 985 eligible infants weighing 2500 g or less and at 37 weeks' or less gestational age, 377 infants were randomly assigned to the intervention group and 608 to the follow-up only group. About two thirds of the infants in each group were in the lighter LBW stratum, and one third were in the heavier LBW stratum.Intervention.—The intervention group received home visits (from neonatal discharge through age 3 years) as well as center-based schooling (from 1 to 3 years of age). Children in both groups received pediatric surveillance.Main Outcome Measures.—Cognitive development, behavioral competence, and health status.Results.—At age 5 years, the intervention group had full-scale IQ scores similar to children in the follow-up only group. However, in the heavier LBW stratum, children in the intervention group had higher full-scale IQ scores (3.7 points higher; P=.03) and higher verbal IQ scores (4.2 points higher; P=.02). No significant differences between intervention and follow-up only groups in cognitive measures at age 5 years were noted in the lighter LBW infants. The intervention and follow-up groups were similar in behavior and health measures regardless of LBW stratum.Conclusion.—The early childhood intervention provided in the first 3 years of life had effects on heavier LBW premature infants' IQ and verbal performance at age 5 years that were not observed for lighter LBW premature infants. The intervention did not affect health or behavior at age 5 years in either LBW stratum.(JAMA. 1994;272:1257-1262

Orthologs Shared among T. thermophila and Selected Eukaryotic Genomes

<p>Venn diagram showing orthologs shared among human, the yeast <i>S. cerevisiae,</i> the apicomplexan <i>P. falciparum,</i> 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.</p

Codon Usage

<div><p>(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)].</p> <p>(B) Principal component analysis of relative synonymous codon usage in <i>T. thermophila.</i> The 232 genes in the tail of the comma-shaped distribution (those with the most biased codon usage) are colored red.</p> <p>(C) Principal component analysis of relative synonymous codon usage in <i>P. falciparum.</i></p></div

Unrooted Consensus Phylogeny of Major Eukaryotic Lineages

<p>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 [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0040286#pbio-0040286-b197" target="_blank">197</a>].</p

Relationship between MIC and MAC Chromosomes

<p>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.</p

Depth of Coverage versus Scaffold Size

<p>Black diamonds indicate all scaffolds; red diamonds, scaffolds capped with telomeres on both ends.</p