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

Jonathan A Eisen ,Mathangi Thiagarajan,Dongying Wu,Lei Sun,Christina Del Toro,Joseph Frankel,Zasha Weinberg,J Michael Cherry,Paolo Amedeo,Jyoti Garg,Kathleen Collins,Jacek Gaertig,Eduardo Orias,Katarzyna Wilamowska,Gerard Manning,Che-Chia Tsao,Yufeng Wang,Qinghu Ren,Martin Wu,Rebecca Barbeau ,Suzanne R Lee ,David E Wilkes ,Kathleen M Karrer ,Nicola J Patron ,Jonathan H Badger ,Sondra Williamson ,Martin A Gorovsky ,Steven L Salzberg ,Hong-Hong Cai ,William H Majoros ,Dorota Włoga ,Joana C Silva ,Aaron P Turkewitz ,Walter L Ruzzo ,David J Asai ,Nicholas A Stover ,Hilary F Ryder ,Maryam Sharafi Farzad ,Roger K Smith ,Robert S Coyne ,Jennifer Wortman ,Arthur L Delcher ,Jane M Carlton ,Eileen P Hamilton ,Balint Stewart ,Ross F Waller ,Ronald E Pearlman ,Brian J Haas ,Nels C Elde ,Cynthia J Krieger ,Luke J Tallon ,Kristie M Jones ,Patrick J Keeling

doi:10.1371/journal.pbio.0040286

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.

Highlights

Tetrahymena thermophila is a single-celled model organism for unicellular eukaryotic biology [1]
The putative T. thermophila tRNA-Sec was identified by analysis of the genome sequence and shown to be transcribed and acylated [61], and we have found that it is expressed and charged and that its charging may be under distinct regulatory control from other tRNAs (Figure S4A)
To better understand what role genes involved in microtubule and cytoskeletal functions might have played in the diversification of this species, we focused analysis on some of the genes with apparent expansions: tubulins, dyneins, and regulatory proteins

Summary

Introduction

Tetrahymena thermophila is a single-celled model organism for unicellular eukaryotic biology [1]. Since it is possible some of the 1,970 gene families could have originated by duplications that occurred prior to the origin of the IES excision process, it is more useful to examine recent duplications We searched for such duplications in multiple ways, including the identification of genes duplicated in the T. thermophila lineage relative to other lineages for which genomes are available (Table S10) and by searching for pairs of paralogs with very similar sequences. T. thermophila has more representatives in each of the four major families than do humans It encodes a much higher number of transporters in the ABC superfamily, voltagegated ion channels (VICs), and P-type ATPases than any other sequenced eukaryotic species (Table 6) including the other free-living protists, the diatom Thalassiosira pseudonana, and the slime mold D. discoideum. The TGD staff is always available to help individual researchers by answering questions, finding information, and generating datasets specific to their needs

Conclusions and Future Plans

Findings

Materials and Methods