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PMID: 16933976 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

PLoS biology ·Vol. 4 ·No. 9 ·2006-09-00 ·Pages e286

Eisen JA, Coyne RS, Wu M, Wu D, Thiagarajan M, Wortman JR, Badger JH, Ren Q, Amedeo P, Jones KM, Tallon LJ, Delcher AL, Salzberg SL, Silva JC, Haas BJ, Majoros WH, Farzad M, Carlton JM, Smith RK, Garg J, Pearlman RE, Karrer KM, Sun L, Manning G, Elde NC, Turkewitz AP, Asai DJ, Wilkes DE, Wang Y, Cai H, Collins K, Stewart BA, Lee SR, Wilamowska K, Weinberg Z, Ruzzo WL, Wloga D, Gaertig J, Frankel J, Tsao CC, Gorovsky MA, Keeling PJ, Waller RF, Patron NJ, Cherry JM, Stover NA, Krieger CJ, del Toro C, Ryder HF, Williamson SC, Barbeau RA, Hamilton EP, Orias E

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.

MeSH Terms
Animals Cells, Cultured Chromosome Mapping/methods Chromosomes Databases, Genetic Eukaryotic Cells/physiology Evolution, Molecular Genome, Protozoan Macronucleus/genetics Micronucleus, Germline/genetics Models, Animal Models, Biological Phylogeny Signal Transduction Tetrahymena thermophila/genetics
Authors & Affiliations
53 authors, click to expand affiliations / ORCID
Eisen Jonathan A
The Institute for Genomic Research, Rockville, Maryland, United States of America. jaeisen@ucdavis.edu
Coyne Robert S
Wu Martin
Wu Dongying
Thiagarajan Mathangi
Wortman Jennifer R
Badger Jonathan H
Ren Qinghu
Amedeo Paolo
Jones Kristie M
Tallon Luke J
Delcher Arthur L
Salzberg Steven L
Silva Joana C
Haas Brian J
Majoros William H
Farzad Maryam
Carlton Jane M
Smith Roger K
Garg Jyoti
Pearlman Ronald E
Karrer Kathleen M
Sun Lei
Manning Gerard
Elde Nels C
Turkewitz Aaron P
Asai David J
Wilkes David E
Wang Yufeng
Cai Hong
Collins Kathleen
Stewart B Andrew
Lee Suzanne R
Wilamowska Katarzyna
Weinberg Zasha
Ruzzo Walter L
Wloga Dorota
Gaertig Jacek
Frankel Joseph
Tsao Che-Chia
Gorovsky Martin A
Keeling Patrick J
Waller Ross F
Patron Nicola J
Cherry J Michael
Stover Nicholas A
Krieger Cynthia J
del Toro Christina
Ryder Hilary F
Williamson Sondra C
Barbeau Rebecca A
Hamilton Eileen P
Orias Eduardo
Conflict of Interest

Competing interests. The authors have declared that no competing interests exist.

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Article Info
Journal
PLoS biology
Abbr.
PLoS Biol
ISSN
1545-7885
DOI
10.1371/journal.pbio.0040286
Email
jaeisen@ucdavis.edu
Published
2006-09-00
Pages
e286
Language
English
Region
United States
NLM ID
101183755
PMCID
PMC1557398
Subset
IM
Grants
NCRR NIH HHS · R01 RR009231 · United States
NLM NIH HHS · R01 LM006845-08 · United States
NCRR NIH HHS · RR-009231 · United States
NIGMS NIH HHS · R01 GM067012 · United States
NLM NIH HHS · R01 LM007938 · United States
NLM NIH HHS · R01 LM006845 · United States
NLM NIH HHS · R01 LM007938-04 · United States
NIGMS NIH HHS · GM067012-03 · United States
Corrections
CommentIn
PMID: 20076635
External Links
PubMed source DOI: 10.1371/journal.pbio.0040286 PMC Full Text View journal details
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