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.
Eisen
Jonathan A
JA
The Institute for Genomic Research, Rockville, Maryland, United States of America. jaeisen@ucdavis.edu
Coyne
Robert S
RS
Wu
Martin
M
Wu
Dongying
D
Thiagarajan
Mathangi
M
Wortman
Jennifer R
JR
Badger
Jonathan H
JH
Ren
Qinghu
Q
Amedeo
Paolo
P
Jones
Kristie M
KM
Tallon
Luke J
LJ
Delcher
Arthur L
AL
Salzberg
Steven L
SL
Silva
Joana C
JC
Haas
Brian J
BJ
Majoros
William H
WH
Farzad
Maryam
M
Carlton
Jane M
JM
Smith
Roger K
RK
Garg
Jyoti
J
Pearlman
Ronald E
RE
Karrer
Kathleen M
KM
Sun
Lei
L
Manning
Gerard
G
Elde
Nels C
NC
Turkewitz
Aaron P
AP
Asai
David J
DJ
Wilkes
David E
DE
Wang
Yufeng
Y
Cai
Hong
H
Collins
Kathleen
K
Stewart
B Andrew
BA
Lee
Suzanne R
SR
Wilamowska
Katarzyna
K
Weinberg
Zasha
Z
Ruzzo
Walter L
WL
Wloga
Dorota
D
Gaertig
Jacek
J
Frankel
Joseph
J
Tsao
Che-Chia
CC
Gorovsky
Martin A
MA
Keeling
Patrick J
PJ
Waller
Ross F
RF
Patron
Nicola J
NJ
Cherry
J Michael
JM
Stover
Nicholas A
NA
Krieger
Cynthia J
CJ
del Toro
Christina
C
Ryder
Hilary F
HF
Williamson
Sondra C
SC
Barbeau
Rebecca A
RA
Hamilton
Eileen P
EP
Orias
Eduardo
E
D000818:Animals; D002478:Cells, Cultured; D002874:Chromosome Mapping / Q000379:methods; D002875:Chromosomes; D030541:Databases, Genetic; D005057:Eukaryotic Cells / Q000502:physiology; D019143:Evolution, Molecular; D018503:Genome, Protozoan; D048648:Macronucleus / Q000235:genetics*; D048631:Micronucleus, Germline / Q000235:genetics; D023421:Models, Animal; D008954:Models, Biological; D010802:Phylogeny; D015398:Signal Transduction; D016808:Tetrahymena thermophila / Q000235:genetics*