title: 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.
authors.affiliation: The Institute for Genomic Research, Rockville, Maryland, United States of America. jaeisen@ucdavis.edu
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Eisen
authors.forename: Robert S
authors.initials: RS
authors.lastname: Coyne
authors.forename: Martin
authors.initials: M
authors.lastname: Wu
authors.forename: Dongying
authors.initials: D
authors.lastname: Wu
authors.forename: Mathangi
authors.initials: M
authors.lastname: Thiagarajan
authors.forename: Jennifer R
authors.initials: JR
authors.lastname: Wortman
authors.forename: Jonathan H
authors.initials: JH
authors.lastname: Badger
authors.forename: Qinghu
authors.initials: Q
authors.lastname: Ren
authors.forename: Paolo
authors.initials: P
authors.lastname: Amedeo
authors.forename: Kristie M
authors.initials: KM
authors.lastname: Jones
authors.forename: Luke J
authors.initials: LJ
authors.lastname: Tallon
authors.forename: Arthur L
authors.initials: AL
authors.lastname: Delcher
authors.forename: Steven L
authors.initials: SL
authors.lastname: Salzberg
authors.forename: Joana C
authors.initials: JC
authors.lastname: Silva
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Haas
authors.forename: William H
authors.initials: WH
authors.lastname: Majoros
authors.forename: Maryam
authors.initials: M
authors.lastname: Farzad
authors.forename: Jane M
authors.initials: JM
authors.lastname: Carlton
authors.forename: Roger K
authors.initials: RK
authors.lastname: Smith
authors.forename: Jyoti
authors.initials: J
authors.lastname: Garg
authors.forename: Ronald E
authors.initials: RE
authors.lastname: Pearlman
authors.forename: Kathleen M
authors.initials: KM
authors.lastname: Karrer
authors.forename: Lei
authors.initials: L
authors.lastname: Sun
authors.forename: Gerard
authors.initials: G
authors.lastname: Manning
authors.forename: Nels C
authors.initials: NC
authors.lastname: Elde
authors.forename: Aaron P
authors.initials: AP
authors.lastname: Turkewitz
authors.forename: David J
authors.initials: DJ
authors.lastname: Asai
authors.forename: David E
authors.initials: DE
authors.lastname: Wilkes
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Wang
authors.forename: Hong
authors.initials: H
authors.lastname: Cai
authors.forename: Kathleen
authors.initials: K
authors.lastname: Collins
authors.forename: B Andrew
authors.initials: BA
authors.lastname: Stewart
authors.forename: Suzanne R
authors.initials: SR
authors.lastname: Lee
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Wilamowska
authors.forename: Zasha
authors.initials: Z
authors.lastname: Weinberg
authors.forename: Walter L
authors.initials: WL
authors.lastname: Ruzzo
authors.forename: Dorota
authors.initials: D
authors.lastname: Wloga
authors.forename: Jacek
authors.initials: J
authors.lastname: Gaertig
authors.forename: Joseph
authors.initials: J
authors.lastname: Frankel
authors.forename: Che-Chia
authors.initials: CC
authors.lastname: Tsao
authors.forename: Martin A
authors.initials: MA
authors.lastname: Gorovsky
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Keeling
authors.forename: Ross F
authors.initials: RF
authors.lastname: Waller
authors.forename: Nicola J
authors.initials: NJ
authors.lastname: Patron
authors.forename: J Michael
authors.initials: JM
authors.lastname: Cherry
authors.forename: Nicholas A
authors.initials: NA
authors.lastname: Stover
authors.forename: Cynthia J
authors.initials: CJ
authors.lastname: Krieger
authors.forename: Christina
authors.initials: C
authors.lastname: del Toro
authors.forename: Hilary F
authors.initials: HF
authors.lastname: Ryder
authors.forename: Sondra C
authors.initials: SC
authors.lastname: Williamson
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Barbeau
authors.forename: Eileen P
authors.initials: EP
authors.lastname: Hamilton
authors.forename: Eduardo
authors.initials: E
authors.lastname: Orias
mesh_terms: 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*