Sequencing the Oxytricha trifallax macronuclear genome: A pilot project

Trends in Genetics

Volumn 19, Issue 11, 2003, Pages 603-607

  Doak, Thomas G ^a   Cavalcanti, Andre R O ^b   Stover, Nicholas A ^b   Dunn, Diane M ^c   Weiss, Robert ^c   Herrick, Glenn ^a   Landweber, Laura F ^b  

^a UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^b PRINCETON UNIVERSITY   (United States)

^c UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; RIBOSOME RNA; SMALL NUCLEOLAR RNA; TRANSFER RNA;

CHROMOSOME; CILIATE; GENE SEQUENCE; GENETIC ANALYSIS; GENOME; INTRON; MACRONUCLEUS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; OXYTRICHA TRIFALLAX; PRIORITY JOURNAL; REVIEW; TELOMERE; UNINDEXED SEQUENCE;

CILIOPHORA; EUKARYOTA; INVERTEBRATA; OXYTRICHA; OXYTRICHA TRIFALLAX; PARAMECIUM; PARAMECIUM TETRAURELIA; PROTOZOA; STERKIELLA HISTRIOMUSCORUM; TETRAHYMENA THERMOPHILA;

EID: 0242380289     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2003.09.013     Document Type: Short Survey

References (32)

1. Collins K. Ciliate telomerase biochemistry. Annu. Rev. Biochem. 68:1999;187-218.
2. Cech T.R. Self-splicing of group I introns. Annu. Rev. Biochem. 59:1990;543-568.
3. Gall J.G. Chromosome structure and the C-value paradox. J. Cell Biol. 91:1981;3-14.
4. Sonneborn T.M. Genetics of cellular differentiation: stable nuclear differentiation in eucaryotic unicells. Annu. Rev. Genet. 11:1977;349-367.
5. Nanney D.L. T. M. Sonneborn: an interpretation. Annu. Rev. Genet. 15:1981;1-9.
6. Wright A.D.G., Lynn D.H. Maximum ages of ciliate lineages estimated using a small subunit rRNA molecular clock: Crown eukaryotes date back to the Paleoproterozoic. Arch. Protistenkd. 148:1997;329-341.
7. Baldauf S.L., et al. A kingdom-level phylogeny of eukaryotes based on combined protein data. Science. 290:2000;972-977.
8. Bahl A., et al. PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Res. 31:2003;212-215.
9. Herrick G. Germline-soma relationships in ciliated protozoa: the inception and evolution of nuclear dimorphism in one-celled animals. Semin. Dev. Biol. 5:1994;3-12.
10. Jahn C.L., Klobutcher L.A. Genome remodeling in ciliated protozoa. Annu. Rev. Microbiol. 56:2002;489-520.
11. Ammermann D., et al. The development of the macronucleus in the ciliated protozoan Stylonychia mytilus. Chromosoma. 45:1974;401-429.
12. Foissner W., Berger H. Identification and ontogenesis of the nomen nudum Hypotrichs (Protozoa: Ciliophora) Oxytricha nova (= Sterkiella nova sp. n.) and O. trifallax (= S. histriomuscorum). Acta Protozool. 38:1999;215-248.
13. Hoffman D.C., et al. Macronuclear gene-sized molecules of hypotrichs. Nucleic Acids Res. 23:1995;1279-1283.
14. Prescott D.M., et al. Coding properties of macronuclear DNA molecules in Sterkiella nova (Oxytricha nova). Protist. 153:2002;71-77.
15. Klobutcher L.A., Herrick G. Developmental genome reorganization in ciliated protozoa: the transposon link. Prog. Nucleic Acid Res. Mol. Biol. 56:1997;1-62.
16. Prescott D.M. Genome gymnastics: unique modes of DNA evolution and processing in ciliates. Nat. Rev. Genet. 1:2000;191-198.
17. Landweber L.F., et al. Evolution and assembly of an extremely scrambled gene. Proc. Natl. Acad. Sci. U.S.A. 97:2000;3298-3303.
18. Hoffman D.C., Prescott D.M. Evolution of internal eliminated seqments and scrambling in the micrnuclear gene encoding DNA polymerase alpha in two Oxytricha species. Nucleic Acids Res. 25:1997;1883-1889.
19. Örtz H.D. Intracellular bacteria in ciliates. Int. Microbiol. 4:2001;143-150.
20. Prescott D.M., Dizick S.J. A unique pattern of intrastrand anomalies in base composition of the DNA in hypotrichs. Nucleic Acids Res. 28:2000;4679-4688.
21. Dönhoff T., Klein A. Timing of differential amplification of macronucleus-destined sequences during macronuclear development in the hypotrichous ciliate Euplotes crassus. Chromosoma. 105:1996;172-179.
22. Doak T.G., et al. Conserved features of TBE1 transposons in ciliated protozoa. Genetica. 101:1997;75-86.
23. Witherspoon D.J., et al. Selection on the protein-coding genes of the TBE1 family of transposable elements in the ciliates Oxytricha fallax and O. trifallax. Mol. Biol. Evol. 14:1997;696-706.
24. Turkewitz A.P., et al. Functional genomics: the coming of age for Tetrahymena thermophila. Trends Genet. 18:2002;35-40.
25. Wen J.P., et al. The processing of macronuclear-destined DNA sequences microinjected into the macronuclear anlagen of the hypotrichous ciliate Stylonchia lemnae. Nucleic Acids Res. 23:1995;1704-1709.
26. Jönsson F., et al. Both subtelomeric regions are required and sufficient for specific DNA fragmentation during macronuclear development in Stylonychia lemnae. Genome Biol. 2:2001;5.
27. Möllenbeck M., et al. The telomerase-associated protein p43 is involved in anchoring telomerase in the nucleus. J. Cell Sci. 116:2003;1757-1761.
28. Pasckha, A. et al. The use of RNAi to analyze gene function in spirotrichous ciliates. Eur. J. Protistol (in press).
29. Sperling L., et al. Random sequencing of Paramecium somatic DNA. Eukaryot. Cell. 1:2002;341-352.
30. Fillingham J.S., et al. Analysis of expressed sequence tags (ESTs) in the ciliated protozoan Tetrahymena thermophila. J. Eukaryot. Microbiol. 49:2002;99-107.
31. Kellis M., et al. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature. 423:2003;241-254.
32. Dawson S.C., Pace N.R. Novel kingdom-level eukaryotic diversity in anoxic environments. Proc. Natl. Acad. Sci. U.S.A. 99:2002;8324-8329.