Jump to ContentJump to Main Navigation
Show Summary Details

Patterns of intron sequence conservation in the genus Tetrahymena

Yichen Zheng / Kristen L. Dimond / Dan Graur / Rebecca A. Zufall
Published Online: 2013-02-27 | DOI: https://doi.org/10.2478/prge-2013-0001



Introns constitute a large fraction of eukaryotic genomes and were once considered neutrally evolving sequences. Recently, however, some introns have been found to harbor sequences that are involved in a variety of regulatory and other functions and show evidence of purifying selection.


We examine the pattern of sequence divergence among ciliates in the genus Tetrahymena. We find that on average introns are more highly conserved than four-fold degenerate sites. Among introns, we find a correlation between conservation strength and both position rank in the gene as well as size of the coding region; the most conserved introns are found closer to the 5’ end of the largest genes.


Our results indicate that Tetrahymena introns experience selective constraint, possibly due to harboring regulatory sequences. We advocate for further experimental study of possible intron functions in Tetrahymena.

Keywords: Intron; Evolution; Ciliate; Tetrahymena

  • Chorev M., Carmel L., The function of introns, Front. Gene, 2012, 3, 55 Google Scholar

  • Barrett L.W., Fletcher S., Wilton S.D., Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements, Cell Mol Life Sci, 2012, 69, 3613-3634 Web of ScienceGoogle Scholar

  • Parsch J., Selective constraints on intron evolution in Drosophila, Genetics, 2003, 165, 1843-1851 Google Scholar

  • Keightley P.D., Gaffney D.J., Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents, PNAS USA, 2003, 100, 13402-13406 Google Scholar

  • Andolfatto P., Adaptive evolution of non-coding DNA in Drosophila, Nature, 2005, 437, 1149-1152 Google Scholar

  • Halligan D.L., Keightley P.D., Ubiquitous selective constraints in the Drosophila genome revealed by genome-wide interspecies comparison, Genome Research, 2006, 16, 875-884 PubMedCrossrefGoogle Scholar

  • Marais G., Nouvellet P., Keightley P.D., Charlesworth B., Intron size and exon evolution in Drosophila, Genetics, 2005, 170, 481-485 Google Scholar

  • Haddrill P.R., Charlesworth B., Halligan D.L., Andolfatto P. Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content, Genome Biology, 2005, 6, R67 CrossrefGoogle Scholar

  • Gazave E., Marqués-Bonet T., Fernando O., Charlesworth B., Navarro A., Patterns and rates of intron divergence between humans and chimpanzees, Genome Biol., 2007, 8, R21 CrossrefWeb of ScienceGoogle Scholar

  • Collins K., Tetrahymena thermophila, In: Wilson L., Matsudaira P. (Eds.), Methods in Cell Biology, Academic Press, 2012 Google Scholar

  • Eisen J.A., Coyne R.S., Wu M., Thiagarajan M., Wortman J.R., Badger J.H., et al., Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote, Plos Biology, 2006, 4, 1620-1642 Google Scholar

  • Jaillon O., Bouhouche K., Gout J.F., Aury J.M., Noel B., Saudemont B., et al., Translational control of intron splicing in eukaryotes, Nature, 2008, 451, 359-362 Web of ScienceGoogle Scholar

  • Hong X., Scofield D.G., Lynch M. Intron size, abundance, and distribution within untranslated regions of genes, Mol Biol Evol, 2006, 23, 2392-2404 Google Scholar

  • Kruger K., Grabowski P.J., Zaug A.J., Sands J., Gottschling D.E., Cech T.R., Self-splicing RNA - auto-excision and autocyclization of the ribosomal-RNA intervening sequence of Tetrahymena, Cell, 1982, 31, 147-157 Google Scholar

  • Stover N.A., Tetrahymena Genome Database (TGD): a new genomic resource for Tetrahymena thermophila research, Nucleic Acids Research, 2006, 34, D500-D503 Google Scholar

  • Edgar R.C., MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, 2004, 5, 113 CrossrefPubMedGoogle Scholar

  • Coyne R.S., Thiagarajan M., Jones K.M., Wortman J.R., Tallon L.J., Haas B.J., et al., Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure, BMC Genomics, 2008, 9, 562 CrossrefWeb of SciencePubMedGoogle Scholar

  • Wuitschick J.D., Karrer K.M., Analysis of genomic G + C content, codon usage, initiator codon context and translation termination sites in Tetrahymena thermophila, Journal of Eukaryotic Microbiology, 1999, 46, 239-247 CrossrefGoogle Scholar

  • Wuitschick J.D., Karrer K.M., Codon usage in Tetrahymena thermophila, Methods Cell Biol., 2000, 62, 565-568 Google Scholar

  • Moabbi A.M., Agarwal N., Kaderi B.E., Ansari A., Role of gene looping in intron-mediated enhancement of transcription. PNAS USA, 2012, 109(22), 8505-8510 Google Scholar

  • Irimia M., Maeso I., Burguera D., Hidalgo-Sánchez M., Puelles L., Roy S.W., et al., Contrasting 5’ and 3’ evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures, Genome Biology, 2011, 3, 551-564 Web of ScienceGoogle Scholar

  • Majewski J., Ott J., Distribution and characterization of regulatory elements in the human genome. Genome Research, 2002, 12, 1827-1836 Google Scholar

  • Jonsson J.J., Foresman M.D., Wilson N., McIvor R.S., Intron requirement for expression of the human purine nucleoside phosphorylase gene, Nucleic Acids Res, 1992, 20(12), 3191-3198 Google Scholar

  • Jonsson J.J., Converse A., McIvor R.S. An enhancer in the first intron of the human purine nucleoside phosphorylaseencoding gene, Gene, 1994, 140(2), 187-193 Google Scholar

  • Hadden T.J., Ryou C., Miller R.E., Elements in the distal 5’-flanking sequence and the first intron function cooperatively to regulate glutamine synthetase transcription during adipocyte differentiation, Nucleic Acids Res, 1997, 25 (19), 3930-3936 Google Scholar

  • Chen J., Hayes P., Roy K., Sirotnak F.M., Two promoters regulate transcription of the mouse folypolyglutamate synthetase gene three tightly clustered Sp1 sites within the first intron markedly enhance activity of promoter B, Gene, 2000, 242(1-2), 257-264 Google Scholar

  • Liu Y., Li H., Tanaka K., Tsumaki N., Yamada Y., Identification of an enhancer sequence within the first intron required for the cartilage-specific transcription of the alpha2(XI) collagen gene, J Biol Chem, 2000, 275(17), 12712-12718 Web of ScienceGoogle Scholar

  • Charron M., Chern J.Y., Wright W.W., The Cathepsin L first intron stimulates gene expression in rat sertoli cells, Biol Reprod, 2007, 76, 813-824 Web of ScienceGoogle Scholar

  • Xiong J., Lu X., Zhou Z., Chang Y., Yuan D., Tian M., et al., Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using deep RNA sequencing, PLoS ONE, 2012, 7(2), e30630 Google Scholar

  • Kim E., Goren A., Ast G., Alternative splicing: current perspectives, Bioessays, 2007, 30, 38-47Web of ScienceGoogle Scholar

About the article

Received: 2012-08-08

Accepted: 2013-01-14

Published Online: 2013-02-27

Citation Information: Protist Genomics, Volume 1, Pages 19–24, ISSN (Online) 2299-100X, DOI: https://doi.org/10.2478/prge-2013-0001.

Export Citation

©2013 Versita Sp. z o.o.. This content is open access.

Comments (0)

Please log in or register to comment.
Log in