Phase distribution of spliceosomal introns: Implications for intron origin

BMC Evolutionary Biology

Volumn 6, Issue , 2006, Pages

  Nguyen, Hung D ^a   Yoshihama, Maki ^a   Kenmochi, Naoya ^a  

^a UNIVERSITY OF MIYAZAKI   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; EUKARYOTE; GENOME; INTRON; NONHUMAN; PREDICTION; SPLICEOSOME; ANIMAL; BIOLOGICAL MODEL; CODON; COMPARATIVE STUDY; EUKARYOTIC CELL; FUNGUS; GENE EXPRESSION REGULATION; GENETICS; HUMAN; INVERTEBRATE; MOLECULAR EVOLUTION; MUTATION; PLANT; STATISTICAL MODEL; VERTEBRATE;

EUKARYOTA;

CODON;

ANIMALS; CODON; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; FUNGI; GENOME; HUMANS; INTRONS; INVERTEBRATES; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTAGENESIS, INSERTIONAL; MUTATION; PLANTS; SPLICEOSOMES; VERTEBRATES;

EID: 33748974763     PISSN: 14712148     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-6-69     Document Type: Article

References (40)

1. Doolittle WF: Genes in pieces: were they ever together? Nature 1978, 272:581-582.
2. Blake CCF: Do genes in pieces imply proteins in pieces? Nature 1978, 273:267.
3. Gilbert W: The exon theory of genes. Cold Spring Harb Symp Quant Biol 1987, 52:901-905.
4. Roy SW: Recent evidence for the exon theory of genes. Genetica 2003, 118:251-266.
5. Cavalier-Smith T: Intron phylogeny: a new hypothesis. Trends Genet 1991, 7:145-148.
6. Palmer JD, Logsdon JM Jr: The recent origins of introns. Curr Opin Genet Dev 1991, 1:470-477.
7. Logsdon JM Jr: The recent origins of spliceosomal introns revisited. Curr Opin Genet Dev 1998, 8:637-648.
8. Fedorov A, Suboch G, Bujakov M, Fedorova L: Analysis of nonuniformity in intron phase distribution. Nucleic Acids Res 1992, 20:2553-2557.
9. Long M, Rosenberg C, Gilbert W: Intron phase correlations and the evolution of the intron/exon structure of genes. Proc Natl Acad Sci USA 1995, 92:12495-12499.
10. Long M, de Souza SJ, Rosenberg C, Gilbert W: Relationship between proto-splice sites and intron phases: evidence from dicodon analysis. Proc Natl Acad Sci USA 1998, 95:219-223.
11. de Souza SJ, Long M, Klein RJ, Roy SW, Lin S, Gilbert W: Toward a resolution of the introns early/late debate: only phase zero introns are correlated with the structure of ancient proteins. Proc Natl Acad Sci USA 1998, 95:5094-5099.
12. Dibb NJ, Newman AJ: Evidence that introns arose at protosplice sites. EMBO J 1989, 8:2015-2021.
13. Qiu WG, Schisler N, Stoltzfus A: The evolutionary gain of spliceosomal introns: sequence and phase preferences. Mol Biol Evol 2004, 21:1252-1263.
14. Sverdlov AV, Rogozin IB, Babenko VN, Koonin EV: Reconstruction of ancestral protosplice sites. Curr Biol 2004, 14:1505-1508.
15. Ruvinsky A, Eskesen ST, Eskesen FN, Hurst LD: Can codon usage bias explain intron phase distribution and exon symmetry? J Mol Evol 2005, 60:99-104.
16. Meunier J, Duret L: Recombination drives the evolution of GC-content in the human genome. Mol Biol Evol 2004, 21:984-990.
17. Roy SW, Lewis BP, Fedorov A, Gilbert W: Footprints of primordial introns on the eukaryotic genome. Trends Genet 2001, 17:496-499.
18. Sverdlov AV, Rogozin IB, Babenko VN, Koonin EV: Evidence of splice signal migration from exon to intron during intron evolution. Curr Biol 2003, 13:2170-2174.
19. Nakao A, Yoshihama M, Kenmochi N: RPG: the Ribosomal Protein Gene database. Nucleic Acids Res 2004, 32:D168-170.
20. Sadusky T, Newman AJ, Dibb NJ: Exon junction sequences as cryptic splice sites: implications for intron origin. Curr Biol 2004, 14:505-509.
21. Stoltzfus A: Molecular evolution: introns fall into place. Curr Biol 2004, 14:R351-R352.
22. Nguyen HD, Yoshihama M, Kenmochi N: New maximum likelihood estimators for eukaryotic intron evolution. PloS Comput Biol 2005, 1:e79.
23. Roy SW, Gilbert W: The evolution of spliceosomal introns: patterns, puzzles and progress. Nat Rev Genet 2006, 7:211-221.
24. Martin W, Koonin EV: Introns and the origin of nucleus-cytosol compartmentalization. Nature 2006, 440:41-45.
25. Roy SW, Gilbert W: Rates of intron loss and gain: implications for early eukaryotic evolution. Proc Natl Acad Sci USA 2005, 102:5773-5778.
26. Yoshihama M, Nakao A, Nguyen HD, Kenmochi N: Analysis of ribosomal protein gene structures: implications for intron evolution. PloS Genet 2006, 2:e25.
27. Rogozin IB, Wolf YI, Sorokin AV, Mirkin BG, Koonin EV: Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr Biol 2003, 13:1512-1517.
28. Csurös M: Likely Scenarios of intron evolution. In Proceedings of the Comparative Genomics: RECOMB 2005 International Workshop: 18-20 September 2005; Dublin Volume 3678. Edited by: McLysaght A, Huson D. Springer-Verlag; Lecture Notes in Bioinformatics :47-60.
29. Csurös M: On the estimation of intron evolution. PLoS Comput Biol 2006, 2:e84.
30. Nguyen HD, Yoshihama M, Kenmochi N: Authors' reply. PLoS Comput Biol 2006, 2:e83.
31. NCBI [http://www.ncbi.nlm.nih.gov/]
32. Fungal Genome Initiative [http://www.broad.mit.edu/annotation/fgi/]
33. JGI Eukaryotic Genomics [http://genome.jgi-psf.org/euk_cur1.html]
34. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
35. Florea L, Hartzell G, Zhang Z, Rubin GM, Miller W: A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res 1998, 8:967-974.
36. Myers EW, Miller W: Optimal alignments in linear space. CABIOS 1988, 4:11-17.
37. TIGR Rice Genome Annotation [http://www.tigr.org/tdb/e2k1/osa1/]
38. Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
39. Felsenstein J, Churchill GA: A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol 1996, 13:93-104.
40. Press WH, Teukolsky SA, Vetterling WT, Flannery BP: Minimization or maximization of functions. In Numerical recipes in C: The art of scientific computing 2nd edition. New York: Cambridge University Press; 1992:394-444.