Conservation versus parallel gains in intron evolution

Nucleic Acids Research

Volumn 33, Issue 6, 2005, Pages 1741-1748

  Sverdlov, Alexander V ^a   Rogozin, Igor B ^a   Babenko, Vladimir N ^a   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; GENE FREQUENCY; GENE INSERTION; GENE SEQUENCE; GENETIC CONSERVATION; INTRON; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; SPECIES DIFFERENCE; STATISTICAL ANALYSIS; STATISTICAL SIGNIFICANCE; ANIMAL; BIOLOGICAL MODEL; HUMAN; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; RNA SPLICING;

ANIMALIA; EUKARYOTA; FUNGI;

ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; HUMANS; INTRONS; MODELS, GENETIC; RNA SPLICE SITES;

EID: 15944384932     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gki316     Document Type: Article

References (33)

1. Lamond,A.I. (1999) RNA splicing. Running rings around RNA. Nature, 397, 655-656.
2. Logsdon,J.M.,Jr (1998) The recent origins of spliceosomal introns revisited. Curr. Opin. Genet. Dev., 8, 637-648.
3. Lynch,M. and Richardson,A.O. (2002) The evolution of spliceosomal introns. Curr. Opin. Genet. Dev., 12, 701-710.
4. Fedorov,A., Merican,A.F. and Gilbert,W. (2002) Large-scale comparison of intron positions among animal, plant, and fungal genes. Proc. Natl Acad. Sci. USA, 99, 16128-16133.
5. Rogozin,I.B., Wolf,Y.I., Sorokin,A.V., Mirkin,B.G. and Koonin,E.V. (2003) Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Curr. Biol., 13, 1512-1517.
6. Dibb,N.J. (1991) Proto-splice site model ofintron origin. J. Theor. Biol., 151, 405-416.
7. Dibb,N.J. and Newman,A.J. (1989) Evidence that introns arose at proto-splice sites. EMBO J., 8, 2015-2021.
8. Sverdlov,A.V., Rogozin,I.B., Babenko,V.N. and Koonin,E.V. (2004) Reconstruction of ancestral protosplice sites. Curr. Biol., 14, 1505-1508.
9. Hankeln,T., Friedl,H., Ebersberger,I., Martin,J. and Schmidt,E.R. (1997) A variable intron distribution in globin genes of Chironomus: Evidence for recent intron gain. Gene, 205, 151-160.
10. Tarrio,R., Rodriguez-Trelles,F. and Ayala,F.J. (2003) A new Drosophila spliceosomal intron position is common in plants. Proc. Natl Acad. Sci. USA, 100, 6580-6583.
11. Qiu,W.G., Schisler,N. and Stoltzfus,A. (2004) The evolutionary gain of spliceosomal introns: Sequence and phase preferences. Mol. Biol. Evol., 21, 1252-1263.
12. Huang,X. (1994) On global sequence alignment. Comput. Appl. Biosci., 10, 227-235.
13. Gelfand,M.S. (1995) Prediction of function in DNA sequence analysis. J. Comput. Biol., 2, 87-115.
14. Rogozin,I.B. and Milanesi,L. (1997) Analysis of donor splice sites in different eukaryotic organisms. J. Mol. Evol., 45, 50-59.
15. Staden,R. (1984) Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res., 12, 505-519.
16. Smith,M.W. (1988) Structure of vertebrate genes: A statistical analysis implicating selection. J. Mol. Evol., 27, 45-55.
17. Stoltzfus,A., Logsdon,J.M.,Jr, Palmer,J.D. and Doolittle,W.F. (1997) Intron 'sliding' and the diversity of intron positions. Proc. Natl Acad. Sci. USA, 94, 10739-10744.
18. Rogozin,I.B., Lyons-Weiler,J. and Koonin,E.V. (2000) Intron sliding in conserved gene families. Trends Genet., 16, 430-432.
19. Mourier,T. and Jeffares,D.C. (2003) Eukaryotic intron loss. Science, 300, 1393.
20. Sverdlov,A.V., Babenko,V.N., Rogozin,I.B. and Koonin,E.V. (2004) Preferential loss and gain of introns in 3′ portions of genes suggests a reverse-transcription mechanism of intron insertion. Gene, 338, 85-91.
21. Stoltzfus,A. (1994) Origin of introns - early or late. Nature, 369, 526-527 author reply 527-528.
22. Fedorov,A., Suboch,G., Bujakov,M. and Fedorova,L. (1992) Analysis of nonuniformity in intron phase distribution. Nucleic Acids Res., 20, 2553-2557.
23. Roy,S.W. and Gilbert,W. (2005) The pattern of intron loss. Proc. Natl Acad. Sci. USA, 102, 713-718.
24. Long,M., de Souza,S.J., Rosenberg,C. and Gilbert,W. (1998) Relationship between 'proto-splice sites' and intron phases: Evidence from dicodon analysis. Proc. Natl Acad. Sci. USA, 95, 219-223.
25. Sverdlov,A.V., Rogozin,I.B., Babenko,V.N. and Koonin,E.V. (2003) Evidence of splice signal migration from exon to intron during intron evolution. Curr. Biol., 13, 2170-2174.
26. Cho,G. and Doolittle,R.F. (1997) Intron distribution in ancient paralogs supports random insertion and not random loss. J. Mol. Evol., 44, 573-584.
27. Gilbert,W. (1987) The exon theory of genes. Cold Spring Harb. Symp. Quant. Biol., 52, 901-905.
28. Sadusky,T., Newman,A.J. and Dibb,N.J. (2004) Exon junction sequences as cryptic splice sites: Implications for intron origin. Curr. Biol., 14, 505-509.
29. Krauss,V., Pecyna,M., Kurz,K. and Sass,H. (2005) Phylogenetic mapping of intron positions: A case study of translation initiation factor eIF2γ. Mol. Biol. Evol., 22, 74-84.
30. Coghlan,A. and Wolfe,K.H. (2004) Origins of recently gained introns in Caenorhabditis. Proc. Natl Acad. Sci. USA, 101, 11362-11367.
31. Rogozin,I.B., Babenko,V.N., Wolf,Y.I. and Koonin,E.V. (2005) Dollo parsimony and reconstruction of genome evolution. In Albert,V.A. (ed.), Parsimony, Phylogeny, and Genomics. Oxford University Press, Oxford, pp. 190-200.
32. Roy,S.W. and Gilbert,W. (2005) Complex early genes. Proc. Natl Acad. Sci. USA, 102, 1986-1991.
33. Mattick,J.S. (1994) Introns: Evolution and function. Curr. Opin. Genet. Dev., 4, 823-831.