Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage

Genome Biology and Evolution

Volumn 3, Issue 1, 2011, Pages 1187-1196

  Moss, Stephen P ^a   Joyce, Domino A ^a   Humphries, Stuart ^a   Tindall, Katherine J ^a   Lunt, David H ^a  

^a UNIVERSITY OF HULL   (United Kingdom)

Author keywords

Comparative genomics pipeline; Genome evolution; Introns; Repeat elements; Teleosts

Indexed keywords

ANIMAL; ARTICLE; COMPARATIVE STUDY; GENETICS; GENOME; INTRON; MOLECULAR EVOLUTION; ZEBRA FISH;

ANIMALS; EVOLUTION, MOLECULAR; GENOME; INTRONS; ZEBRAFISH;

DANIO; DANIO RERIO; TELEOSTEI;

EID: 84859136419     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evr090     Document Type: Article

References (57)

1. Adams MD, Rudner DZ, Rio DC. 1996. Biochemistry and regulation of pre-mRNA splicing. Curr Opin Cell Biol. 8:331-339. (Pubitemid 26179212)
2. Aparicio S, et al. 2002. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301-1310. (Pubitemid 34913162)
3. Benson G. 1999. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27:573-580. (Pubitemid 29210025)
4. Benton MJ, Donoghue PCJ. 2007. Paleontological evidence to date the tree of life. Mol Biol Evol. 24:26-53. (Pubitemid 46026279)
5. Bergman CM, Quesneville H. 2007. Discovering and detecting transpos-able elements in genome sequences. Brief Bioinform. 8:382-392. (Pubitemid 350186918)
6. Bosco G, Campbell P, Leiva-Neto JT, Markow TA. 2007. Analysis of Drosophila species genome size and satellite DNA content reveals significant differences among strains as well as between species. Genetics 177:1277-1290. (Pubitemid 350277032)
7. Boulesteix M, Weiss M, Biémont C. 2006. Differences in genome size between closely related species: the Drosophila melanogaster species subgroup. Mol Biol Evol. 23:162-167. (Pubitemid 41785963)
8. Burnette JM, Miyamoto-Sato E, Schaub MA, Conklin J, Lopez AJ. 2005. Subdivision of large introns in Drosophila by recursive splicing at nonexonic elements. Genetics 170:661-674. (Pubitemid 40980668)
9. Castillo-Davis CI, Mekhedov SL, Hartl DL, Koonin EV, Kondrashov FA. 2002. Selection for short introns in highly expressed genes. Nat Genet. 31:415-418. (Pubitemid 35154453)
10. Chamary J-V, Hurst LD. 2004. Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage. Mol Biol Evol. 21:1014-1023. (Pubitemid 38658209)
11. Coghlan A, Wolfe KH. 2004. Origins of recently gained introns in Caenorhabditis. Proc Natl Acad Sci U S A. 101:11362-11367. (Pubitemid 39038352)
12. Deutsch M, Long M. 1999. Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res. 27:3219-3228. (Pubitemid 29355739)
13. Flicek P, et al. 2010. Ensembl 2011. Nucleic Acids Res. 39:D800-D806.
14. Frischmeyer PA, Dietz HC. 1999. Nonsense-mediated mRNA decay in health and disease. Hum Mol Genet. 8:1893-1900. (Pubitemid 29458667)
15. Gaffney DJ, Keightley PD. 2006. Genomic selective constraints in murid noncoding DNA. PLoS Genet. 2:e204.
16. Gazave E, Marqué s-Bonet T, Fernando O, Charlesworth B, Navarro A. 2007. Patterns and rates of intron divergence between humans and chimpanzees. Genome Biol. 8:R21.
17. Haffter P, et al. 1996. The identification of genes with unique and essential functions in the development of the zebrafish, Danio rerio. Development 123:1-36. (Pubitemid 27056733)
18. Hankeln T, Friedl H, Ebersberger I, Martin J, Schmidt ER. 1997. A variable intron distribution in globin genes of Chironomus: evidence for recent intron gain. Gene 205:151-160. (Pubitemid 28029609)
19. Hatton AR, Subramaniam V, Lopez AJ. 1998. Generation of alternative Ultrabithorax isoforms and stepwise removal of a large intron by resplicing at exon-exon junctions. Mol Cell. 2:787-796. (Pubitemid 128378986)
20. Hawkins JS, Kim H, Nason JD, Wing RA, Wendel JF. 2006. Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium. Genome Res. 16:1252-1261. (Pubitemid 44506958)
21. Hughes AL, Yeager M. 1997. Comparative evolutionary rates of introns and exons in murine rodents. J Mol Evol. 45:125-130. (Pubitemid 27323517)
22. Iwamoto M, Maekawa M, Saito A, Higo H, Higo K. 1998. Evolutionary relationship of plant catalase genes inferred from exon-intron structures: isozyme divergence after the separation of monocots and dicots. Theor Appl Genet. 97:9-19. (Pubitemid 28376700)
23. Jaillon O, et al. 2004. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957.
24. Jeffares DC, Penkett CJ, Bähler J. 2008. Rapidly regulated genes are intron poor. Trends Genet. 24:375-378.
25. Jurka J, et al. 2005. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110:462-467. (Pubitemid 41159923)
26. Kim E, Magen A, Ast G. 2007. Different levels of alternative splicing among eukaryotes. Nucleic Acids Res. 35:125-131. (Pubitemid 46189837)
27. Kimura T, et al. 2004. Large-scale isolation of ESTs from medaka embryos and its application to medaka developmental genetics. Mech Dev. 121:915-932. (Pubitemid 38813147)
28. Lander ES, et al. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921. (Pubitemid 32165345)
29. Li W, Tucker AE, Sung W, Thomas WK, Lynch M. 2009. Extensive, recent intron gains in Daphnia populations. Science 326:1260-1262.
30. Lin C-F, Mount SM, Jarmo1owski A, Makaowski W. 2010. Evolutionary dynamics of U12-type spliceosomal introns. BMC Evol Biol. 10:47.
31. Ló pez-Bigas N, Audit B, Ouzounis C, Parra G, Guigó R. 2005. Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett. 579:1900-1903. (Pubitemid 40404028)
32. Lynch M, Conery JS. 2003. The origins of genome complexity. Science 302:1401-1404. (Pubitemid 37452183)
33. Majewski J, Ott J. 2002. Distribution and characterization of regulatory elements in the human genome. Genome Res. 12:1827-1836. (Pubitemid 35469931)
34. Marais G, Nouvellet P, Keightley PD, Charlesworth B. 2005. Intron size and exon evolution in Drosophila. Genetics 170:481-485. (Pubitemid 40800007)
35. Mills RE, Bennett EA, Iskow RC, Devine SE. 2007. Which transposable elements are activeinthe human genome? Trends Genet. 23:183-191. (Pubitemid 46497510)
36. Mironov AA, Fickett JW, Gelfand MS. 1999. Frequent alternative splicing of human genes. Genome Res. 9:1288-1293. (Pubitemid 30042512)
37. Morgulis A, Gertz EM, Schäffer AA, Agarwala R. 2006. WindowMasker: window-based masker for sequenced genomes. Bioinformatics 22:134-141. (Pubitemid 43205398)
38. Neafsey DE, Palumbi SR. 2003. Genome size evolution in pufferfish: a comparative analysis of diodontid and tetraodontid pufferfish genomes. Genome Res. 13:821-830. (Pubitemid 36621742)
39. Roest Crollius H, Weissenbach J. 2005. Fish genomics and biology. Genome Res. 15:1675-1682. (Pubitemid 41780397)
40. Rogers J. 1989. How were introns inserted into nuclear genes? Trends Genet. 5:213-216. (Pubitemid 19171787)
41. Roy SW, Gilbert W. 2006. The evolution of spliceosomal introns: patterns, puzzles and progress. Nat Rev Genet. 7:211-221. (Pubitemid 43361532)
42. Schwartz SH, et al. 2008. Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res. 18:88-103.
43. Sela N, Kim E, Ast G. 2010. The role of transposable elements in the evolution of non-mammalian vertebrates and invertebrates. Genome Biol. 11:R59.
44. Sharp PA. 1985. On the origin of RNA splicing and introns. Cell 42:397-400.
45. Sharpton TJ, Neafsey DE, Galagan JE, Taylor JW. 2008. Mechanisms of intron gain and loss in Cryptococcus. Genome Biol. 9:R24.
46. Shepard S, McCreary M, Fedorov A. 2009. The peculiarities of large intron splicing in animals. PloS One. 4:e7853.
47. Smit AF. 1999. Interspersed repeats and other mementos of transpos-able elements in mammalian genomes. Curr Opin Genet Dev. 9:657-663.
48. Smit AFA, Hubley R, Green P. 2011. RepeatMasker Open-3.3.0 [computer program]. Seattle (WA): Institute for Systems Biology [cited 2011 September 16]. Available from: http://www.repeat masker.org
49. Stabenau A, et al. 2004. The Ensembl core software libraries. Genome Res. 14:929-933. (Pubitemid 38660512)
50. Stajich JE, Dietrich FS, Roy SW. 2007. Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biol. 8: R223.
51. Stajich JE, et al. 2002. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 12:1611-1618. (Pubitemid 35175100)
52. Stein LD, et al. 2003. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol. 1:E45.
53. Venter JC, et al. 2001. The sequence of the human genome. Science 291:1304-1351.
54. Wagner A. 2005. Energy constraints on the evolution of gene expression. Mol Biol Evol. 22:1365-1374. (Pubitemid 40734188)
55. Yandell M, et al. 2006. Large-scale trends in the evolution of gene structures within 11 animal genomes. PLoS Comput Biol. 2:e15.
56. Zhu L, et al. 2009. Patterns of exon-intron architecture variation of genes in eukaryotic genomes. BMC Genomics. 10:47.
57. Zhuang YA, Goldstein AM, Weiner AM. 1989. UACUAAC is the preferred branch site for mammalian mRNA splicing. Proc Natl Acad Sci U S A. 86:2752-2756. (Pubitemid 19112619)