Table of Contents Author Guidelines Submit a Manuscript
International Journal of Genomics
Volume 2013, Article ID 671316, 11 pages
http://dx.doi.org/10.1155/2013/671316
Research Article

Effects of Taxon Sampling in Reconstructions of Intron Evolution

Belozersky Institute for Physicochemical Biology, Lomonosov Moscow State University, Moscow 119991, Russia

Received 15 October 2012; Accepted 2 January 2013

Academic Editor: Yuri Panchin

Copyright © 2013 Mikhail A. Nikitin and Vladimir V. Aleoshin. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. S. W. Roy and W. Gilbert, “Complex early genes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 6, pp. 1986–1991, 2005. View at Publisher · View at Google Scholar · View at Scopus
  2. H. D. Nguyen, M. Yoshihama, and N. Kenmochi, “New maximum likelihood estimators for eukaryotic intron evolution,” PLoS Computational Biology, vol. 1, no. 7, article e79, 2005. View at Publisher · View at Google Scholar · View at Scopus
  3. W. G. Qiu, N. Schisler, and A. Stoltzfus, “The evolutionary gain of spliceosomal introns: sequence and phase preferences,” Molecular Biology and Evolution, vol. 21, no. 7, pp. 1252–1263, 2004. View at Publisher · View at Google Scholar · View at Scopus
  4. H. Le Hir, A. Nott, and M. J. Moore, “How introns influence and enhance eukaryotic gene expression,” Trends in Biochemical Sciences, vol. 28, no. 4, pp. 215–220, 2003. View at Publisher · View at Google Scholar · View at Scopus
  5. F. Raible, K. Tessmar-Raible, K. Osoegawa et al., “Evolution: vertebrate-type intron-rich genes in the marine annelid Platynereis dumerilii,” Science, vol. 310, no. 5752, pp. 1325–1326, 2005. View at Publisher · View at Google Scholar · View at Scopus
  6. J. C. Sullivan, A. M. Reitzel, and J. R. Finnerty, “A high percentage of introns in human genes were present early in animal evolution: evidence from the basal metazoan Nematostella vectensis,” Genome Informatics, vol. 17, no. 1, pp. 219–229, 2006. View at Google Scholar · View at Scopus
  7. M. Srivastava, E. Begovic, J. Chapman et al., “The Trichoplax genome and the nature of placozoans,” Nature, vol. 454, no. 7207, pp. 955–960, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. M. Srivastava, O. Simakov, J. Chapman et al., “The Amphimedon queenslandica genome and the evolution of animal complexity,” Nature, vol. 466, no. 7307, pp. 720–726, 2010. View at Publisher · View at Google Scholar · View at Scopus
  9. N. King, M. J. Westbrook, S. L. Young et al., “The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans,” Nature, vol. 451, no. 7180, pp. 783–788, 2008. View at Publisher · View at Google Scholar · View at Scopus
  10. J. E. Stajich, F. S. Dietrich, and S. W. Roy, “Comparative genomic analysis of fungal genomes reveals intron-rich ancestors,” Genome Biology, vol. 8, no. 10, article R223, 2007. View at Publisher · View at Google Scholar · View at Scopus
  11. M. Csurös, I. B. Rogozin, and E. V. Koonin, “Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach,” Molecular Biology and Evolution, vol. 25, no. 5, pp. 903–911, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. S. W. Roy and D. Penny, “A very high fraction of unique intron positions in the intron-rich diatom Thalassiosira pseudonana indicates widespread intron gain,” Molecular Biology and Evolution, vol. 24, no. 7, pp. 1447–1457, 2007. View at Publisher · View at Google Scholar · View at Scopus
  13. T. Y. James, F. Kauff, C. L. Schoch et al., “Reconstructing the early evolution of Fungi using a six-gene phylogeny,” Nature, vol. 443, no. 7113, pp. 818–822, 2006. View at Publisher · View at Google Scholar · View at Scopus
  14. C. W. Dunn, A. Hejnol, D. Q. Matus et al., “Broad phylogenomic sampling improves resolution of the animal tree of life,” Nature, vol. 452, no. 7188, pp. 745–749, 2008. View at Publisher · View at Google Scholar · View at Scopus
  15. H. Philippe, N. Lartillot, and H. Brinkmann, “Multigene analyses of bilaterian animals corroborate the monophyly of Ecdysozoa, Lophotrochozoa, and protostomia,” Molecular Biology and Evolution, vol. 22, no. 5, pp. 1246–1253, 2005. View at Publisher · View at Google Scholar · View at Scopus
  16. K. S. Pick, H. Philippe, F. Schreiber et al., “Improved phylogenomic taxon sampling noticeably affects nonbilaterian relationships,” Molecular Biology and Evolution, vol. 27, no. 9, pp. 1983–1987, 2010. View at Publisher · View at Google Scholar · View at Scopus
  17. K. Meusemann, B. M. Von Reumont, S. Simon et al., “A phylogenomic approach to resolve the arthropod tree of life,” Molecular Biology and Evolution, vol. 27, no. 11, pp. 2451–2464, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. K. M. Kjer, “Aligned 18S and insect phylogeny,” Systematic Biology, vol. 53, no. 3, pp. 506–514, 2004. View at Publisher · View at Google Scholar · View at Scopus
  19. D. Bhattacharya and L. Medlin, “Algal phylogeny and the origin of land plants,” Plant Physiology, vol. 116, no. 1, pp. 9–15, 1998. View at Google Scholar · View at Scopus
  20. T. R. Bachvaroff, S. M. Handy, A. R. Place, and C. F. Delwiche, “Alveolate phylogeny inferred using concatenated ribosomal proteins,” Journal of Eukaryotic Microbiology, vol. 58, no. 3, pp. 223–233, 2011. View at Publisher · View at Google Scholar · View at Scopus
  21. C. Burge and S. Karlin, “Prediction of complete gene structures in human genomic DNA,” Journal of Molecular Biology, vol. 268, no. 1, pp. 78–94, 1997. View at Publisher · View at Google Scholar · View at Scopus
  22. M. Csuros, J. A. Holey, and I. B. Rogozin, “In search of lost introns,” Bioinformatics, vol. 23, no. 13, pp. i87–i96, 2007. View at Google Scholar
  23. M. Csuros, I. B. Rogozin, and E. V. Koonin, “A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes,” PLoS Computational Biology, vol. 7, no. 9, 2011. View at Google Scholar