In search of lost introns
rös 1,*1Department of Computer Science and Operations Research, Université de Montréal, Québec, Canada, 2Department of Computer Science, Saint John's University and the College of St. Benedict, Collegeville, MN, USA and 3National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
*To whom correspondence should be addressed.
 |
Abstract |
|---|
Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon–intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution, require adequate computational tools.
We describe novel computational methods for studying spliceosomal intron evolution. Our goal is to give a reliable characterization of the dynamics of intron evolution. Our algorithmic innovations address the identification of orthologous introns, and the likelihood-based analysis of intron data. We discuss a compression method for the evaluation of the likelihood function, which is noteworthy for phylogenetic likelihood problems in general. We prove that after O(n
) preprocessing time, subsequent evaluations take O(n/log ) time almost surely in the Yule–Harding random model of n-taxon phylogenies, where is the input sequence length.
We illustrate the practicality of our methods by compiling and analyzing a data set involving 18 eukaryotes, which is more than in any other study to date. The study yields the surprising result that ancestral eukaryotes were fairly intron-rich. For example, the bilaterian ancestor is estimated to have had more than 90% as many introns as vertebrates do now.
Availability: The Java implementations of the algorithms are publicly available from the corresponding author's site http://www.iro.umontreal.ca/~csuros/introns/. Data are available on request.
Contact: csuros{at}iro.umontreal.ca
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  M. D. Wilkerson, Y. Ru, and V. P. Brendel Common introns within orthologous genes: software and application to plants Brief Bioinform, November 1, 2009; 10(6): 631 - 644. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Csuros Malin: maximum likelihood analysis of intron evolution in eukaryotes Bioinformatics, July 1, 2008; 24(13): 1538 - 1539. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. Tarrio, F. J. Ayala, and F. Rodriguez-Trelles From the Cover: Alternative splicing: A missing piece in the puzzle of intron gain PNAS, May 20, 2008; 105(20): 7223 - 7228. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Csuros, I. B. Rogozin, and E. V. Koonin Extremely Intron-Rich Genes in the Alveolate Ancestors Inferred with a Flexible Maximum-Likelihood Approach Mol. Biol. Evol., May 1, 2008; 25(5): 903 - 911. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
S. W. Roy and M. Irimia Rare Genomic Characters Do Not Support Coelomata: Intron Loss/Gain Mol. Biol. Evol., April 1, 2008; 25(4): 620 - 623. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 M. Irimia and S. W. Roy Spliceosomal introns as tools for genomic and evolutionary analysis Nucleic Acids Res., March 1, 2008; 36(5): 1703 - 1712. [Abstract] [Full Text] [PDF]
|
|