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Nucleic Acids Research Advance Access originally published online on February 7, 2008
Nucleic Acids Research 2008 36(5):1703-1712; doi:10.1093/nar/gkn012
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Nucleic Acids Research, 2008, Vol. 36, No. 5 1703-1712
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Molecular Biology

Spliceosomal introns as tools for genomic and evolutionary analysis

Manuel Irimia1 and Scott William Roy2,*

1Departament de Genètica, Universitat de Barcelona, Barcelona, Spain and 2National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA

*To whom correspondence should be addressed. Tel: 301 496 8941; Fax: 301 480 2288; Email: scottwroy{at}gmail.com

Received December 1, 2007. Revised January 7, 2008. Accepted January 8, 2008.

Over the past 5 years, the availability of dozens of whole genomic sequences from a wide variety of eukaryotic lineages has revealed a very large amount of information about the dynamics of intron loss and gain through eukaryotic history, as well as the evolution of intron sequences. Implicit in these advances is a great deal of information about the structure and evolution of surrounding sequences. Here, we review the wealth of ways in which structures of spliceosomal introns as well as their conservation and change through evolution may be harnessed for evolutionary and genomic analysis. First, we discuss uses of intron length distributions and positions in sequence assembly and annotation, and for improving alignment of homologous regions. Second, we review uses of introns in evolutionary studies, including the utility of introns as indicators of rates of sequence evolution, for inferences about molecular evolution, as signatures of orthology and paralogy, and for estimating rates of nucleotide substitution. We conclude with a discussion of phylogenetic methods utilizing intron sequences and positions.

The authors wish it to be known that, in their opinion, the authors should be regarded as joint First Authors.


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