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Nucleic Acids Research 2004 32(12):3724-3733; doi:10.1093/nar/gkh686
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Published online 14 July 2004

Nucleic Acids Research, Vol. 32 No. 12 © Oxford University Press 2004; all rights reserved

Prevalence of intron gain over intron loss in the evolution of paralogous gene families

Vladimir N. Babenko, Igor B. Rogozin, Sergei L. Mekhedov and Eugene V. Koonin*

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bldg 38A, Bethesda, MD 20894, USA

* To whom correspondence should be addressed: Tel: +1 301 435 5913; Fax: +1 301 435 7794; Email: koonin{at}ncbi.nlm.nih.gov

Received May 12, 2004; Revised June 5, 2004; Accepted June 16, 2004

The mechanisms and evolutionary dynamics of intron insertion and loss in eukaryotic genes remain poorly understood. Reconstruction of parsimonious scenarios of gene structure evolution in paralogous gene families in animals and plants revealed numerous gains and losses of introns. In all analyzed lineages, the number of acquired new introns was substantially greater than the number of lost ancestral introns. This trend held even for lineages in which vertical evolution of genes involved more intron losses than gains, suggesting that gene duplication boosts intron insertion. However, dating gene duplications and the associated intron gains and losses based on the molecular clock assumption showed that very few, if any, introns were gained during the last ~100 million years of animal and plant evolution, in agreement with previous conclusions reached through analysis of orthologous gene sets. These results are generally compatible with the emerging notion of intensive insertion and loss of introns during transitional epochs in contrast to the relative quiet of the intervening evolutionary spans.


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