Skip Navigation

Nucleic Acids Research 2004 32(12):3724-3733; doi:10.1093/nar/gkh686
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (1125K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (36)
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Babenko, V. N.
Right arrow Articles by Koonin, E. V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Babenko, V. N.
Right arrow Articles by Koonin, E. V.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Mol Biol EvolHome page
A. D. Cutter, A. Dey, and R. L. Murray
Evolution of the Caenorhabditis elegans Genome
Mol. Biol. Evol., June 1, 2009; 26(6): 1199 - 1234.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
G. Pavesi, F. Zambelli, C. Caggese, and G. Pesole
Exalign: a new method for comparative analysis of exon-intron gene structures
Nucleic Acids Res., May 1, 2008; 36(8): e47 - e47.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
C. Martens, K. Vandepoele, and Y. Van de Peer
Whole-genome analysis reveals molecular innovations and evolutionary transitions in chromalveolate species
PNAS, March 4, 2008; 105(9): 3427 - 3432.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
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]

Home page
 Mol Biol EvolHome page
Y.-H. Loh, S. Brenner, and B. Venkatesh
Investigation of Loss and Gain of Introns in the Compact Genomes of Pufferfishes (Fugu and Tetraodon)
Mol. Biol. Evol., March 1, 2008; 25(3): 526 - 535.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. K. Basu, I. B. Rogozin, O. Deusch, T. Dagan, W. Martin, and E. V. Koonin
Evolutionary Dynamics of Introns in Plastid-Derived Genes in Plants: Saturation Nearly Reached but Slow Intron Gain Continues
Mol. Biol. Evol., January 1, 2008; 25(1): 111 - 119.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. W. Roy and D. Penny
On the Incidence of Intron Loss and Gain in Paralogous Gene Families
Mol. Biol. Evol., August 1, 2007; 24(8): 1579 - 1581.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
L. Carmel, Y. I. Wolf, I. B. Rogozin, and E. V. Koonin
Three distinct modes of intron dynamics in the evolution of eukaryotes
Genome Res., July 1, 2007; 17(7): 1034 - 1044.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
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
Mol. Biol. Evol., July 1, 2007; 24(7): 1447 - 1457.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
H. D. Nguyen, M. Yoshihama, and N. Kenmochi
The Evolution of Spliceosomal Introns in Alveolates
Mol. Biol. Evol., May 1, 2007; 24(5): 1093 - 1096.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
J. Coulombe-Huntington and J. Majewski
Characterization of intron loss events in mammals
Genome Res., January 1, 2007; 17(1): 23 - 32.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
S. Foret and R. Maleszka
Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera)
Genome Res., November 1, 2006; 16(11): 1404 - 1413.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
S. W. Roy and D. Penny
Large-scale intron conservation and order-of-magnitude variation in intron loss/gain rates in apicomplexan evolution
Genome Res., October 1, 2006; 16(10): 1270 - 1275.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. W. Roy, M. Irimia, and D. Penny
Very Little Intron Gain in Entamoeba histolytica Genes Laterally Transferred from Prokaryotes
Mol. Biol. Evol., October 1, 2006; 23(10): 1824 - 1827.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
D. G. Knowles and A. McLysaght
High Rate of Recent Intron Gain and Loss in Simultaneously Duplicated Arabidopsis Genes
Mol. Biol. Evol., August 1, 2006; 23(8): 1548 - 1557.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
S. W. Roy and D. L. Hartl
Very little intron loss/gain in Plasmodium: Intron loss/gain mutation rates and intron number
Genome Res., June 1, 2006; 16(6): 750 - 756.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. W. Roy and W. Gilbert
Rates of intron loss and gain: Implications for early eukaryotic evolution
PNAS, April 19, 2005; 102(16): 5773 - 5778.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. W. Roy and W. Gilbert
Complex early genes
PNAS, February 8, 2005; 102(6): 1986 - 1991.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.