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Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage

Moss, Stephen P.; Joyce, Domino A.; Humphries, Stuart; Tindall, Katherine J.; Lunt, David H.


Stephen P. Moss

Stuart Humphries

Katherine J. Tindall


We have developed a bioinformatics pipeline for the comparative evolutionary analysis of Ensembl genomes and have used it to analyze the introns of the five available teleost fish genomes. We show our pipeline to be a powerful tool for revealing variation between genomes that may otherwise be overlooked with simple summary statistics. We identify that the zebrafish, Danio rerio, has an unusual distribution of intron sizes, with a greater number of larger introns in general and a notable peak in the frequency of introns of approximately 500 to 2,000 bp compared with the monotonically decreasing frequency distributions of the other fish. We determine that 47% of D. rerio introns are composed of repetitive sequences, although the remainder, over 331 Mb, is not. Because repetitive elements may be the origin of the majority of all noncoding DNA, it is likely that the remaining D. rerio intronic sequence has an ancient repetitive origin and has since accumulated so many mutations that it can no longer be recognized as such. To study such an ancient expansion of repeats in the Danio, lineage will require further comparative analysis of fish genomes incorporating a broader distribution of teleost lineages. © The Author(s) 2010.


Moss, S. P., Joyce, D. A., Humphries, S., Tindall, K. J., & Lunt, D. H. (2011). Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage. Genome Biology and Evolution, 3(1), 1187-1196.

Journal Article Type Article
Acceptance Date Aug 30, 2011
Online Publication Date Sep 13, 2011
Publication Date Nov 1, 2011
Deposit Date Nov 13, 2014
Publicly Available Date Oct 27, 2022
Journal Genome biology and evolution
Print ISSN 1759-6653
Electronic ISSN 1759-6653
Publisher Oxford University Press
Peer Reviewed Peer Reviewed
Volume 3
Issue 1
Pages 1187-1196
Keywords Genetics; Ecology, Evolution, Behavior and Systematics
Public URL
Publisher URL
Additional Information This is a copy of an article published in Genome biology and evolution, 2011, v.3 available at


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©The Author(s) 2011. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (, which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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