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MBE Advance Access published online on May 23, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl017
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© 2006 The Authors 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.
Accepted May 16, 2006

Research Article

High Rate of Recent Intron Gain and Loss in Simultaneously Duplicated Arabidopsis genes

David G. Knowles 1 and Aoife McLysaght 1 *

1 Smurfit Institute of Genetics, University of Dublin, Trinity College Dublin, Dublin 2, Ireland

* To whom correspondence should be addressed.
Aoife McLysaght, E-mail: aoife.mclysaght{at}tcd.ie


  Abstract

We examined the gene structure of a set of 2563 Arabidopsis thaliana paralogous pairs that were duplicated simultaneously 20-60 million years ago by tetraploidy. Out of a total of 23,164 introns in these genes we found that 10,004 pairs have been conserved, and 578 introns have been inserted or deleted in the time since the duplication event. This intron insertion/deletion rate of 2.7x10-3 - 9.1x10-4 per site per million years is high in comparison to previous studies. At least 56 introns were gained and 39 lost based on parsimony analysis of the phylogenetic distribution of these introns. We found weak evidence that genes undergoing intron gain and loss are biased with respect to gene ontology terms. Gene pairs that experienced at least two intron insertions or deletions show evidence of enrichment for membrane location and transport and transporter activity function. We do not find any relationship of intron flux to expression level or G+C content of the gene. Detection of a bias in the location of intron gains and losses within a gene depends on the method of measurement: an intragene method indicates that events (specifically intron losses) are biased towards the 3’ end of the gene. Despite the relatively recent acquisition of these introns, we found only one case where we could identify the mechanism of intron origin - the TOUCH3 gene has experienced two tandem, partial, internal gene duplications which duplicated a pre-existing intron and also created a novel, alternatively-spliced intron which makes use of a duplicated pair of cryptic splice sites.

Keywords: intron gain and loss; Arabidopsis thaliana; intron evolution; genome evolution.
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