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Patterns and rates of intron divergence between humans and chimpanzees

Elodie Gazave1, Tomàs Marqués-Bonet1, Olga Fernando12, Brian Charlesworth3 and Arcadi Navarro4*

Author Affiliations

1 Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Carrer Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain

2 Instituto de Tecnologia Química e Biológica (ITQB), Universidade Nova de Lisboa, Av. da República (EAN) 2781-901 Oeiras, Lisboa, Portugal

3 Institute of Evolutionary Biology, University of Edinburgh, West Mains Road, Edinburgh, Scotland, EH7 3JT, UK

4 Institucio Catalana de Recerca i Estudis Avancats (ICREA), Unitat de Biologia Evolutiva, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Carrer Dr Aiguader 88, 08003 Barcelona, Catalonia, Spain

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Genome Biology 2007, 8:R21  doi:10.1186/gb-2007-8-2-r21

Published: 19 February 2007

Abstract

Background

Introns, which constitute the largest fraction of eukaryotic genes and which had been considered to be neutral sequences, are increasingly acknowledged as having important functions. Several studies have investigated levels of evolutionary constraint along introns and across classes of introns of different length and location within genes. However, thus far these studies have yielded contradictory results.

Results

We present the first analysis of human-chimpanzee intron divergence, in which differences in the number of substitutions per intronic site (Ki) can be interpreted as the footprint of different intensities and directions of the pressures of natural selection. Our main findings are as follows: there was a strong positive correlation between intron length and divergence; there was a strong negative correlation between intron length and GC content; and divergence rates vary along introns and depending on their ordinal position within genes (for instance, first introns are more GC rich, longer and more divergent, and divergence is lower at the 3' and 5' ends of all types of introns).

Conclusion

We show that the higher divergence of first introns is related to their larger size. Also, the lower divergence of short introns suggests that they may harbor a relatively greater proportion of regulatory elements than long introns. Moreover, our results are consistent with the presence of functionally relevant sequences near the 5' and 3' ends of introns. Finally, our findings suggest that other parts of introns may also be under selective constraints.