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Open Access Research article

Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication

Jörg Lehmann1, Carina Eisenhardt2, Peter F Stadler13456 and Veiko Krauss1*

Author Affiliations

1 Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany

2 Genetics Group, Department of Biology II, University of Leipzig, Johannisallee 21-23, 04103 Leipzig, Germany

3 Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany

4 RNomics Group, Fraunhofer Institute for Cell Therapy and Immunology, Perlickstraße 1, 04103 Leipzig, Germany

5 Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17, 1090 Wien, Austria

6 Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA

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BMC Evolutionary Biology 2010, 10:156  doi:10.1186/1471-2148-10-156

Published: 26 May 2010

Abstract

Background

Positions of spliceosomal introns are often conserved between remotely related genes. Introns that reside in non-conserved positions are either novel or remnants of frequent losses of introns in some evolutionary lineages. A recent gain of such introns is difficult to prove. However, introns verified as novel are needed to evaluate contemporary processes of intron gain.

Results

We identified 25 unambiguous cases of novel intron positions in 31 Drosophila genes that exhibit near intron pairs (NIPs). Here, a NIP consists of an ancient and a novel intron position that are separated by less than 32 nt. Within a single gene, such closely-spaced introns are very unlikely to have coexisted. In most cases, therefore, the ancient intron position must have disappeared in favour of the novel one. A survey for NIPs among 12 Drosophila genomes identifies intron sliding (migration) as one of the more frequent causes of novel intron positions. Other novel introns seem to have been gained by regional tandem duplications of coding sequences containing a proto-splice site.

Conclusions

Recent intron gains sometimes appear to have arisen by duplication of exonic sequences and subsequent intronization of one of the copies. Intron migration and exon duplication together may account for a significant amount of novel intron positions in conserved coding sequences.