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Open Access Research article

Birth and death of gene overlaps in vertebrates

Izabela Makałowska1*, Chiao-Feng Lin23 and Krisitina Hernandez2

Author Affiliations

1 The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA

2 Institute of Molecular Evolutionary Genetics and Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA

3 Institute of Bioinformatics, University of Muenster, 48149 Muenster, Germany

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BMC Evolutionary Biology 2007, 7:193  doi:10.1186/1471-2148-7-193

Published: 16 October 2007



Between five and fourteen per cent of genes in the vertebrate genomes do overlap sharing some intronic and/or exonic sequence. It was observed that majority of these overlaps are not conserved among vertebrate lineages. Although several mechanisms have been proposed to explain gene overlap origination the evolutionary basis of these phenomenon are still not well understood. Here, we present results of the comparative analysis of several vertebrate genomes. The purpose of this study was to examine overlapping genes in the context of their evolution and mechanisms leading to their origin.


Based on the presence and arrangement of human overlapping genes orthologs in rodent and fish genomes we developed 15 theoretical scenarios of overlapping genes evolution. Analysis of these theoretical scenarios and close examination of genomic sequences revealed new mechanisms leading to the overlaps evolution and confirmed that many of the vertebrate gene overlaps are not conserved. This study also demonstrates that repetitive elements contribute to the overlapping genes origination and, for the first time, that evolutionary events could lead to the loss of an ancient overlap.


Birth as well as most probably death of gene overlaps occurred over the entire time of vertebrate evolution and there wasn't any rapid origin or 'big bang' in the course of overlapping genes evolution. The major forces in the gene overlaps origination are transposition and exaptation. Our results also imply that origin of overlapping genes is not an issue of saving space and contracting genomes size.