Abstract
Previous studies of repetitive elements (REs) have implicated a mechanistic role in generating new chimerical genes. Such examples are consistent with the classic model for exon shuffling, which relies on non-homologous recombination. However, recent data for chromosomal aberrations in model organisms suggest that ectopic homology-dependent recombination may also be important. Lack of a dataset comprising experimentally verified young duplicates has hampered an effective examination of these models as well as an investigation of sequence features that mediate the rearrangements. Here we use ∼7,000 cDNA probes (∼112,000 primary images) to screen eight species within the Drosophila melanogaster subgroup and identify 17 duplicates that were generated through ectopic recombination within the last 12 mys. Most of these are functional and have evolved divergent expression patterns and novel chimeric structures. Examination of their flanking sequences revealed an excess of repetitive sequences, with the majority belonging to the transposable element DNAREP1 family, associated with the new genes. Our dataset strongly suggests an important role for REs in the generation of chimeric genes within these species.
Highlights
Gene duplication followed by the acquisition of novel molecular function is a fundamental process underlying biological diversity
Many new genes have been found to originate through dispersed gene duplication and exon/domain shuffling
What recombination mechanisms were involved in the duplication and the shuffling processes? Lack of the intermediate products of recombination that share adequate sequence identity between homologous sequences, or the parental sequences from which the new genes were derived, often makes answering these questions difficult
Summary
Gene duplication followed by the acquisition of novel molecular function is a fundamental process underlying biological diversity. Breakpoint analyses on these datasets revealed little or no sequence identity between the loci recombined, supporting a NHR model While these experiments show such a model is possible for exon shuffling, it remains an open question how frequently such processes in non-artificial systems, and over evolutionary time, will contribute to the formation of fixed chimeric genes. Another potential NHR mechanism that can mediate nonhomologous recombination is through the activity of transposable elements (TEs). ¤ Current address: Ingenieur de Recherche en Bioinformatique Equipe Genomique Evolutive des Vertebres, Institut de Genomique Fonctionnelle de Lyon (IGFL)— Ecole Normale Superieure de Lyon (ENSL) 46, Lyon, France
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