Several mechanisms have been proposed to account for the origination of new genes. Despite extensive case studies, the general principles governing this fundamental process are still unclear at the whole genome level. Here we unveil genome-wide patterns for the mutational mechanisms leading to new genes, and their subsequent lineage-specific evolution at different time nodes in the D. melanogaster species subgroup. We find that, 1) tandem gene duplication has generated about 80% of the nascent duplicates that are limited to single species (D. melanogaster or D. yakuba); 2) the most abundant new genes shared by multiple species (44.1%) are dispersed duplicates, and are more likely to be retained and be functional; 3) de novo gene origination from non-coding sequences plays an unexpectedly important role during the origin of new genes, and is responsible for 11.9% of the new genes; 4) retroposition is also an important mechanism, and had generated approximately 10% new genes; 5) about 30% of the new genes in the D. melanogaster species complex recruited various genomic sequences and formed chimeric gene structures, suggesting structure innovation as an important way to help fixation of new genes; and 6) the rate of the origin of new functional genes is estimated to be 5 to 11 genes per million years in the D. melanogaster subgroup. Finally, we survey gene frequencies among 19 strains from all over the world for D. melanogaster-specific new genes, and reveal that 44.4% of them show copy number polymorphisms within population. In conclusion, we provide a panoramic picture for origin of new genes in Drosophila species.

http://www.ncbi.nlm.nih.gov/pubmed/18550802?dopt=Abstract
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Klaas Vandepoele, PhD
Tel. 32 (0)9 33 13822
VIB Department of Plant Systems Biology, Ghent University
Technologiepark 927, 9052 Gent, Belgium
E-mail: Klaas.Vandepoele@psb.ugent.be
Website: http://bioinformatics.psb.ugent.be/
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Not shy of a spark, a knife twists at the thought 
that I should fall short of the mark