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PMID: 18550802 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

On the origin of new genes in Drosophila.

Genome research ·Vol. 18 ·No. 9 ·2008-09-00 ·Pages 1446-55

Zhou Q, Zhang G, Zhang Y, Xu S, Zhao R, Zhan Z, Li X, Ding Y, Yang S, Wang W

Abstract

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 Drosophila melanogaster species subgroup. We find that (1) tandem gene duplication has generated approximately 80% of the nascent duplicates that are limited to single species (D. melanogaster or Drosophila 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 noncoding 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% of the new genes; (5) approximately 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 five to 11 genes per million years in the D. melanogaster subgroup. Finally, we survey gene frequencies among 19 globally derived strains for D. melanogaster-specific new genes and reveal that 44.4% of them show copy number polymorphisms within a population. In conclusion, we provide a panoramic picture for the origin of new genes in Drosophila species.

MeSH Terms
Animals Chimerism Drosophila melanogaster/genetics Evolution, Molecular Genes, Duplicate Genes, Insect Genome, Insect Phylogeny Tandem Repeat Sequences
Authors & Affiliations
10 authors, click to expand affiliations / ORCID
Zhou Qi
CAS-Max Planck Junior Research Group, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
Zhang Guojie
Zhang Yue
Xu Shiyu
Zhao Ruoping
Zhan Zubing
Li Xin
Ding Yun
Yang Shuang
Wang Wen
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.076588.108
Published
2008-09-00
Epub
2008-00-11
Pages
1446-55
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC2527705
Subset
IM
External Links
PubMed source DOI: 10.1101/gr.076588.108 PMC Full Text View journal details
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