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Updated: Jul 8, 2026
10:17
Multi-target Chromogenic Whole-mount In Situ Hybridization for Comparing Gene Expression Domains in Drosophila Embryos
Published on: January 31, 2016
Coordinated evolution of co-expressed gene clusters in the Drosophila transcriptome
Jason G Mezey1, Sergey V Nuzhdin, Fangfei Ye
1Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853, USA. jgm45@cornell.edu
BMC Evolutionary Biology
|January 9, 2008
Summary
Gene expression in physically clustered genes evolves coordinately across Drosophila species. This coordinated evolution is linked to adaptive sequence changes, suggesting a connection between transcriptome and sequence evolution.
Area of Science:
- Genomics
- Evolutionary Biology
- Transcriptomics
Background:
- Eukaryotic transcriptomes often exhibit co-expression of physically clustered genes.
- This organization suggests coordinated gene expression evolution may be common.
- Understanding transcriptome evolution requires studying gene clusters with interdependent expression.
Purpose of the Study:
- To investigate the coordinated evolution of gene expression in physically clustered genes.
- To determine the relationship between coordinated expression evolution and adaptive sequence evolution.
- To explore the role of local regulatory mechanisms in gene cluster evolution.
Main Methods:
- Gene expression was measured using microarrays across seven Drosophila melanogaster subgroup species.
- Correlation structure of gene expression was analyzed using principal component analysis of correlation matrices.
- Patterns of co-expression were assessed at different scales within and across species.
Main Results:
- Physically clustered genes show coordinated expression evolution across many genomic locations.
- Co-expression clusters within species showed under-representation of adaptively evolving genes.
- Clusters exhibiting co-evolution of expression across species were enriched for adaptively evolving genes.
Conclusions:
- Co-evolution of expression in gene clusters is prevalent in the Drosophila melanogaster subgroup.
- A link exists between adaptive sequence evolution and coordinated gene expression evolution.
- Local gene regulation may drive the connection between adaptive sequence evolution and coordinated expression.
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