title: Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution.
abstract: BACKGROUND
  The physical organization and chromosomal localization of genes within genomes is known to play an important role in their function. Most genes arise by duplication and move along the genome by random shuffling of DNA segments. Higher order structuring of the genome occurs in eukaryotes, where groups of physically linked genes are co-expressed. However, the contribution of gene duplication to gene order has not been analyzed in detail, as it is believed that co-expression due to recent duplicates would obscure other domains of co-expression.
  
  
  RESULTS
  We have catalogued ordered duplicated genes in Drosophila melanogaster, and found that one in five of all genes is organized as tandem arrays. Furthermore, among arrays that have been spatially conserved over longer periods than would be expected on the basis of random shuffling, a disproportionate number contain genes encoding developmental regulators. Using in situ gene expression data for more than half of the Drosophila genome, we find that genes in these conserved clusters are co-expressed to a much higher extent than other duplicated genes.
  
  
  CONCLUSIONS
  These results reveal the existence of functional constraints in insects that retain copies of genes encoding developmental and regulatory proteins as neighbors, allowing their co-expression. This co-expression may be the result of shared cis-regulatory elements or a shared need for a specific chromatin structure. Our results highlight the association between genome architecture and the gene regulatory networks involved in the construction of the body plan.
authors.affiliation: Instituto de Investigaciones Biomédicas CSIC-UAM, Arturo Duperier 4, 28029 Madrid, Spain. cquijano@bsc.es
authors.forename: Carlos
authors.initials: C
authors.lastname: Quijano
authors.forename: Pavel
authors.initials: P
authors.lastname: Tomancak
authors.forename: Jesus
authors.initials: J
authors.lastname: Lopez-Marti
authors.forename: Mikita
authors.initials: M
authors.lastname: Suyama
authors.forename: Peer
authors.initials: P
authors.lastname: Bork
authors.forename: Marco
authors.initials: M
authors.lastname: Milan
authors.forename: David
authors.initials: D
authors.lastname: Torrents
authors.forename: Miguel
authors.initials: M
authors.lastname: Manzanares
mesh_terms: D000818:Animals; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D005786:Gene Expression Regulation; D020131:Genes, Duplicate
chemical_list: D029721:Drosophila Proteins