title: Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture.
abstract: BACKGROUND
  The biological dimensions of genes are manifold. These include genomic properties, (e.g., X/autosomal linkage, recombination) and functional properties (e.g., expression level, tissue specificity). Multiple properties, each generally of subtle influence individually, may affect the evolution of genes or merely be (auto-)correlates. Results of multidimensional analyses may reveal the relative importance of these properties on the evolution of genes, and therefore help evaluate whether these properties should be considered during analyses. While numerous properties are now considered during studies, most work still assumes the stereotypical solitary gene as commonly depicted in textbooks. Here, we investigate the Drosophila melanogaster genome to determine whether deviations from the stereotypical gene architecture correlate with other properties of genes.
  
  
  RESULTS
  Deviations from the stereotypical gene architecture were classified as the following gene constellations: Overlapping genes were defined as those that overlap in the 5-prime, exonic, or intronic regions. Chromatin co-clustering genes were defined as genes that co-clustered within 20 kb of transcriptional territories. If this scheme is applied the stereotypical gene emerges as a rare occurrence (7.5%), slightly varied schemes yielded between approximately 1%-50%. Moreover, when following our scheme, paired-overlapping genes and chromatin co-clustering genes accounted for 50.1 and 42.4% of the genes analyzed, respectively. Gene constellation was a correlate of a number of functional and evolutionary properties of genes, but its statistical effect was approximately 1-2 orders of magnitude lower than the effects of recombination, chromosome linkage and protein function. Analysis of datasets on male reproductive proteins showed these were biased in their representation of gene constellations and evolutionary rate Ka/Ks estimates, but these biases did not overwhelm the biologically meaningful observation of high evolutionary rates of male reproductive genes.
  
  
  CONCLUSIONS
  Given the rarity of the solitary stereotypical gene, and the abundance of gene constellations that deviate from it, the presence of gene constellations, while once thought to be exceptional in large Eukaryote genomes, might have broader relevance to the understanding and study of the genome. However, according to our definition, while gene constellations can be significant correlates of functional properties of genes, they generally are weak correlates of the evolution of genes. Thus, the need for their consideration would depend on the context of studies.
authors.affiliation: Department of Ecology and Evolutionary Biology, Rice University, 6100 Main Street, MS 170, Houston, Texas 77005, USA.
authors.forename: Shuwei
authors.initials: S
authors.lastname: Li
authors.forename: Ching-Hua
authors.initials: CH
authors.lastname: Shih
authors.forename: Michael H
authors.initials: MH
authors.lastname: Kohn
mesh_terms: D000818:Animals; D002875:Chromosomes / Q000235:genetics; D017124:Conserved Sequence; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D020440:Gene Duplication; D017344:Genes, Insect / Q000235:genetics*; D008297:Male; D011995:Recombination, Genetic / Q000235:genetics