Rapid sequence divergence rates in the 5 prime regulatory regions of young Drosophila melanogaster duplicate gene pairs

Abstract

While it remains a matter of some debate, rapid sequence evolution of the coding sequences of duplicate genes is characteristic for early phases past duplication, but long established duplicates generally evolve under constraint, much like the rest of the coding genome. As for coding sequences, it may be possible to infer evolutionary rate, selection, and constraint via contrasts between duplicate gene divergence in the 5 prime regions and in the corresponding synonymous site divergence in the coding regions. Finding elevated rates for the 5 prime regions of duplicated genes, in addition to the coding regions, would enable statements regarding the early processes of duplicate gene evolution. Here, 1 kb of each of the 5 prime regulatory regions of Drosophila melanogaster duplicate gene pairs were mapped onto one another to isolate shared sequence blocks. Genetic distances within shared sequence blocks (d 5' ) were found to increase as a function of synonymous (d S ), and to a lesser extend, amino-acid (d A ) site divergence between duplicates. The rate d 5' /d S was found to rapidly decay from values > 1 in young duplicate pairs (d S < 0.3) to 0.28 or less in older duplicates (d S > 0.8). Such rapid rates of 5 prime evolution exceeding 1 (~neutral) predominantly were found to occur in duplicate pairs with low amino-acid site divergence and that tended to be co-regulated when assayed on microarrays. Conceivably, functional redundancy and relaxation of selective constraint facilitates subsequent positive selection on the 5 prime regions of young duplicate genes. This might promote the evolution of new functions (neofunctionalization) or division of labor among duplicate genes (subfunctionalization). In contrast, similar to the vast portion of the non-coding genome, the 5 prime regions of long-established gene duplicates appear to evolve under selective constraint, indicating that these long-established gene duplicates have assumed critical functions.

Diversification at Transcription Factor Binding Sites within a Species and the Implications for Environmental Adaptation

“…Indeed, it has been previously shown that there is a significant negative relationship between the expression correlation of duplicate genes and K a (Gu et al, 2002). Similar results have been obtained when analyzing duplicate genes in Arabidopsis thaliana, Drosophila melanogaster and humans (Ganko, Meyers and Vision, 2007;Kohn, 2008;Park and Makova, 2009). To-gether these results indicate that functional change of diverging duplicate genes at the coding sequence level is coupled with change in transcription factor binding sites and expression.…”

Evolutionary divergence and limits of conserved non-coding sequence detection in plant genomes

“…BLASTN implements a local alignment strategy whereas DIALIGN combines local alignment to seed subsequent global alignment. Both of these tools have previously been used in other CNS investigations ( 6 , 8 , 85 , 86 ). A case study using a known heat shock element ( 74 , 75 ) shows that both DIALIGN and BLASTN were successful in identifying the motif TTCnnGAA, with DIALIGN being more sensitive ( Figure 3 ).…”

A critical assessment of cross-species detection of gene duplicates using comparative genomic hybridization

“…Similarly, a selective advantage for spatially or temporally divided expression can produce highly conserved protein coding regions (a type of subfunctionalization) due to mutations in the enhancer regions [ 54 ]. Such changes in enhancer regions have been reported to occur in recent duplicates [ 55 ]. In some cases, novel function may come about with only a small level of sequence divergence of the protein coding region.…”