Allelic imbalance in Drosophila hybrid heads: exons, isoforms and evolution.

Using RNA-seq technology, a comprehensive assessment of cis regulatory divergence in interspecific hybrid female heads was conducted and patterns of sequence evolution (Begun et al. 2007) within causal loci were examined. Genotype specific references were shown to virtually eliminate the map bias plaguing this technology. A novel Bayesian model, which uses allele representation in F1 hybrid DNA sequence reads as a prior, was used to estimate allele frequencies in RNA sequences. Overall design: There are three independent replicate samples of D. melanogaster - D. simulans F1 hybrid interspecific RNA from head tissues. RNA samples were sequenced (one lane per replicate) on a GAIIX with 54 bp paired end reads. One gDNA sample was collected for the same genotype and 3 technical replicates were run on a GAIIX with 36 bp paired end reads. The DNA data was deposited to SRA (accession SRA048616).