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Cytorace-3 is a laboratory evolved hybrid lineage of  Drosophila nasuta nasuta  males and  Drosophila nasuta albomicans  females currently passing ~850 generations. To assess interracial hybridization effects on gene expression in Cytorace-3 we profiled the transcriptomes of mature ovaries and testes by employing Illumina sequencing technology and  de novo  transcriptome assembling strategies. We found 26% of the ovarian, and 14% of testis genes to be differentially expressed in Cytorace-3 relative to the expressed genes in the parental gonadal transcriptomes. About 5% of genes exhibited additive gene expression pattern in the ovary and 3% in the testis, while the remaining genes were misexpressed in Cytorace-3. Nearly 772 of these misexpressed genes in the ovary and 413 in the testis were either over- or under-dominant. Genes following  D. n. nasuta  dominance was twice (270 genes) than  D. n. albomicans  dominance (133 genes) in the ovary. In contrast, only 105 genes showed  D. n. nasuta  dominance and 207 showed  D. n. albomicans  dominance in testis transcriptome. Of the six expression inheritance patterns, conserved inheritance pattern was predominant for both ovary (73%) and testis (85%) in Cytorace-3. This study is the first to provide an overview of the expression divergence and inheritance patterns of the transcriptomes in an independently evolving distinct hybrid lineage of  Drosophila . This recorded expression divergence in Cytorace-3 surpasses that between parental lineages illustrating the strong impact of hybridization driving rapid gene expression changes.

De novo assembly, annotation and gene expression profiles of gonads of Cytorace-3, a hybrid lineage of Drosophila nasuta nasuta and D. n. albomicans