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Background  Maternal RNAs play a critical role in early development. Variation in the diversity and levels of maternally derived gene transcripts may be central to the origin of phenotypic novelty -- a longstanding problem in evolution and development. By studying maternal transcriptomes within and between divergent species, a better understanding of the evolutionary forces acting on maternal RNA allocation is possible.    Results  We present the first maternal transcriptome of the red flour beetle,  Tribolium castaneum . Using a tiled whole-genome microarray, we found that 58.2% of  T. castaneum  genes are maternally loaded into eggs. Comparison of known  Drosophila melanogaster  maternal genes to our results showed widespread conservation of maternal expression with  T. castaneum . Additionally, we found that many genes previously reported as having sex or tissue specific expression in  T. castaneum  were also maternally loaded. Identification of such pleiotropy is vital for proper modeling and testing of evolutionary theory using empirical data. The microarray design also allowed the detection of 2315 and 4060 novel transcriptionally active regions greater in length than 100 bp in unfertilized and fertilized  T. castaneum  eggs, respectively. These transcriptionally active regions represent novel exons of potentially unknown genes for future study.    Conclusions  Our results lay a foundation for utilizing  T. castaneum  as a model for understanding the role of maternal genes in evolution.

Identification of maternally-loaded RNA transcripts in unfertilized eggs of Tribolium castaneum