Digital differential expression analysis of early embryonic de novo assembled sexed transcriptomes of Ceratitis capitata, a world-wide agricultural pest, to identify new sex-specific and sex-biased genes.

The agricultural pest Ceratitis capitata, also known as the Mediterranean fruit fly or Medfly, belongs to the Tephritidae family, which includes a large number of damaging pest species. The knowledge of the life-cycle and of the biology of pest species opens new chances to develop eco-sustainable control strategies, alternative to pesticides. Reproduction and sex determination are at the same time crucial aspects to understand insect biology and optimal targets to limit their population growth and diffusion. In the Medfly, where XY (males) and XX (females) sexual chromosomes are present, the primary signal of sex determination, constituted by a dominant factor linked to the Y-chromosome, is still uknown. To identify this factor and to search for new early sex-biased genes we applied Illumina sequencing to RNA from 8-10 hours and 23-25 hours after egg laying (AEL) embryos of C. capitata, leading to define about 20,000 novel unique reconstructed transcripts. We utilized short reads mapping and counting, using BOWTIE and SAMTOOLS software, and the EdgeR software to evaluate and compare the expression levels of the reconstructed transcripts between sexed embryonic samples and stages. We identified about 3000 male-biased and about 1000 female-biased transcripts at 8-10h AEL. Selected candidate transcripts are under validation by qPCR expression analyses and RNAi functional analyses