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Background  Cryptic prophages are genetically defective in their induction and propagation, and are simply regarded as genetic remnants. There are several putative cryptic WO prophages in the sequenced  Wolbachia  genomes. Whether they are lytic is unclear and their functions are poorly understood. Only three open reading frames (ORFs) in cryptic WO prophages have been reported to be actively transcribed.    Results  In this study, we comprehensively examined the transcription of the only cryptic WO prophage (WOSol) in a  Wolbachia  strain that infects a fig wasp,  Ceratosolen solmsi  (Agaonidae, Chalcidoidea). By analyzing the transcriptions of all the ORFs of WOSol in both sexes of  C. solmsi , using qualitative and quantitative methods, we demonstrated that i) a high percentage of ORFs are actively transcribed (59%, 17/29); ii) the expression of these ORFs is highly sex-specific, with a strong male bias (three in females and 15 in males); iii) an  ank  (ankyrin-domain-containing) gene actively transcribed in both wasp sexes is more highly expressed in males.    Conclusions  A large proportion of the genes in the cryptic WO prophage WOSol are expressed, which overturns the concept that cryptic prophages are simply genetically defective. The highly sex-specific expression patterns of these genes in the host suggest that they play important roles in  Wolbachia  biology and its reproductive manipulation of its insect host, particularly through the males.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-893) contains supplementary material, which is available to authorized users.

Large proportion of genes in one cryptic WO prophage genome are actively and sex-specifically transcribed in a fig wasp species