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To explore the transcriptome of Musca domestica larvae and to identify unique sequences, we used massively parallel pyrosequencing on the Roche 454-FLX platform to generate a substantial EST dataset of this fly. As a result, we obtained a total of 249,555 ESTs with an average read length of 373 bp. These reads were assembled into 13,206 contigs and 20,556 singletons. Using BlastX searches of the Swissprot and Nr databases, we were able to identify 4,814 contigs and 8,166 singletons as unique sequences. Subsequently, the annotated sequences were subjected to GO analysis and the search results showed a majority of the query sequences were assignable to certain gene ontology terms. In addition, functional classification and pathway assignment were performed by KEGG and 2,164 unique sequences were mapped into 184 KEGG pathways in total. As the first attempt on large-scale RNA sequencing of M. domestica, this general picture of the transcriptome can establish a fundamental resource for further research on functional genomics.

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This review paper deals with the immunological response in marine fish infected by Cryptocaryon irritans and discussed the practical difficulties in the development of potential molecular remedies. Browsing through the literature, it is understood that the development of molecular diagnostic tool to detect the early infection in fish by C. irritans is under progress. Once it is successfully established, the possible application of this technique could be suggested for even the non‐specific treatments such as copper‐based medications and bare‐bottomed quarantine of culture tanks. However, prior protection of healthy fish from C. irritans could be accomplished through proper immunization by infective theronts. In this case, a well‐suited in vitro culture technique is necessary to harvest theronts in large scale. Recent immunological and transcriptome studies predicted that the components related to local immune response are more effective against C. irritans than their systemic counterparts. However, in vivo experiments to prove the effect of these antiparasitic molecular components are meagre. Though molecular vaccines, developed from the well‐characterized 34 kDa immobilization antigen (iAg), responded well, these remedies fail to have a uniform impact against antigenically different strains (serotypes). More research is recommended to identify common protective epitopes from different serotypes. Also, studying the adjuvant effects of various innate responsive components like cytokines is significant. The suggested studies would be immensely helpful to develop effective vaccines against C. irritans infection and thereby optimize the aquaculture practices.