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Background  Gibel carp is an important aquaculture species in China, and a herpesvirus, called as  Carassius auratus  herpesvirus ( Ca HV), has hampered the aquaculture development. Diverse gynogenetic clones of gibel carp have been identified or created, and some of them have been used as aquaculture varieties, but their resistances to herpesvirus and the underlying mechanism remain unknown.    Results  To reveal their susceptibility differences, we firstly performed herpesvirus challenge experiments in three gynogenetic clones of gibel carp, including the leading variety clone A + , candidate variety clone F and wild clone H. Three clones showed distinct resistances to  Ca HV. Moreover, 8772, 8679 and 10,982 differentially expressed unigenes (DEUs) were identified from comparative transcriptomes between diseased individuals and control individuals of clone A + , F and H, respectively. Comprehensive analysis of the shared DEUs in all three clones displayed common defense pathways to the herpesvirus infection, activating IFN system and suppressing complements. KEGG pathway analysis of specifically changed DEUs in respective clones revealed distinct immune responses to the herpesvirus infection. The DEU numbers identified from clone H in KEGG immune-related pathways, such as “chemokine signaling pathway”, “Toll-like receptor signaling pathway” and others, were remarkably much more than those from clone A +  and F. Several IFN-related genes, including  Mx1 ,  viperin ,  PKR  and others, showed higher increases in the resistant clone H than that in the others.  IFNphi3 ,  IFI44-like  and  Gig2  displayed the highest expression in clone F and  IRF1  uniquely increased in susceptible clone A + . In contrast to strong immune defense in resistant clone H, susceptible clone A +  showed remarkable up-regulation of genes related to apoptosis or death, indicating that clone A +  failed to resist virus offensive and evidently induced apoptosis or death.    Conclusions  Our study is the first attempt to screen distinct resistances and immune responses of three gynogenetic gibel carp clones to herpesvirus infection by comprehensive transcriptomes. These differential DEUs, immune-related pathways and IFN system genes identified from susceptible and resistant clones will be beneficial to marker-assisted selection (MAS) breeding or molecular module-based resistance breeding in gibel carp.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3945-6) contains supplementary material, which is available to authorized users.

Distinct herpesvirus resistances and immune responses of three gynogenetic clones of gibel carp revealed by comprehensive transcriptomes