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Background  Accompanied with rapid growth and high density aquaculture, gibel carp has been seriously threatened by  Carassius auratus  herpesvirus ( Ca HV) since 2012. In previous study, distinct  Ca HV resistances and immune responses were revealed in the diseased individuals of three gibel carp gynogenetic clones (A + , F and H). However, little is known about the gene expression changes in the survivors after  Ca HV challenge, particularly their differences of innate and adaptive immune system between susceptible clone and resistant clone.    Results  We firstly confirmed the  Ca HV carrier state in the survivors of three gibel carp clones after  Ca HV challenge by evaluating the abundances of five  Ca HV genes. The assay of viral loads indicated the resistant clone H possessed not only stronger resistance but also higher tolerance to  Ca HV. Then, 2818, 4047 and 3323 differentially expressed unigenes (DEUs) were screened from the head-kidney transcriptome profiles of survivors compared with controls from clone A + , F and H. GO and KEGG analysis suggested that a persistent immune response might sustain in resistant clone H and F, while susceptible clone A +  had a long-term impact on the circulatory system which was consistent with the major symptoms of bleeding caused by  Ca HV. Among the top 30 enriched pathways of specifically up-regulated DEUs in respective clones, 26, 7 and 15 pathways in clone H, F and A +  were associated with infections, diseases, or immune-related pathways respectively. In addition, 20 pathways in clone F belonged to “metabolism” or “biogenesis”, and 7 pathways involved in “circulatory system” were enriched in clone A + . Significantly, we revealed the differential expression changes of IFN system genes and immunoglobulin (Ig) genes among the survivors of three clones. Finally, myosins and Igs were identified as co-expression modules which were positively or negatively correlated to  Ca HV viral loads respectively.    Conclusions  Our results revealed the common and distinct gene expression changes in immune and circulatory system in the survivors of three gibel carp gynogenetic clones with different  Ca HV resistances. The current study represents a paradigm of differential innate and adaptive immune reactions in teleost, and will be beneficial to the disease-resistance breeding of gibel carp.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5777-z) contains supplementary material, which is available to authorized users.

Differential expression of innate and adaptive immune genes in the survivors of three gibel carp gynogenetic clones after herpesvirus challenge