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Integrated analysis of mRNA and viral miRNA expression profiles in the kidney of Carassius auratus gibelio response to cyprinid herpesvirus 2

ABSTRACT: MiRNAs are small non-coding single stranded RNAs that play crucial roles in numerous biological processes. Vertebrate herpesviruses encode multiple viral miRNAs that modulate host and viral genes. However, the roles of viral miRNAs in invertebrates have not been fully determined. Here, we used high-throughput sequencing to analyse miRNA and mRNA expression proﬁles of Carassius auratus gibelio in response to infection by cyprinid herpesvirus 2 (CyHV-2). RNA sequencing obtained 26,664 assembled transcripts, including 2,978 differentially expressed genes, among which 12 were validated by qRT-PCR. Based on small RNA (sRNA) sequencing and secondary structure predictions, we identified 17 CyHV-2 encoded miRNAs. Target prediction for the viral miRNAs identiﬁed >1,109 host and virus gene target pairs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis of the viral miRNAs revealed diverse affected immune signalling pathways, including the RIG-I-like receptor, the Toll-like receptor and the JAK-STAT signalling pathways. Finally, we presented a functional analysis of CyHV-2-encoded ORF60 and host gene TLR5, both of which are targeted by CyHV-2 miRNA miR-C1.

ORGANISM(S): Carassius gibelio

PROVIDER: GSE90626 | GEO | 2018/01/01

SECONDARY ACCESSION(S): PRJNA355239

REPOSITORIES: GEO

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Project description:Gibel carp (Carassius gibelio) is a cyprinid fish that originated in eastern Eurasia and is considered as invasive in European freshwater ecosystems. The populations of gibel carp in Europe are mostly composed of asexually reproducing triploid females (i.e., reproducing by gynogenesis) and sexually reproducing diploid females and males. Although some cases of coexisting sexual and asexual reproductive forms are known in vertebrates, the molecular mechanisms maintaining such coexistence are still in question. Both reproduction modes are supposed to exhibit evolutionary and ecological advantages and disadvantages. To better understand the coexistence of these two reproduction strategies, we performed transcriptome profile analysis of gonad tissues (ovaries), and studied the differentially expressed reproduction-associated genes in sexual and asexual females. We used high-throughput RNA sequencing to generate transcriptomic profiles of gonadal tissues of triploid asexual females and males, diploid sexual males and females of gibel carp, as well as diploid individuals from two closely-related species, C. auratus and Cyprinus carpio. Using SNP clustering, we showed the close similarity of C. gibelio and C. auratus with a basal position of C. carpio to both Carassius species. Using transcriptome profile analyses, we showed that many genes and pathways are involved in both gynogenetic and sexual reproduction in C. gibelio; however, we also found that 1500 genes, including 100 genes involved in cell cycle control, meiosis, oogenesis, embryogenesis, fertilization, steroid hormone signaling and biosynthesis were differently expressed in the ovaries of asexual and sexual females. We suggest that the overall downregulation of reproduction-associated pathways in asexual females, and their maintenance in sexual ones, allow for their stable coexistence, integrating the evolutionary and ecological advantages and disadvantages of the two reproductive forms. However, we showed that many sexual-reproduction-related genes are maintained and expressed in asexual females, suggesting that gynogenetic gibel carp retains the genetic toolkits for meiosis and sexual reproduction. These findings shed new light on the evolution of this asexual and sexual complex.

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Integrated analysis of mRNA and viral miRNA expression profiles in the kidney of Carassius auratus gibelio response to cyprinid herpesvirus 2

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