Long noncoding RNA and mRNA expression profiling following igf3 knockdown in common carp (Cyprinus carpio)

Growth and reproduction are two major physiological processes that are closely related in vertebrates, and IGFs are key factors that regulate the growth and reproduction axis. As a novel IGF system member, igf3 plays an important role in gonadal development of teleost fish. Although studies have reported the abnormal expression of igf3 in fish gonad, whether the igf3 regulates the expression of long noncoding RNAs (lncRNAs) in gonad remains unknown. In this study, a igf3 knockdown common carp (Cyprinus carpio) model was established by RNA interference. Than RNA sequencing of transcriptome in C. carpio after igf3 knockdown was performed. A total of 327,169,410 and 306,305,018 clean reads were identified from control and igf3-dsRNA group, respectively. After a stringent filtering, RNA-seq yielded 14199 lncRNA and 106932 mRNA transcripts with 124 and 353 differentially expressed lncRNAs and mRNAs. Gene Ontology analysis revealed that the target genes of differentially expressed lncRNAs and mRNAs mainly regulated male genitalia development, female gonad development, cellular response to gonadotropin-releasing hormone, insulin-like growth factor-activated receptor activity and insulin-like growth factor binding. Kyoto Encyclopedia of Genes and Genomes analysis showed that the target genes of differentially expressed lncRNAs and mRNAs mainly involved in pathways associated with insulin signaling pathway, GnRH signaling pathway, Wnt signaling pathway, PI3K-Akt signaling pathway and TGF-beta signaling pathway. The lncRNA-mRNA co-expression network highlight the inter-regulation of the differentially expressed lncRNAs and mRNAs in gonad. Our results provide essential data regarding differentially expressed lncRNAs and mRNAs after igf3 knockdown, which may be useful to elucidate the role of igf3 in the gonadal development of C. carpio. lncRNAs and mRNAs after igf3 knockdown in common carp were detected by deep sequencing using Illumina HiSeq X (BioProject Accession: PRJNA493964).