Transcriptome-wide identification and functional investigation of circular RNA in the teleost large yellow croaker (Larimichthys crocea)

•We evaluated the performance of the two computational identification pipelines to circRNA in large yellow croaker.•We first identified and validated circRNA from the RNA-seq datasets in large yellow croaker.•The parent genes of the detected circRNAs were analyzed by GO and KEGG.•We also predicted that some identified L. crocea circRNA have abundant microRNA-binding sites.

Circular RNA (circRNA) was first reported over thirty years ago. With the development of high-throughput sequencing technologies, circRNA has been identified in an increasing number of species. However, few studies on circRNA have been reported in teleost fish. Accumulating transcriptome and phenotype data enable us to probe the biological functions of circRNA in fish species. Here, we report the identification of circRNAs from RNA sequencing (RNA-seq) data in large yellow croaker (Larimichthys crocea), a commercially important marine fish in China and East Asia. Using the computational identification, 975 circular RNAs were detected, of which three were validated by experiments. GO and KEGG analyses revealed the biological functions of genes hosting the circRNAs were enriched in the progression of translation initiation, macromolecule metabolism and binding. Notably, we found that many circRNAs in large yellow croaker had abundant microRNA-binding sites. A total of 363 the identified circRNAs had more than five miRNA-binding sites, among which twenty-two had more than ten binding sites for the miRNA-430 and the let-7 family. Our study confirmed the presence of circRNAs in large yellow croaker for the first time, providing a valuable reference for circRNA identification in fish species. Meanwhile, this work confirmed that the RNA-seq data from the traditional linear transcriptome library could be used for preliminary circRNA identification, which may offer an important reference for preliminary circRNA investigations in other species.