The Identification And Functional Classification Of Circular RNA In The Teleost Large Yellow Croaker (Larimichthys Crocea)

The circular RNA was reported thirty years ago.Recently,with the development of high-throughput sequencing technology,circular RNA has been identified in an increasing number of species.However,few studies on circular RNA have been reported in teleost fish.Large yellow croaker(Larimichthys crocea)is a commercially important marine fish in China and East Asia,and accumulating transcriptome and phenotype data enable us to probe the biological functions of circular RNA in large yellow croaker.Here,we used the simulation data from the genome of large yellow croaker to evaluate the two bioinformatics pipeline of detecting circular RNA.And then we used the appropriate pipeline to carry out the circular RNA from the real transcript data sets of large yellow croaker.At the same time,we used the NGS to sequence the gonads of male and female fish,in order to study the expression of circular RNA in gonads.And the differential expression of the circular RNA between male and female gonads was studied.Our study confirmed the presence of circular RNA in large yellow croaker for the first time,providing a valuable reference for circular RNA identification in fish species.Meanwhile,the results will provided the important information about the composition of the transcriptome of large yellow croaker and the regulation of these components.The main results are as follows:1.We used the simulation data which have different circular and linear transcripts to evaluate the two computational pipelines of identifying circular RNA.The results showed that under the condition of low circular RNA,the true positive circular RNA was higher by CIRCexplorer.However,in the case of high circular transcripts,the true positive of circular RNA detected by CIRI was significantly increased,and the number of circular RNAs detected was more.In contrast,the true positive of CIRCexplorer has declined,and the number of circular RNA identified is still low.2.According to the results of the simulation,we use CIRCexplorer to carry out the circular RNA from the traditional transcriptome data set of large yellow croaker.Finally,975 circular RNA were detected,of which 65.95% were derived from the exon of the coding gene.Then we randomly selected the three circular RNA to verify,the results confirmed that two of them are circular RNA.GO and KEGG analyses revealed the biological functions of genes hosting the circular RNA were enriched in the progression of translation initiation,macromolecule metabolism and binding.Notably,we found that many circular RNA in large yellow croaker had abundant microRNA-binding sites.A total of 363 the identified circular RNAs 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.3.We used the sequencing of circular RNA to analysis the expression of circular RNA in the gonad of large yellow croaker.Finally,we detected a total of 6115 circular RNAs from the male and female gonads,of which 2693 were specifically expressed in the male gonad and 1053 were specifically expressed in the female gonad.And there were 621 circular RNA higher expressed in female and 1065 higher expressed in male.The coding genes of these differential circular RNAs were analyzed by enrichment of GO and KEGG.The results showed that coding genes of the male and female gonadal RNA had significant differences in lipid metabolism pathway,progesterone-mediated oocyte maturation and ubiquitin mediated proteolysis.We also found that the circular RNA in gonad of large yellow croaker had abundant miRNA-binding sites,and the network analysis showed that the network of circRNA-miRNA-mRNA in gonad was complexed.