Identification Of MicroRNAs In Large Yellow Croaker(Larimichthys Crocea) Using An Integrated Comparative And Ab Initio Approach

The large yellow croaker?Larimichthys crocea?is an economic marine fish with highest output in China,and it's very important to research for this species.Since the miRNAs'discovery at the turn of the century,more and more scientists have been focusing on the study of miRNAs as the result of the fact that miRNAs play a vital role in regulating a series of biological processes and there are lots of researches about miRNAs in many species especially in the model organisms,whereas the researches related miRNAs in large yellow croaker are pretty rare.Researching the miRNAs'function in large yellow croaker and discovering the miRNAs could make us know better about the basic knowledge of economic genetic traits and provide an effective way to improve characters in large yellow croaker.In this work,we employed an integrated strategy combining homology-based and ab initio approach to predict miRNAs from the genome and transcriptome of large yellow croaker.We predicted the miRNA target genes and annotated all these target genes.we also studied the miRNA-related SNP which can influence miRNA target genes.Detailed results and conclusions are as follows:1.Based on the theory that mature miRNAs are conservative among different species,273 and 54 miRNAs were gained from genome an transcriptome sequence of large yellow croaker respectively,and after remove the redundant miRNA sequences,a total number of 284 miRNAs were gained.According to the theory that miRNAs can convene into a cluster,we also identified131 novel miRNAs by using an ab initio method.All of these miRNAs could provide materials for further miRNA function studies in large yellow croaker.2.The length of mature miRNAs vary from 16 nt to 27 nt with an average length of 21.74 nt,and the majority length is 22 nt,which account for about 33.3% of all mature miRNAs.In the study about base composition of each site of miRNA,we also found adenine had the lower frequency than any other nucleotides in the 23^rd site.The phylogenetic analysis of miR-12,miR-22,miR-34 and miR-203 sequences reveled that conversation and diversification of miRNA precursors.3.Miranda and RNAhybrid were used to predict target genes of all 418 miRNA sequences and 16142 and 23510 target genes were gained respectively.In order to reduce the false positive results,we only adopt the intersection of two results and at last,16053 target genes were gained.For further study,all these target genes were used to GO and KEGG annotation analysis.4.According to the SNP distribution in large yellow croaker genome,22 SNP were found in19 miRNAs.Mature miRNA regions had the lowest SNP frequency when compared with other vicinity regions and this results reveled miRNAs in large yellow croaker were also conservative.miRNA target genes were also predicted at the affection of miRNA-related SNP and the results indicated the miRNA-related SNP can increase the number of miRNA target genes.