Identification And Differentially Expressed Analysis Of MiRNA In Muscovy Duck

MicroRNAs(miRNAs)are a kind of non-coding small molecule RNAs,which play important roles in regulating a variety of biological processes in eukarya.These results should provide greater insight into the roles of miRNAs in poultry,providing more information for identifying genes related to Muscovy duck reproductive performance development.In this study,the identification and differentially expressed analysis of miRNAs by use of the Hisque 2500 SE50 sequencing technology combined with bioinformatics analysis were based on the construction of nesting and laying Moscovy duck ovary tissues cDNA libraries.We then predicted the target genes of differentially expressed miRNAs and analyzed the function of target genes.The results show that:1.Hisque 2500 SE50 sequencing of the two libraries generated 7966848(laying)and 9612842(nesting)raw reads,respectively.After discarding the low-quality sequences,trimming the 3'adaptor sequences and removing the 5' adaptor contaminations,6824590 clean reads ranging from 18 to 30 nucleotides were generated for the laying library,and 8242042 clean reads were generated for the nesting library.2.The sequence length distribution of nesting and laying libraries shows the same trend.We found a peak around 20-24nt,and the most abundant group of short RNAs was 22 nt long.The 20-24nt size group of nesting libraries was 91.1%,while The 20-24nt size group was 94.1%in laying libraries.This suggested that the length of small RNAs of two libraries are not significant difference in the overall composition,but the distributions of miRNA with different length are difference.3.we systemically examined the base composition of the unique tags from the two libraries.The miRNA first nucleotide bias of both libraries showed Uridine(U)dominated the first position,while U was the favor nucleotide bias at each position.4.By the Bioinformatics analysis,372 novel miRNA genes were identified from two libraries.Out of 372 novel miRNA genes,344 were Conservative novel miRNA.5.106 new miRNAs were differentially expressed between the laying and nesting Muscovy duck groups,of which 102(11 unconservative miRNAs and 91 conservative miRNAs)were significantly up-regulated and 4(1 unconservative miRNA and 3 unconservative miRNAs)were significantly down-regulated in nesting group.6.284 out of 372 novel miRNA genes were predicted to have10,685 targets.We predicted 5039 target genes for 106 differentially expressed miRNAs.GO and KEGG Pathway analysis showed these target genes of the differentially expressed miRNAs associated with the many biological processes,suggesting that they may play important roles in the nesting Muscovy duck.In present paper,comparative profile of the miRNA in laying and nesting muscovy duck ovary tissues were analysized,the results show that miRNA may play an key role in the nesting Muscovy duck tissues,it provides a useful resource for future studies on the role of miRNAs,lay the foundation for further study of muscovy duck molecular mechanism in egg laying and reproduction.