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【目的】预测鉴定甜橙miRNA及其作用机制和功能,为深入研究挖掘甜橙miRNA及其抗病相关miRNA的作用等提供翔实的基因信息。【方法】利用高通量测序技术、相关的生物信息学软件和数据库,构建甜橙小RNA文库,然后以甜橙基因组为参考基因组,进行甜橙miRNA鉴定和靶基因预测;利用GO和KEGG数据库对靶基因进行功能分析。【结果】成功构建了甜橙小RNA文库:获得12 617 944条小RNA序列分属于3 065 625种小RNA序列,获得序列中24 nt长的序列最多,占到序列的49.3%。鉴定出2 199 561条miRNA,其中已知miRNA638 722条,分属52种miRNA家族,候选miRNA1 560 839条,分属204种miRNA。已知的52种保守miRNA基因预测出927个靶基因位点,候选miRNA中有154种预测出1 777个靶基因位点。GO数据库对靶基因分类显示,甜橙miRNA调控的靶基因主要参与多细胞互作、转录本调控和细胞组成等生物学途经和分子功能方面。KEGG数据库中病原物与寄主互作亚库分析结果显示,靶基因主要与抗性蛋白、转录因子和抗病酶等关联。【结论】预测鉴定出一批甜橙miRNA及其调控的靶基因,为进一步研究提供了参考信息。
【Objective】 The objective of this study is to predict and identify the mechanism and function of sweet orange miRNAs and to provide informative gene information for further study on the function of miRNAs in sweet orange and their miRNAs for disease resistance. 【Method】 The sweet orange small RNA library was constructed by using high-throughput sequencing technology and related bioinformatics software and database. Then the sweet orange genome was used as the reference genome to identify the sweet orange miRNAs and predict the target genes. Using GO and KEGG database Functional analysis of target genes. 【Result】 A small RNA library of sweet orange was constructed successfully. 12 617 944 small RNA sequences belonging to 3 065 625 small RNA sequences were obtained. The sequences with 24 nt length were the most, accounting for 49.3% of the sequence length. A total of 2 199 561 miRNAs were identified, of which 722 miRNAs were known, belonging to 52 miRNA families and 560 839 candidate miRNAs, belonging to 204 miRNAs. The known 52 conserved miRNA genes predicted 927 target loci and 154 of the candidate miRNAs predicted 1 777 target loci. The classification of target genes by GO database showed that the target genes regulated by sweet orange miRNA are mainly involved in biological pathway and molecular function such as multi-cell interaction, transcriptional regulation and cell composition. The results of the sub-database of pathogen-host interaction in KEGG database showed that the target genes were mainly associated with resistance proteins, transcription factors and anti-disease enzymes. 【Conclusion】 A batch of sweet orange miRNAs and their target genes were identified and predicted, which provided reference information for further research.