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Identification of miRNAs and Their Target Genes Using Deep Sequencing and Degradome Analysis in Trifoliate Orange [Poncirus trifoliate (L.) Raf]

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An Erratum to this article was published on 24 September 2011

Abstract

To identify novel as well as conserved miRNAs in citrus, deep sequencing of small RNA library combined with microarray was performed in precocious trifoliate orange (an early flowering mutant of trifoliate orange, Poncirus trifoliata L. Raf.), resulting in the obtainment of a total of 114 conserved miRNAs belonging to 38 families and 155 novel miRNAs. The miRNA star sequences of 39 conserved miRNAs and 27 novel miRNAs were also discovered among newly identified miRNAs, providing additional evidence for the existence of miRNAs. Through degradome sequencing, 172 and 149 genes were identified as targets of conserved miRNAs and novel miRNAs, respectively. GO and KEGG annotation revealed that high ranked miRNA-target genes were those implicated in biological and metabolic processes. To characterize those miRNAs expressed at the juvenile and adult development stages of citrus, further analysis on the expression profiles of these miRNAs through hybridizing the commercial microarray and real-time PCR was performed. The results revealed that some miRNAs were down-regulated at adult stage compared with juvenile stage. Detailed comparison of the expression patterns of some miRNAs and corresponding target genes revealed the negative correlation between them, while few of them are positively correlated.

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Acknowledgments

We are grateful to Prof. Han-Hui Kuang for his helpful discussion and help in revising this manuscript. This research was supported financially by the National Natural Science Foundation of China (grant nos. 30971973, 31071777, 30921002). The Science Foundation of the Doctoral Subject Point of the Chinese Ministry of Education (grant no. 20090146110009), the Fundamental Research Funds for the Central Universities (2011QC037, 2010BQ044), and the 863 Project of China.

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Authors and Affiliations

  1. Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, 430070, China

    Jin-Zhi Zhang, Xiao-Yan Ai, Wen-Wu Guo, Shu-Ang Peng, Xiu-Xin Deng & Chun-Gen Hu

  2. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Wen-Wu Guo & Xiu-Xin Deng

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  1. Jin-Zhi Zhang
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  2. Xiao-Yan Ai
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Correspondence to Chun-Gen Hu.

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An erratum to this article can be found at http://dx.doi.org/10.1007/s12033-011-9455-x.

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Zhang, JZ., Ai, XY., Guo, WW. et al. Identification of miRNAs and Their Target Genes Using Deep Sequencing and Degradome Analysis in Trifoliate Orange [Poncirus trifoliate (L.) Raf]. Mol Biotechnol 51, 44–57 (2012). https://doi.org/10.1007/s12033-011-9439-x

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