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BMC Genomics. 2019 Jun 28;20(1):534. doi: 10.1186/s12864-019-5879-7.

Construction and analysis of degradome-dependent microRNA regulatory networks in soybean.

Author information

1
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
2
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China. huangji@njau.edu.cn.

Abstract

BACKGROUND:

Usually the microRNA (miRNA)-mediated gene regulatory network (GRN) is constructed from the investigation of miRNA expression profiling and target predictions. However, the higher/lower expression level of miRNAs does not always indicate the higher/lower level of cleavages and such analysis, thus, sometimes ignores the crucial cleavage events. In the present work, the degradome sequencing data were employed to construct the complete miRNA-mediated gene regulatory network in soybean, unlike the traditional approach starting with small RNA sequencing data.

RESULTS:

We constructed the root-, cotyledon-, leaf- and seed-specific miRNA regulatory networks with the degradome sequencing data and the forthcoming verification of miRNA profiling analysis. As a result, we identified 205 conserved miRNA-target interactions (MTIs) involved with 6 conserved gma-miRNA families and 365 tissue-specific MTIs containing 24 root-specific, 45 leaf-specific, 63 cotyledon-specific and 225 seed-specific MTIs. We found a total of 156 miRNAs in tissue-specific MTIs including 18 tissue-specific miRNAs, however, only 3 miRNAs have consistent tissue-specific expression. Our study showed the degradome-dependent miRNA regulatory networks (DDNs) in four soybean tissues and explored their conservations and specificities.

CONCLUSIONS:

The construction of DDNs may provide the complete miRNA-Target interactions in certain plant tissues, leading to the identification of the conserved and tissue-specific MTIs and sub-networks. Our work provides a basis for further investigation of the roles and mechanisms of miRNA-mediated regulation of tissue-specific growth and development in soybean.

KEYWORDS:

DDN; Degradome; Regulatory network; Soybean; microRNA

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