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

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.

Fig. 1

Degradome-dependent miRNA regulatory networks in soybean. The width of edges are gradient from 1 to 7, corresponding to the number of degradome libraries that verified the same MTIs. The color of edges represents the category of cleavage of highest degradome count (red is Cat_1 level, and blue is Cat_2).The grey-green circles represent targets, the grey-green squares represent target gene-encoding protein families (indicating biological function), blue circles are expression-non-changed miRNAs and orange ones are tissue-specific miRNAs

Fig. 2

Venn diagram of diversity of gma-miRNA-Target relations in different tissues. The numbers in the picture show number of miRNA-Target relations’ distribution in root, leaf, cotyledon, and seed (including seed coat)

Fig. 3

Comparisons of verified MTIs in different tissues. a Comparison of verified MTIs and DEM regulated MTIs in root; b Comparison of verified MTIs and DEM regulated MTIs in cotyledon; c Comparison of verified MTIs and DEM regulated MTIs in seed; d Comparison of verified MTIs and DEM regulated MTIs in leaf

Fig. 4

Tissue-conserved gma-miRNA family regulatory networks. a gma-miR166 family regulatory network; b gma-miR160 family regulatory network; c gma-miR171family regulatory network; d gma-miR1510 and e gma-miR167 regulatory networks

Fig. 5

gma-miR171 mediated gene regulatory networks a Cotyledon-specific DDN b Seed-specific DDN c Conserved DDN; d Degradome verified cleavage t-plot of (a) (b) (c) *DDN, Degradome-Dependent MicroRNA-mediated networks. Red verticals in (d) are degradome count of the MTIs in figure titles, which show the cleavage level of MTIs

Fig. 6

Exemplified tissue-specific subnetworks. a Leaf-specific DDN mediated by cotyledon-specific miRNA5674 and miRNA1508c b Cotyledon-specific miRNA159-mediated subnetwork c Root-specifc DDN regulated by miRNA1510b-3p and miRNA2109-5p; d Seed-specific miRNA164-mediated subnetworks. *DDN, Degradome-Dependent MicroRNA-mediated networks, ‘Tissues’ described whether the MTIs are conserved or tissue-specific.

Fig. 7

Interacted networks between different gma-miRNA families. a Co-interacted network of gma-miR 319 family and gma-miR4996, sub-network of Fig.3a; b Verified t-plot of gma-miR4996/Glyma.13 g219900, Y-aix represents degradome abundance(TP10M), X-aix represents nucleotide position (nt), the aligned region of microRNA on mRNA. c Verified t-plot of gma-miR319l/Glyma.13 g219900. d Verified t-plot of gma-miR319f/Glyma.13 g219900

Fig. 8

The gma-miR167 family regulatory network. a Gma-miRNA167 family regulatory networks (including miR 167a/b/c/d/e/f/g/j); b Gma-miRNA167k regulatory network; c Mature gma-miRNA167 sequence variation. The bases in red are sequence variations, the grey box is homologous part of gma-miRNA167 family, and the green box is homologous part of gma-miRNA167a/b/c/d/e/f/g/j