Interplay of gene expression and regulators under salinity stress in gill of Labeo rohita

Abstract

Background: Labeo rohita is the most preferred freshwater carp species in India. The concern of increasing salinity concentration in freshwater bodies due to climate change may greatly impact the aquatic environment. Gills are one of the important osmoregulatory organs and have direct contact with external environment. Hence, the current study is conducted to understand the gill transcriptomic response of L. rohita under hypersalinity environment.

Results: Comprehensive analysis of differentially expressed long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and mRNAs was performed in gills of L. rohita treated with 2, 4, 6 and 8ppt salinity concentrations. Networks of lncRNA-miRNA-mRNA revealed involvement of 20, 33, 52 and 61 differentially expressed lncRNAs, 11, 13, 26 and 21 differentially expressed miRNAs in 2, 4, 6 and 8ppt groups between control and treatment respectively. These lncRNA-miRNA pairs were regulating 87, 214, 499 and 435 differentially expressed mRNAs (DE mRNAs) in 2, 4, 6 and 8ppt treatments respectively. Functional analysis of these genes showed enrichment in pathways related to ion transportation and osmolyte production to cope with induced osmotic pressure due to high salt concentration. Pathways related to signal transduction (MAPK, FOXO and phosphatidylinositol signaling), and environmental information processing were also upregulated under hypersalinity. Energy metabolism and innate immune response pathways also appear to be regulated. Protein turnover was high at 8ppt as evidenced by enrichment of the proteasome and aminoacyl tRNA synthesis pathways, along with other enriched KEGG terms such as apoptosis, cellular senescence and cell cycle.

Conclusion: Altogether, the RNA-seq analysis provided valuable insights into competitive endogenous (lncRNA-miRNA-mRNA) regulatory network of L. rohita under salinity stress. L. rohita is adapting to the salinity stress by means of upregulating protein turnover, osmolyte production and removing the damaged cells using apoptotic pathway and regulating the cell growth and hence diverting the essential energy for coping with salinity stress.

Keywords: Gill transcriptome; Labeo rohita; Salinity stress; ceRNA network.

Fig. 1

Volcano plot of differentially expressed genes identified between control and 2ppt (1a), 4ppt (1b), 6ppt (1c) and 8ppt (1d) salinity treated L. rohita. The X-axis signifies Log2FoldChange value and Y-axis signifies –Log10 p-value. The ash color dots indicates non-significant genes, blue dots indicates significantly down regulated and orange dots indicates significantly up regulated genes

Fig. 2

Hub genes identified using CytoHubba plugin with maximal clique centrality (MCC) algorithm on Cytoscape for 2ppt (2a), 4ppt (2b), 6ppt (2c) and 8ppt (2d) salinity treatments. Edges represent protein-protein interaction. Red nodes represent genes with highest MCC score and yellow nodes represent genes with low MCC scores. Blue nodes represent the genes that are directly interacted with hubgenes

Fig. 3

a) Two-graph ROC curve where red line indicate specificity of mRNA and blue line indicates specificity of lncRNA b) Different classes of lncRNA identified in gill transcriptome of Labeo Rohita

Fig. 4

lncRNA-miRNA-mRNA integrated network of 2ppt treatment. Green colour diamonds, orange colour triangles, and circles represent lncRNA, miRNA and mRNA respectively. Red and blue colour circles represent up and down regulated mRNAs respectively. Network includes 259 edges and 118 nodes with 20, 11and 87 lncRNAs, miRNAs and mRNAs respectively

Fig. 5

lncRNA-miRNA-mRNA integrated network of 4ppt treatment. Green colour diamonds, orange colour triangles, and circles represent lncRNA, miRNA and mRNA respectively. Red and blue colour circles represent up and down regulated mRNAs respectively. Network includes 824 edges and 260 nodes with 33, 13 and 214 lncRNAs, miRNAs and mRNAs respectively

Fig. 6

lncRNA-miRNA-mRNA integrated network of 6ppt treatment. Green colour diamonds, orange colour triangles, and circles represent lncRNA, miRNA and mRNA respectively. Red and blue colour circles represent up and down regulated mRNAs respectively. Network includes 2688 edges and 577 nodes with 52, 26 and 499 lncRNAs, miRNAs and mRNAs respectively

Fig. 7

lncRNA-miRNA-mRNA integrated network of 8ppt treatment. Green colour diamonds, orange colour triangles, and circles represent lncRNA, miRNA and mRNA respectively. Red and blue colour circles represent up and down regulated mRNAs respectively. Network includes 3533 edges and 517 nodes with 61, 21 and 435 lncRNAs, miRNAs and mRNAs respectively