Integrative miRNA-mRNA network analysis to identify crucial pathways of salinity adaptation in brain transcriptome of Labeo rohita

Frontiers in Genetics

Genetics

Aparna Chaudhari¹  Nitin Shukla²  Amrutlal K. Patel²  Chaitanya G. Joshi²  Ishan Raval²  Harshini Vemula²  Vivek Shrivastava³  Sujit Kumar³ 

[1] Central Institute of Fisheries Education, Mumbai, Maharashtra, India;Gujarat Biotechnology Research Centre, Gandhinagar, Gujarat, India;Postgraduate Institute of Fisheries Education and Research, Kamdhenu University, Gandhinagar, Gujarat, India;

关键词: brain transcriptome;    Labeo rohita;    hub genes;    miRNA-mRNA regulatory network;    salinity adaptation;   

DOI  :  10.3389/fgene.2023.1209843

 received in 2023-04-21, accepted in 2023-08-17,  发布年份 2023

来源: Frontiers

【 摘 要 】

Introduction: Brain being the master regulator of the physiology of animal, the current study focuses on the gene expression pattern of the brain tissue with special emphasis on regulation of growth, developmental process of an organism and cellular adaptation of Labeo rohita against unfavourable environmental conditions.Methods: RNA-seq study was performed on collected brain samples at 8ppt salt concentration and analyzed for differential gene expression, functional annotation and miRNA-mRNA regulatory network.Results: We found that 2450 genes were having significant differential up and down regulation. The study identified 20 hub genes based on maximal clique centrality algorithm. These hub genes were mainly involved in various signaling pathways, energy metabolism and ion transportation. Further, 326 up and 1214 down regulated genes were found to be targeted by 7 differentially expressed miRNAs i.e., oni-miR-10712, oni-miR-10736, ssa-miR-221-3p, ssa-miR-130d-1-5p, ssa-miR-144-5p and oni-miR-10628. Gene ontology analysis of these differentially expressed genes led to the finding that these genes were involved in signal transduction i.e., calcium, FOXO, PI3K-AKT, TGF-β, Wnt and p53 signalling pathways. Differentially expressed genes were also involved in regulation of immune response, environmental adaptation i.e., neuroactive ligand-receptor interaction, ECM-receptor interaction, cell adhesion molecules and circadian entrainment, osmoregulation and energy metabolism, which are critical for salinity adaptation.Discussion: The findings of whole transcriptomic study on brain deciphered the miRNA-mRNA interaction patterns and pathways associated with salinity adaptation of L. rohita.

【 授权许可】

Unknown   
Copyright © 2023 Shukla, Vemula, Raval, Kumar, Shrivastava, Chaudhari, Patel and Joshi.