The Pacific white shrimp, Penaeus vannamei, is a euryhaline species that can tolerate extremely low salinity levels. Whereas, molecular mechanisms underlying low salinity tolerance, including upstream functional regulators, remain elusive in penaeid shrimp. In this study, P. vannamei was exposed to low salinity stress through degrading salinity from 30‰ to 3‰ gradually, and potential osmoregulatory mechanisms were investigated by ATAC-seq and RNA-seq analyses.
As expected, the chromatin accessibility was positively correlated with the gene expression levels. Whereas only a part of differentially expressed genes (DEGs, 36.8%) was associated with the differential chromatin accessibility; and the expression of these genes may be regulated by cis-regulatory elements, e.g. transcription factors (TFs). These genes were enriched in betaine synthesis pathway and PI3K-Akt signaling pathway and so on.
Based on the sequences of differential accessible regions, nine TFs and their potential binding sites (TFBS) were identified throughout the genome. Among the nine TFs, seven of them were newly identified to be associated with salinity adaptation. Characteristics of these nine TFs, including potential functions, expression profiles, consensus TFBS motifs, and the functional enrichment and expression profiles of their potentially targeted genes, were thoroughly investigated. Among these TFs, ZBTB has the largest number of specific target genes and functional enrichment of target genes showed pathways that closely associated with salinity adaptation, including amino acid metabolism and lipids metabolism pathways.
Knocking down the expression of ZBTB resulted in the significantly increasing mortality rate under both acute and chronic low-salinity stresses. DAP-seq sequencing and analysis of ZBTB confirmed the locations of TFBSs and targeted genes, which provided a comprehensive perspective for understanding the regulatory network of this TF.
These findings provide insights into the regulatory mechanism of salinity tolerance to improve genetic breeding and desalination aquaculture of penaeid shrimp.