Identification of common transcriptional responses to salinity of two halophytes: Bruguiera gymnorrhiza and Populus euphratica

Salinity stress is a major environmental factor that limits plant growth and development. This study identified common differentially expressed genes (DEGs) of two halophyte species, Populus euphratica and Bruguiera gymnorrhiza, using a meta-analysis of retrieved microarray datasets. A total of 27 commonly up-regulated DEGs were identified, including NAC1, GBSS1, NIR1, APR1, and ChlAKR, with the most positive fold changes. Additionally, 37 commonly down-regulated DEGs, such as GASA1, GLT1, MSS1, and APS1 showed the most negative fold changes. Gene Ontology analysis indicated that these DEGs are mainly involved in responses to stimuli, chemicals, or metals. Several transcription factors responsive to salinity stress were identified, including up-regulated families such as NAC, bZIP, ERF, MYB, and LBD, while NAC was the only down-regulated family. Gene network analysis highlighted five hub genes: NIR1, APR1, APR3, HY5, and MS2, of which only MS2 was down-regulated. Among microRNA families, miR5658 (up-regulated) and miR169 (down-regulated) were the most frequent. Promoter analysis revealed cis-acting elements binding to 11 conserved motifs, including AP2/EREBP and C2H2 classes, potentially regulating key responses to abiotic stress in halophytes. These findings may provide insights that could inform strategies for genetic engineering of crops. The relative expression of the NIR1 gene in P. euphratica leaves was significantly induced by NaCl, with higher expression under 500 mM peaking at 48 h (10-fold). Expression decreased at 72 h but remained above control levels, showing a time- and concentration-dependent response.