NIN-like protein (NLP) transcription factors are key regulators of plant nitrate signaling and stress responses. Although extensively studied in Arabidopsis thaliana and various crops, it has rarely been reported in woody plants, particularly in drought-tolerant tree species. In this study, 10 PeNLP genes were identified in the drought-tolerant tree Populus euphratica Oliv. through comparative genomics. These genes were unevenly distributed across seven chromosomes, and the gene-family expansion was mainly driven by whole-genome duplication (WGD). Analysis of conserved domains showed that PeNLPs contained 4–10 characteristic motifs, and most members possessed the typical RWP-RK and PB1-related domains. Collinearity analysis identified 18 NLP orthologous gene pairs between P. euphratica and its relatives (Populus pruinosa and Salix sinopurpurea), which exceeded the 15 pairs detected between P. euphratica and A. thaliana, indicating that the NLP family is more conserved within the Salicaceae. Phylogenetic analysis divided PeNLPs into three subfamilies, and their promoter regions harbored diverse cis-acting elements associated with hormone signaling, environmental stress, growth, and light response. Transcriptome and qRT-PCR analyses further demonstrated that PeNLPs were generally downregulated under drought stress. Overall, this study systematically characterized the evolution, structure, and drought responsiveness of the PeNLPs, providing a theoretical basis and genetic resources for improving nitrogen use efficiency and drought resistance in trees.

The WUSCHEL-related homeobox (WOX) gene family plays crucial roles in plant growth, development, and stress responses. In this study, a comprehensive genome-wide analysis of WOX genes was conducted in three Populus species, P. euphratica, P. pruinosa, and P. deltoides. A total of 16, 16, and 21 WOX genes were identified, respectively, and classified into three clades (ancient, intermediate, and WUS/modern) based on phylogenetic relationships. Structural analyses revealed highly conserved homeodomain motifs and similar exon–intron organizations, indicating strong evolutionary conservation. Furthermore, synteny analyses demonstrated that whole-genome duplication or segmental duplication events were the primary drivers of WOX gene family expansion, with most duplicated gene pairs undergoing purifying selection. Promoter analysis identified abundant cis-acting elements related to light responsiveness, hormone signaling, and stress responses. Notably, transcriptomic profiling during seed germination under drought and salt stress revealed distinct interspecific expression patterns and temporal dynamics between the two desert poplars. Specifically, members such as PeWox11 and PpWox2 were significantly induced, suggesting their potential involvement in abiotic stress adaptation. These findings provide comprehensive insights into the evolutionary conservation and divergence of WOX genes in Populus, establishing a theoretical foundation for the molecular breeding of stress-tolerant woody plants.