WRKY transcription factors are widely distributed in higher plants and play important roles in many biological processes, including stress resistance. The recently published genome sequence of yellowhorn, an oil tree with robust resistance to cold, drought, heat, salt and alkali, provides an excellent opportunity to identify and characterize the entire yellowhorn WRKY protein family and a basis for the study of abiotic stress resistance of WRKY gene family in forest species. In the present comprehensive analysis of WRKY transcription factors in yellowhorn, 65 WRKY genes were identified and defined based on their location on the chromosome. According to their structure and phylogenetic relationships, XsWRKY genes clustered into WRKY groups I–III. Segmental duplication events played a significant role in the expansion of WRKY gene family. Furthermore, transcriptomic data and real-time quantitative PCR analysis showed that expression of XsWRKY genes responding to salt and drought stresses and a hormone treatment. We also determined structures of the encoded proteins, cis-elements of the promoter region, and expression patterns. These results provide a foundation for the study of the biological function of WRKY transcription factors in yellowhorn.

In plants, alternative splicing (AS) is a crucial post-transcriptional regulatory mechanism that generates diverse mature transcripts from precursor mRNA, with the resulting functional proteins regulating a wide range of plant life activities. The regulation of AS is intricate and complex, playing pivotal roles in controlling plant biological processes like seed germination, flowering time control, growth, and development, as well as responses to abiotic and biotic stresses. The regulation of AS is a multilayered and intricately coordinated network system, primarily involving two core components: cis-regulatory elements and trans-acting factors on pre-mRNA. The precise execution of AS relies on the splicing factors by recognizing cis-elements to modulate splice site selection. Regulated by their own sequence variation, environmental cues, and identification of different spliceosomes, functional genes enable AS to achieve precise spatiotemporal regulation, thereby allowing plants to dynamically respond to developmental signals and environmental challenges. Here, we provide a comprehensive overview of AS patterns, functional genes, and splicing factors undergoing AS and its regulatory mechanisms during different processes, highlighting how AS-mediated gene regulation contributes to plant development and stress response, and offering potential strategies for improving plant adaptation by manipulation of AS-regulated genes.

The basic leucine zipper (bZIP) transcription factor family is one of the largest and most diverse families in plants, regulating plant growth and development and playing an essential role in response to abiotic and biotic stresses. However, little is known about the biological functions of bZIP proteins in yellowhorn (Xanthoceras sorbifolium). Recently, 64 XsbZIP genes were identified in the yellowhorn genome and found to be disproportionately distributed in linkage groups. The XsbZIP proteins clustered into 11 groups based on their phylogenetic relationships with AtbZIP, ZmbZIP and GmbZIP proteins. Five intron patterns in the basic and hinge regions and additional conserved motifs were defined, both supporting the group classification and possibly contributing to their functional diversity. Compared to tandem duplication, the segment duplication greatly contributed to the expansion of yellowhorn bZIP genes. In addition, most XsbZIP genes harbor several stress responsive cis-elements in their promoter regions. Moreover, the RNA-seq and qRT-PCR data indicated XsbZIP genes were extensively involved in response to various stresses, including salt (NaCl), cold and abscisic acid, with possibly different molecular mechanisms. These results provide a new understanding of the biological functions of bZIP transcription factors in yellowhorn.

Yellowhorn (Xanthoceras sorbifolium Bunge) is an oil-bearing tree species in northern China. In this study, we used yellowhorn from Heilongjiang to analyze the morphological and physiological changes of fruit development and conducted transcriptome sequencing. The results showed that the fruit experienced relatively slow growth from fertilization to DAF20 (20 days after flowering). From DAF40 to DAF60, the fruit entered an accelerated development stage, with a rapid increase in both transverse and longitudinal diameters, and the kernel contour developed completely at DAF40. From DAF60 to DAF80, the transverse and vertical diameters of the fruit developed slowly, and the overall measures remained stable until maturity. The soluble sugar, starch, and anthocyanin content gradually accumulated until reaching a peak at DAF80 and then rapidly decreased. RNA-seq analysis revealed differentially expressed genes (DEGs) in the seed coat and kernel, implying that seed components have different metabolite accumulation mechanisms. During the stages of seed kernel development, k-means clustering separated the DEGs into eight sub-classes, indicating gene expression shifts during the fruit ripening process. In subclass 8, the fatty acid biosynthesis pathway was enriched, suggesting that this class was responsible for lipid accumulation in the kernel. WGCNA revealed ten tissue-specific modules for the 12 samples among 20 modules. We identified 54 fatty acid biosynthesis pathway genes across the genome, of which 14 was quantified and confirmed by RT-qPCR. Most genes in the plastid synthesis stage showed high expression during the DAF40–DAF60 period, while genes in the endoplasmic reticulum synthesis stage showed diverse expression patterns. EVM0012847 (KCS) and EVM0002968 (HCD) showed similar high expression in the early stages and low expression in the late stages. EVM0022385 (HCD) exhibited decreased expression from DAF40 to DAF60 and then increased from DAF60 to DAF100. EVM0000575 (KCS) was increasingly expressed from DAF40 to DAF60 and then decreased from DAF60 to DAF100. Finally, we identified transcription factors (TFs) (HB-other, bHLH and ARF) that were predicted to bind to fatty acid biosynthesis pathway genes with significant correlations. These results are conducive to promoting the transcriptional regulation of lipid metabolism and the genetic improvement in terms of high lipid content of yellowhorn.

Beet (Beta vulgaris L.) is an important economic crop widely cultivated across various regions worldwide. Its agricultural significance lies not only in its high sugar yield but also in its positive impact on agro-ecosystems and the economic value of its by-products. However, beet production and quality are adversely affected by multiple abiotic and biotic stresses, including pathogen infection, drought, salinity, and extreme temperatures. In recent years, numerous key stress-responsive genes have been identified, including BvPAL, BvPR, and Rz1-4, which mediate responses to biotic stresses, and BvM14-SAMS2, BvINT1;1, BvHMA3, BvCOLD1, and BvALKBH10B, which enhance tolerance to abiotic stresses. Meanwhile, core transcription factors such as bHLH, HSP, WRKY, and SPL show differential expression under stresses, suggesting that they may regulate stress-related genes and constitute major transcriptional modules enabling beet to withstand adverse conditions. In this study, we summarize the changes in beet under different stress conditions, combining gene information to reveal key regulatory changes in stress responses and how these molecular processes contribute to stress adaptation. This not only provides a theoretical basis for the improvement of beet stress tolerance and yield, but also offers potential directions for future breeding strategies in practical applications.

Salt stress severely limits plant growth, particularly in woody species. In this study, a time-course transcriptomic analysis (0–24 h NaCl treatment) revealed a clear time-dependent transcriptional reprogramming pattern in Betula platyphylla, characterized by rapid early activation followed by gradual stabilization. The response can be divided into three phases: early stress perception and signaling (1–3 h), mid-stage metabolic and hormonal reprogramming (5–9 h), and late-stage homeostasis and physiological adaptation (12–24 h). Early responses are dominated by signal transduction, the middle phase by metabolic reorganization and enhanced translation, and the late phase by redox and cellular homeostasis. Compared to the limited role of the Dehydration-Responsive Element-Binding protein (DREB) pathway, Abscisic acid (ABA) and Jasmonic acid (JA) signaling appear to play more central regulatory roles. Further analyses revealed the coordinated temporal activation of Reactive oxygen species (ROS), Salt Overly Sensitive (SOS), and ABA pathways: ROS shows an early burst followed by antioxidant activation; the SOS pathway regulates ion homeostasis via the Calcineurin B-like protein (CBL)-CBL-interacting protein kinase (CIPK) module; and ABA signaling progresses from biosynthesis to downstream transcriptional regulation. Protein interaction network analysis further identifies ABA signaling as a central hub integrating Ca²⁺ signaling, ROS metabolism, and ion transport. Overall, B. platyphylla responds to salt stress through a temporally coordinated regulatory network, providing new molecular insights into salt tolerance mechanisms in woody plants.