Alfalfa (Medicago sativa L.) is an important forage legume and soil salinization seriously affects its growth and yield. In a previous study, we identified a salt-tolerant variety ‘Gongnong NO.1’ and a salt-sensitive variety ‘Sibeide’. To unravel the molecular mechanism involved in salt stress, we conducted transcriptomic analysis on these two cultivars grown under 0 and 250 mM NaCl treatments for 0, 12, and 24 h. Totals of 336, and 548 differentially expressed genes (DEGs) in response to NaCl were, respectively, identified in the ‘Gongnong NO.1’ and ‘Sibeide’ varieties. The Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway enrichment analysis showed that the DEGs were classified in carbohydrate metabolism, energy production, transcription factor, and stress-associated pathway. Expression of MsHPCA1, encoding a putative H₂O₂ receptor, was responsive to both NaCl and H₂O₂ treatment. MsHPCA1 was localized in cell membrane and overexpression of MsHPCA1 in alfalfa increased salt tolerance and H₂O₂ content. This study will provide new gene resources for the improvement in salt tolerance in alfalfa and legume crops, which has important theoretical significance and potential application value.

Background: Transposable elements (TEs) and noncoding sequences are major components of the genome, yet their functional contributions to long noncoding RNAs (lncRNAs) are not well understood. Although many lncRNAs originating from TEs (TE-lncRNAs) have been identified across various organisms, their characteristics and regulatory roles, particularly in insects, remain largely unexplored. This study integrated multi-omics data to investigate TE-lncRNAs in D. melanogaster, focusing on the influence of transposons across different omics levels. Results: We identified 16,118 transposons overlapping with lncRNA sequences that constitute 2119 TE-lncRNAs (40.4% of all lncRNAs) using 256 public RNA-seq samples and 15 lncRNA-seq samples of Drosophila S2 cells treated with heavy metals. Of these, 67.2% of TE-lncRNAs contain more than one TE. The LTR/Gypsy family was the most common transposon insertion. Transposons preferred to insert into promoters, transcription starting sites, and intronic regions, especially in chromosome ends. Compared with lncRNAs, TE-lncRNAs showed longer lengths, a lower conservation, and lower levels but a higher specificity of expression. Multi-omics data analysis revealed positive correlations between transposon insertions and chromatin openness at the pre-transcriptional level. Notably, a total of 516 TE-lncRNAs provided transcriptional factor binding sites through transposon insertions. The regulatory network of a key transcription factor was rewired by transposons, potentially recruiting other transcription factors to exert regulatory functions under heavy metal stress. Additionally, 99 TE-lncRNAs were associated with m⁶A methylation modification sites, and 115 TE-lncRNAs potentially provided candidate small open reading frames through transposon insertions. Conclusions: Our data analysis demonstrated that TEs contribute to the regulation of lncRNAs. TEs not only promote the transcriptional regulation of lncRNAs, but also facilitate their post-transcriptional and epigenetic regulation.

Sunflower (Helianthus annuus) is highly susceptible to infection by the root parasitic plant Orobanche cumana during its growth. In establishing connections with the sunflower root system, O. cumana induces the hydrolysis and remodeling of the host cell wall. Xyloglucan endotransglucosylase/hydrolase (XTH), a member of glycoside hydrolase family 16 (GH16), is a key enzyme involved in the hydrolysis and synthesis of xyloglucan, playing a critical role in cell wall modification and reconstruction. However, the involvement of XTH families in the interaction between sunflower and O. cumana remains unclear. In this study, we showed that the expression level of HaXTH2 was upregulated in sunflowers following O. cumana infection. Overexpression of HaXTH2 loosens host primary cell walls and represses lignin-based defense responses at the early infection stage, thereby facilitating haustorial penetration across cortical tissues and xylem bridge formation to support normal parasitism of O. cumana. Functional analysis revealed that HaXTH2 and its homolog, HaXTH2-1, facilitate O. cumana infection, whereas OcXTH2, an O. cumana homolog, suppresses this process. Furthermore, HaXTH2, HaXTH2-1, and OcXTH2 are localized to the cell wall. Domain truncation analysis revealed that the GH16 domain alone from HaXTH2 and HaXTH2-1 enhance parasitic susceptibility, while the xyloglucan endotransglycosylase C-terminal domain (XET_C) domain does not. Mutation analysis identified Y20 in HaXTH2 and H96 in HaXTH2-1 as key amino acid sites regulating O. cumana parasitism. This study expands our understanding of the functions of XTHs in plant–plant interactions and provides a theoretical basis for further development of O. cumana-resistant sunflower cultivars.

The adaxial–abaxial axes play a crucial role in normal leaf growth. While recent studies have explored the molecular mechanisms underlying these developmental processes, the functions of BELL homologous genes remain insufficiently understood. In this study, we demonstrate that silencing the SlBL4 gene in tomatoes ( Solanum lycopersicum cv. Micro-Tom) affects leaf polarity development. RNA sequencing (RNA-seq) analysis indicates that SlBL4 regulates numerous differentially expressed genes (DEGs) associated with leaf polarity, auxin transporters, LOB domain-containing proteins, chlorophyll accumulation, and chloroplast development. Furthermore, SlBL4 positively regulated the expression of SlGH3.1 , SlGH3.2 , and SlLOB4 genes associated with leaf growth polarity. These findings elucidate the roles of SlBL4 and propose a novel function for BELL genes in regulating plant leaf polarity.