Biology subjects

Ru, D.

Publications and source records attributed to Ru, D..

3 recordsLinked to original sources

bioRxiv2026

Genome-wide investigation of WRKY gene family in Lagenaria siceraria

BackgroundA significant family of transcription factors known as WRKY genes include many physiological functions and environmental adaptations. However, insufficient information was previously available about the WRKY genes in Lagenaria siceraria, a crucial crop with substantial economic significance. The recent publication of the whole-genome sequence of L. siceraria has allowed us to perform a genome-wide investigation of the organization of the WRKY genes in L. siceraria. ResultsIn the present study, 57 L. siceraria WRKY (LsiWRKY) genes were identified and given new names based on their relative chromosomal distribution. The 57 LsiWRKYs were further divided into three major groups and several subgroups based on their structural and phylogenetic properties. Segmentation duplication events have played a major role in the expansion of the WRKY gene family in L. siceraria. Phylogenetic comparisons of the Group III WRKY genes provide valuable insights into the evolutionary characteristics of WRKY genes in L. siceraria. Additionally, RNA-seq analysis revealed distinct expression pattern of WRKY genes across different tissues. ConclusionsThis study presents a preliminary analysis of the WRKY gene family in L. siceraria, including their structural characteristics, evolutionary traits, and tissue-specific expression patterns. The systematic insights provided here serve as a foundation for further functional studies aimed at enhancing L. siceraria crops. This knowledge holds promise for improving the cultivation and yield of L. siceraria, thereby contributing to agricultural advancements.

genomics↗

bioRxiv2025

Transcriptomics uncovers molecular mechanisms underlying salt-inhibited root growth in Festuca rubra

Salt stress markedly inhibits root growth in Festuca rubra, while shoot development remains largely unaffected. Transcriptomic analysis identified 68,062 differentially expressed genes (DEGs) under salt stress. Upregulated genes were found significantly enriched in pathways related to methionine, melatonin, and suberin biosynthesis-processes likely contributing to stress adaptation through root growth suppression and maintenance of ion homeostasis. In contrast, genes associated with gibberellin biosynthesis, abscisic acid (ABA) response, and sugar signaling were downregulated, indicating complex hormonal and metabolic reprogramming. Notably, paradoxical regulation of gibberellin and ethylene signaling pathways suggests the presence of finely tuned mechanisms that balance growth and stress responses. These findings shed light on the molecular basis of root-specific salt stress responses in F. rubra and enhance our understanding of its adaptive strategies under saline conditions.

plant biology↗

bioRxiv2020

Human Identical Sequences of SARS-CoV-2 Promote Clinical Progression of COVID-19 by Upregulating Hyaluronan via NamiRNA-Enhancer Network

The COVID-19 pandemic is a widespread and deadly public health crisis. The pathogen SARS-CoV-2 replicates in the lower respiratory tract and causes fatal pneumonia. Although tremendous efforts have been put into investigating the pathogeny of SARS-CoV-2, the underlying mechanism of how SARS-CoV-2 interacts with its host is largely unexplored. Here, by comparing the genomic sequences of SARS-CoV-2 and human, we identified five fully conserved elements in SARS-CoV-2 genome, which were termed as "human identical sequences (HIS)". HIS are also recognized in both SARS-CoV and MERS-CoV genome. Meanwhile, HIS-SARS-CoV-2 are highly conserved in the primate. Mechanically, HIS-SARS-CoV-2, behaving as virus-derived miRNAs, directly target to the human genomic loci and further interact with host enhancers to activate the expression of adjacent and distant genes, including cytokines gene and angiotensin converting enzyme II (ACE2), a well-known cell entry receptor of SARS-CoV-2, and hyaluronan synthase 2 (HAS2), which further increases hyaluronan formation. Noteworthily, hyaluronan level in plasma of COVID-19 patients is tightly correlated with severity and high risk for acute respiratory distress syndrome (ARDS) and may act as a predictor for the progression of COVID-19. HIS antagomirs, which downregulate hyaluronan level effectively, and 4-Methylumbelliferone (MU), an inhibitor of hyaluronan synthesis, are potential drugs to relieve the ARDS related ground-glass pattern in lung for COVID-19 treatment. Our results revealed that unprecedented HIS elements of SARS-CoV-2 contribute to the cytokine storm and ARDS in COVID-19 patients. Thus, blocking HIS-involved activating processes or hyaluronan synthesis directly by 4-MU may be effective strategies to alleviate COVID-19 progression.

molecular biology↗