Functional and evolutionary comparative analysis of the DIR gene family in Nicotiana tabacum L. and Solanum tuberosum L.

BACKGROUND: The dirigent (DIR) genes encode proteins that act as crucial regulators of plant lignin biosynthesis. In Solanaceae species, members of the DIR gene family are intricately related to plant growth and development, playing a key role in responding to various biotic and abiotic stresses. It will be of great application significance to analyze the DIR gene family and expression profile under various pathogen stresses in Solanaceae species. RESULTS: A total of 57 tobacco NtDIRs and 33 potato StDIRs were identified based on their respective genome sequences. Phylogenetic analysis of DIR genes in tobacco, potato, eggplant and Arabidopsis thaliana revealed three distinct subgroups (DIR-a, DIR-b/d and DIR-e). Gene structure and conserved motif analysis showed that a high degree of conservation in both exon/intron organization and protein motifs among tobacco and potato DIR genes, especially within members of the same subfamily. Total 8 pairs of tandem duplication genes (3 pairs in tobacco, 5 pairs in potato) and 13 pairs of segmental duplication genes (6 pairs in tobacco, 7 pairs in potato) were identified based on the analysis of gene duplication events. Cis-regulatory elements of the DIR promoters participated in hormone response, stress responses, circadian control, endosperm expression, and meristem expression. Transcriptomic data analysis under biotic stress revealed diverse response patterns among DIR gene family members to pathogens, indicating their functional divergence. After 96 h post-inoculation with Ralstonia solanacearum L. (Ras), tobacco seedlings exhibited typical symptoms of tobacco bacterial wilt. The qRT-PCR analysis of 11 selected NtDIR genes displayed differential expression pattern in response to the bacterial pathogen Ras infection. Using line 392278 of potato as material, typical symptoms of potato late blight manifested on the seedling leaves under Phytophthora infestans infection. The qRT-PCR analysis of 5 selected StDIR genes showed up-regulation in response to pathogen infection. Notably, three clustered genes (NtDIR2, NtDIR4, StDIR3) exhibited a robust response to pathogen infection, highlighting their essential roles in disease resistance. CONCLUSION: The genome-wide identification, evolutionary analysis, and expression profiling of DIR genes in response to various pathogen infection in tobacco and potato have provided valuable insights into the roles of these genes under various stress conditions. Our results could provide a basis for further functional analysis of the DIR gene family under pathogen infection conditions.

Bioinformatics study on different gene expression profiles of fibroblasts and vascular endothelial cells in keloids.

ABSTRACT: Keloid is a benign fibroproliferative skin tumor. The respective functions of fibroblasts and vascular endothelial cells in keloid have not been fully studied. The purpose of this study is to identify the respective roles and key genes of fibroblasts and vascular endothelial cells in keloids, which can be used as new targets for diagnosis or treatment.The microarray datasets of keloid fibroblasts and vascular endothelial cells were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were screened out. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used for functional enrichment analysis. The search tool for retrieval of interacting genes and Cytoscape were used to construct protein-protein interaction (PPI) networks and analyze gene modules. The hub genes were screened out, and the relevant interaction networks and biological process analysis were carried out.In fibroblasts, the DEGs were significantly enriched in collagen fibril organization, extracellular matrix organization and ECM-receptor interaction. The PPI network was constructed, and the most significant module was selected, which is mainly enriched in ECM-receptor interaction. In vascular endothelial cells, the DEGs were significantly enriched in cytokine activity, growth factor activity and transforming growth factor-ß (TGF-ß) signaling pathway. Module analysis was mainly enriched in TGF-ß signaling pathway. Hub genes were screened out separately.In summary, the DEGs and hub genes discovered in this study may help us understand the molecular mechanisms of keloid, and provide potential targets for diagnosis and treatment.