Systematic Identification of the GH28 Gene Family in the Pathogenic Fungus Cytospora pyri and Functional Verification of the Candidate Virulence Gene VP1G_08835

Genome-Wide Characterization of the Botryosphaeria dothidea GH28 Family Reveals BdGH28_3 Contributes to Virulence on Chinese Hickory

Chinese hickory (Carya cathayensis Sarg.) is an economically important tree species widely cultivated in southeastern China, where trunk canker disease caused by Botryosphaeria dothidea poses a serious threat to tree health and production. Pectin-degrading enzymes are important virulence-associated factors that facilitate fungal colonization and host tissue maceration, but their evolutionary diversification and functional roles in B. dothidea during woody host infection remain poorly understood. Comparative genomic analysis revealed lineage-specific variation in the GH28 glycoside hydrolase family among the examined Botryosphaeriaceae species, with B. dothidea exhibiting an expanded GH28 repertoire relative to the analyzed species. Expression analysis and functional assays revealed that BdGH28_3 showed the highest transcript abundance during infection stage and contributed to the full virulence of B. dothidea. A predicted protein–protein interaction (PPI) network suggested potential associations between BdGH28_3 and other pectinolytic enzymes, including polygalacturonases, pectin lyases, and pectinesterases. Collectively, these findings identify GH28 diversification as a distinctive feature of the B. dothidea genome and establish BdGH28_3 as a virulence-associated member, providing a foundation for investigating GH28-mediated pathogenicity in woody hosts.

Insights into the dirigent gene family in banana: genome-wide identification and role in biotic and abiotic stress tolerance

COMPARATIVE GENOMIC ANALYSIS OF CORE AND ACCESSORY GENES IN RUST FUNGI REVEALS PATHOGENICITY-ASSOCIATED GENE FAMILIES IN Phakopsora pachyrhizi

This study highlights that core and accessory gene families have shaped P. pachyrhizi-soybean interactions, identifying promising targets for functional studies aimed at elucidating host-adaptation mechanisms in rust fungi.

Genome-Wide Identification and Bioinformatics Analysis of Thaumatin-like Proteins in Aegiceras corniculatum

Background: The mangrove ecosystem serves as a vital coastal ecotone, providing essential ecological services, such as water purification, shoreline protection, and biodiversity maintenance. Fungal pathogens threaten mangrove health and contribute to ecosystem degradation, but the molecular mechanisms underlying disease resistance in mangroves remain poorly explored. Introdustion: Thaumatin-like proteins (TLPs), belonging to the pathogenesis-related-5 (PR-5) family, play a crucial role in antifungal defense in plants. Method and results: In this study, we identified 23 TLP family members in the mangrove Aegiceras corniculatum. The genes encoding TLP family members were unevenly distributed on chromosomes. Collinearity analyses showed that TLP family members in A. corniculatum underwent multiple gene duplication events, and Ka/Ks calculations revealed that these duplicated genes were predominantly under purifying selection. Among the 23 TLPs, AcTLP19 was significantly upregulated after Botrytis cinerea infection. Subcellular localization prediction and experiments revealed the extracellular localization of AcTLP19. Conclusions: Heterologous expression and antibacterial tests showed that recombinant AcTLP19 had no direct antifungal activity against B. cinerea or Fusarium oxysporum under the tested conditions, leaving open the possibility that it contributes to mangrove defense through indirect mechanisms, or that its antifungal activity was not captured under the specific assay conditions. This study advances our knowledge of mangrove stress responses and may contribute to future conservation strategies.

Genome-Wide Characterization and Expression Profiling of the Chitinase Gene Family in Radish (Raphanus sativus L.) Under Clubroot Stress

Clubroot, caused by the obligate biotrophic protist Plasmodiophora brassicae (P. brassicae), is a destructive soil-borne disease that severely threatens the production of radish (Raphanus sativus L.). Although chitinases are known to execute critical defense functions by degrading pathogen chitin, a comprehensive genome-wide characterization of the radish chitinase (RsChi) gene family and its specific role in clubroot resistance remains lacking. Here, we systematically identified 24 RsChi genes in the radish genome, characterizing their chromosomal distribution, structural organization, and promoter regulatory networks. These genes are unevenly distributed across seven chromosomes and cluster into four subfamilies, with tandem duplication driving family expansion, particularly on Chromosome 3. Promoter analysis revealed a significant enrichment of jasmonic acid- and abscisic acid-responsive cis-elements, implicating RsChi genes in hormone-mediated defense signaling. Using qRT-PCR to profile expression dynamics during P. brassicae infection across contrasting radish lines, we identified strong genotype- and stage-specific transcriptional responses. Notably, TRs0x1c000780 remained transcriptionally silent prior to infection but was specifically induced over 10-fold in the resistant line at 28 days post-inoculation. This infection-triggered induction positions TRs0x1c000780 as a promising candidate defense gene. Together, these findings provide structural and functional insights into the RsChi family and highlight candidate targets for breeding clubroot-resistant radish cultivars.

Comparative genome-wide analysis of CAD (Cinnamyl Alcohol Dehydrogenase) gene family in Medicago truncatula and Lotus japonicus and their expression profiles in response to various abiotic abiotic stresses

The CAD (Cinnamyl Alcohol Dehydrogenase) gene family is a key determinant for lignin biosynthesis in plants. In legumes, CAD enzymes are involved in the development of vascular tissues such as xylem and Casparian strip and they contribute to the production of antimicrobial and antifungal compounds. Thereby, it offers defense against pathogens and pests. Despite their biological significance, a comparative genome-wide analysis of the CAD gene family in Medicago truncatula and Lotus japonicus has not been explored. Therefore, we conducted a comparative genome-wide study to investigate the characteristics and potential role of CAD genes in these two model legume species. A total of 51 CAD genes were identified in M. truncatula (MtCAD) and 35 in L. japonicus (LjCAD). The CAD proteins are prominently characterized by ADH_N and ADH_zinc_N domains that were distributed in 8 and 6 chromosomes of MtCAD and LjCAD, respectively. Structural organization and conserved motif analysis indicated notable similarities between MtCAD and LjCAD proteins. However, considering the ancestry and functionality and based on the evolutionary analysis, LjCAD showed more similarities with Arabidopsis than MjCAD. Gene duplication analysis identified twelve duplicated gene pairs in MtCAD and eight in LjCAD, including both tandem and segmental duplication events. Most MtCAD and LjCAD were found in the cytoplasm with some of the cis-acting regulatory elements associated with stress responses. Gene Ontology annotation suggested that most MtCAD genes were associated with biological processes whereas LjCAD genes are mainly enriched in molecular functions. Both MtCAD and LjCAD showed potential roles in secondary metabolite production. Three substantial transcription factor families such as bZIP, C2H2, and ERF and several unique microRNAs were predicted to target MtCAD and LjCAD in regulating their gene expression against certain abiotic stressors for instance cold, freezing, drought, and heat. The MtCAD and LjCAD expressed highly in stress-responsive tissues such as nodule, root, immature flower, seed, and leaf. Meanwhile, RNA-sequencing data further highlighted several potential stress-responsive genes. In M. truncatula, The MtCAD1, MtCAD3, MtCAD9, MtCAD15, MtCAD23, MtCAD27, and MtCAD47 exhibited higher expression under cold, drought, and freezing stress compared with control conditions. Whereas in L. japonicus, LjCAD6, LjCAD8, and LjCAD11 showed higher expression under cold, drought, and heat stress. Thus, these genes may serve as promising candidates for improving abiotic stress tolerance and provide molecular insights into their functional roles for future crop improvement programs and experimental validation.