Search Results (121)

Marine microbiomes play an important role in coastal marine environments. This study examined microbial communities in beach waters and sands at six recreational beaches to identify the fingerprints of anthropogenic influences. Samples were collected from four metropolitan areas in the U.S., within Miami, Florida; Seattle, Washington; Newport Beach, California and in Australia within Adelaide. Samples were analyzed for enterococci and fungi by culture. Reverse-transcription droplet digital PCR (RT-ddPCR) was performed for pepper mild mottle virus (PMMoV). Next-generation sequencing was carried out to elucidate the microbial diversity and predict antibiotic resistance. Enterococci concentrations surpassed the U.S. EPA marine water quality guideline value in the seawater samples from Seattle and Adelaide, and fungal concentration exceeded the WHO guideline in the sand of North Star Beach, California. Low levels of PMMoV were detected in seawater and sand from multiple locations. Chloroflexi and Acidobacteria were the most abundant bacterial phyla in sand, while Marinimicrobia and Cyanobacteria dominated in seawater. Beach sand had higher bacterial and fungal diversity than seawater, of which the most abundant fungal genera include taxa of potential pathogens. Predicted antibiotic resistance genes showed high levels of beta-lactam and multidrug resistance genes in all samples. This study contributes to the understanding of anthropogenic impact on the coastal environment, emphasizing the need for human health protection measures. Full article

Phytophthora blight, caused by the oomycete pathogen Phytophthora capsici, is a devastating disease that severely constrains pepper (Capsicum annuum) production, leading to significant yield reduction and quality deterioration. Pathogen infection elicits a host immune response that involves extensive transcriptional reprogramming, during which transcription factors (TFs) act as key regulatory hubs linking upstream signaling cascades to downstream defense gene expression networks. NAC TFs represent a plant-specific gene family and play crucial roles in plant growth, development, and response to various stresses. However, the infection-responsive transcriptional dynamics and functions of NAC TFs during pepper–P. capsici interactions remain poorly elucidated. In this study, transcriptome profiling and RT-qPCR analysis of pepper plants challenged with P. capsici identified three NAC TF genes—CaNAC61, CaNAC79, and CaNAC92—that were consistently upregulated at the infection stages. Subcellular localization assays demonstrated that all these three proteins localize to the nucleus. Silencing of CaNAC61, CaNAC79, or CaNAC92 in pepper conferred enhanced resistance to P. capsici. In contrast, their transient overexpression in pepper leaves significantly promoted lesion expansion and suppressed transcript levels of the defense marker genes CaPR1, CaDEF1, and CaLOX1. Consistently, heterologous overexpression in transgenic Nicotiana benthamiana further validated CaNAC61, CaNAC79, and CaNAC92 as negative regulators in resistance to P. capsici. Collectively, our findings demonstrated that CaNAC61, CaNAC79, and CaNAC92 negatively regulate plant resistance to P. capsici, expanding the functional diversity of NAC TFs in plant immune responses and providing valuable candidate targets for genetic improvement against Phytophthora blight. Full article

Verticillium wilt caused by Verticillium dahliae poses a severe threat to pepper (Capsicum annuum) production worldwide. Kunitz trypsin inhibitors (KTIs) play crucial roles in plant disease resistance, yet research on the CaKTI gene family in pepper, especially regarding its regulatory functions in resistance to V. dahliae, remains limited. In this study, members of the CaKTI gene family were systematically identified in the pepper genome, followed by comprehensive analyses of their physicochemical properties, phylogeny, chromosomal localization, conserved motifs, cis-acting elements in promoters, and expression profiles. A total of 22 CaKTI genes were identified, all harboring the beta-trefoil_STI superfamily domain. They were unevenly distributed across four chromosomes, with evident tandem duplication events, and exhibited tissue-specific and developmental stage-specific expression patterns. In the Verticillium-resistant pepper cultivar, five candidate CaKTI genes (CaKTI9, CaKTI6, CaKTI17, CaKTI18, and CaKTI22) were significantly induced and upregulated, particularly in roots, and their expression might be modulated by the methyl jasmonate signaling pathway. This study reveals the molecular features, evolutionary conservation, and defense-associated expression patterns of CaKTI genes in pepper and provides a preliminary exploratory basis for future research on disease resistance and molecular breeding. Full article

RNA-binding proteins (RBPs), specifically those containing K Homology (KH) domains, are critical for post-transcriptional regulation and abiotic stress responsiveness in plants. However, systematic characterization of the KHD gene family in potato (Solanum tuberosum L.) remains unreported. Here, we identified 83 StKHD genes unevenly distributed across 12 potato chromosomes, which clustered into five subgroups with conserved gene structures and motif compositions. Most StKHD proteins were predicted to localize to the nucleus, confirmed experimentally for StKHD-41 via transient expression in Nicotiana benthamiana. Collinearity analysis revealed 23, 22, 19, and 4 orthologous pairs with Arabidopsis, tomato, pepper, and tobacco, respectively. Promoter analysis showed distribution of hormone- and stress-responsive cis-elements, while interaction network analysis predicted 39 StKHDs interacting with 137 proteins. Tissue-specific profiling revealed broad expression of several StKHDs, and specific members displayed consistent expression changes under abiotic stresses, correlating with TC-rich repeat enrichment. RT-qPCR validated that StKHD-41 responded rapidly to JA, moderately to SA/GA, and slowly to ABA, with significant upregulation under drought and salt stress by day 2. This study provides a foundation for understanding StKHD functions and identifies targets for enhancing potato stress resistance. Full article

The genus Capsicum comprises several species that are vital vegetable and spice crops cultivated worldwide, possessing significant economic, nutritional, and ornamental value due to their diverse fruit morphologies, colors, spiciness levels, and stress resistance. Historically, the large genome size (approximately 3 Gb) and high proportion of repetitive sequences (over 80% transposable elements) have constrained in-depth analysis of structural variations and functional genes within Capsicum species. However, recent advances in long-read sequencing, Hi-C scaffolding, and genome assembly have enabled the production of multiple high-quality and telomere-to-telomere (T2T) Capsicum genomes, which have ushered in a new era of research at the nuclear, organellar, and pan-genome levels. The publication of these omics resources has greatly expanded our understanding of the evolution of agronomically and environmentally relevant traits in peppers and their wild relatives. This review systematically summarizes recent progress in reference genomes, pan-genomes, and organellar genomes of the genus Capsicum, highlighting the enhancement of key breeding trait analyses through omics data, and outlines future integrated breeding strategies to provide theoretical and methodological references for genetic improvement and molecular breeding in pepper. Full article

Insect infestation poses a significant threat to global agriculture by impairing plant growth and reducing crop yields. The western flower thrip (WFT) causes substantial damage through both direct feeding and transmission of plant viruses. Although the jasmonic acid (JA) signaling pathway is known to participate in plant defense against WFTs, the underlying molecular mechanisms in non-model crops such as peppers, remain largely elusive. This study investigates the role of suppressor of prosystemin-mediated responses2 (Spr2) within JA-mediated defense against WFTs in pepper. Through an integrated approach employing virus-induced gene silencing (VIGS), transcription analysis, phytohormone quantification, insect behavior assays and life history investigations, we demonstrated that silencing CaSpr2 significantly reduced JA and JA-Ile accumulation, and led to a strong feeding preference of WFTs for CaSpr2-silenced plants. Furthermore, the adult lifespan, survival rate, female fecundity, oviposition rate, and population parameters of WFTs were significantly improved on CaSpr2-silenced plants. Spr2 functions as an essential component within the JA signaling pathway, thereby playing a critical role in conferring resistance to WFTs in cultivated pepper. These findings provide profound insights and practical implications for breeding thrips-resistant cultivars in non-model plants, through genetic manipulation of JA signaling, offering a promising avenue for sustainable agricultural pest management. Full article

Research on the CBP gene family in plants is scarce, with only sporadic reports on its association with immune responses. No systematic study has explored how CBP family genes regulate pepper resistance against Phytophthora capsici. Here, we focused on pepper CaCBP2, an RNA-binding protein, whose expression was significantly induced by P. capsici. Functional validation via VIGS and heterologous overexpression confirmed CaCBP2 as a negative regulator of pepper resistance to P. capsici. Based on physiological assays, transcriptome sequencing and WGCNA, we speculate it may mediate immune responses by regulating antioxidant systems, defense hormone metabolism, and disease resistance-related genes. Our findings fill the relevant research gap, enrich the role of RNA-binding proteins in plant anti-phytophthora defense, and provide a novel target for crop disease-resistant breeding. Full article

Aspergillus fumigatus, a saprophytic fungus, causes aspergillosis, primarily affecting the immunocompromised. The efficacy of triazole antifungals is compromised by resistance that has developed both clinically and environmentally. Widespread agricultural use of similar triazole fungicides selects for resistant genotypes, leading to potential food contamination and compromising treatment. This study assessed the presence of azole-resistant A. fumigatus in minimally processed food items commonly consumed in Brazil. A total of 25 commercial samples, including black pepper, yerba mate, and green coffee beans, were collected from different regions. Forty-two A. fumigatus isolates were recovered and screened for susceptibility to agricultural and clinical triazoles by determining EC₅₀ values for tebuconazole (0.04–0.7 µg/mL), itraconazole (0.06–0.5 µg/mL), and voriconazole (0.07–0.15 µg/mL). Sequence analysis of the CYP51A gene revealed the presence of M172V mutation, none of which are associated with resistance. Microsatellite genotyping indicated high genotypic diversity and genetic relatedness among isolates from different food sources. Although no azole-resistant phenotypes were identified, the consistent recovery of A. fumigatus from products not directly exposed to azole fungicides highlights the need for continued surveillance. Agricultural environments remain critical hotspots for the emergence and dissemination of resistance, reinforcing the importance of integrated One Health strategies in antifungal resistance monitoring. Full article

The pepper Bs2 resistance gene confers resistance to susceptible Solanaceae plants against pathogenic strains of Xanthomonas campestris pv. vesicatoria carrying the avrBs2 avirulence gene. Previously, we generated Bs2-transgenic Citrus sinensis plants that exhibited enhanced resistance to citrus canker caused by Xanthomonas citri subsp. citri (Xcc), although the underlying mechanisms remained unknown. To elucidate the molecular basis of the early defense response, we performed a comparative transcriptomic analysis of Bs2-expressing and non-transgenic plants 48 h after Xcc inoculation. A total of 2022 differentially expressed genes (DEGs) were identified, including 1356 up-regulated and 666 down-regulated genes. In Bs2-plants, 36.8% of the up-regulated DEGs were associated with defense responses and biotic stress. Functional annotation revealed major changes in genes encoding receptor-like kinases, transcription factors, hormone biosynthesis enzymes, pathogenesis-related proteins, secondary metabolism, and cell wall modification. Among hormone-related pathways, genes linked to ethylene biosynthesis and signaling were the most strongly regulated. Consistently, endogenous ethylene levels increased in Bs2-plants following Xcc infection, and treatment with an ethylene-releasing compound enhanced resistance in non-transgenic plants. Overall, our results indicate the Bs2 expression activates a complex defense network in citrus and may represent a valuable strategy for controlling canker and other Xanthomonas-induced diseases. Full article

Pepper blight, caused by Phytophthora capsici, significantly impacts plant health and reduces crop yields, resulting in severe economic losses. Developing resistant varieties and identifying resistance targets through transcriptomic sequencing, along with elucidating their underlying resistance mechanisms, represent pivotal strategies for disease control. In this study, 11 resistant pepper varieties were identified from 21 varieties; among these, the highly resistant line 19K23 and the susceptible line QM were selected for further analysis. Transcriptome sequencing of root samples from both varieties was conducted on day 2 and day 5 after inoculation with P. capsici. Analysis of differentially expressed genes between the resistant variety and susceptible variety revealed pathways such as photosynthesis, oxidoreductase activity, plant-pathogen interaction, and secondary metabolism. Six key biological processes were highlighted among the highly differentially expressed genes, with porphyrin and chlorophyll metabolism activated early in 19K23. The Ras family, MAPK signaling, hormone signal transduction, and GPI-anchor biosynthesis were implicated in resistance. Importantly, secondary metabolism and lipid metabolism pathways such as phenylpropanoid biosynthesis, isoquinoline alkaloid biosynthesis, and unsaturated fatty acid biosynthesis appeared to play pivotal roles. Additionally, cell wall synthesis and structure, as well as stress response processes, were important. These findings enhance understanding of pepper resistance mechanisms against P. capsici and offer valuable molecular insights for future research on genetic regulation and resistance breeding. Full article

Phototropins (PHOTs) are plant blue-light receptors that mediate crucial physiological processes such as phototropism, chloroplast movement, stomatal opening, and flowering. However, the PHOT family genes remain poorly characterized in pepper. Here, we identified and molecularly cloned two PHOT genes (CaPHOT1 and CaPHOT2) in pepper, which were phylogenetically classified into distinct groups with their homologs from rice, maize, tomato, and Arabidopsis. These genes exhibit conserved gene structures, implying functional conservation during evolution. Subcellular localization analysis confirmed that both CaPHOT1 and CaPHOT2 are localized to the plasma membrane. Expression profiling revealed that both CaPHOT1 and CaPHOT2 were expressed in all tissues, with the highest transcripts in leaves and the lowest in roots. Notably, RNA-seq data revealed that the expression of CaPHOT1 was up-regulated by JA and SA, whereas CaPHOT2 showed no significant changes. Furthermore, CaPHOT1 and CaPHOT2 displayed divergent expression patterns upon Phytophthora capsici infection (PCI). Furthermore, transient overexpression of CaPHOT1 in pepper enhanced susceptibility to PCI, indicating its negative role in disease resistance. Our findings identified the CaPHOT gene family in pepper and functionally demonstrated that CaPHOT1 negatively regulates resistance to PCI, thereby providing insights for future research on PHOTs in other plant species. Full article

Chilli veinal mottle virus (ChiVMV) causes severe yield losses in pepper across Asia. It is very urgent to study the host plant resistance to control this viral disease. As a type of defense response gene, pathogenesis-related protein 1 (PR1) is a well-established defense marker against fungal/bacterial pathogens, and its role in virus resistance remains unclear. Here, we cloned CaPR1 from the ChiVMV-highly resistant pepper variety ‘Perennial’. The 477 bp ORF encodes a 17.65 kDa basic protein containing a conserved CAP-PR1 domain. The subcellular localization of CaPR1 revealed that it was located in the plasma membrane, endoplasmic reticulum (ER), and nucleus. RT-qPCR revealed leaf-predominant expression, with earlier and stronger induction in the highly resistant than the highly susceptible variety after ChiVMV inoculation (6.4-fold at 2 days post-inoculation). The overexpression of CaPR1 in tobacco significantly increased resistance, reducing disease index by 25% and viral coat protein accumulation. Our findings identified CaPR1 as a positive regulator of ChiVMV resistance, providing a molecular target for pepper breeding. In addition, exogenous SA treatment increased the resistance of the highly susceptible cultivar ‘Guijiao 12’ to ChiVMV, and 0.25 mM had a greater effect. Full article

This article provides a comprehensive analysis of Virus-Induced Gene Silencing (VIGS), which is an effective tool for studying the functional genomics of organisms that are poorly amenable to genomic editing. The VIGS method is grounded in the plant’s post-transcriptional gene silencing (PTGS) machinery and utilizes recombinant viral vectors to trigger systemic suppression of endogenous plant gene expression, leading to visible phenotypic changes that enable gene function characterization. This article details the application of VIGS in model organisms (Arabidopsis thaliana, Nicotiana benthamiana) and a wide range of crops, with a special focus on the Solanaceae family, particularly pepper (Capsicum annuum L.). This review analyzes the design and structural elements of viral vectors used for VIGS, such as Tobacco Rattle Virus (TRV), Broad Bean Wilt Virus 2 (BBWV2), Cucumber Mosaic Virus (CMV), geminiviruses (CLCrV, ACMV), and satellite virus-based systems. It also critically examines the key factors that determine silencing efficiency. These factors encompass insert design, agroinfiltration methodology, plant developmental stage, agroinoculum concentration, plant genotype, and environmental factors (temperature, humidity, photoperiod). Particular attention is given to optimization strategies, such as the use of viral suppressors of RNA silencing (VSRs). This article concludes with the achievements in using VIGS to identify pepper genes governing fruit quality (color, biochemical composition, pungency), resistance to biotic (bacteria, oomycetes, insects) and abiotic (temperature, salt, osmotic stress) factors, as well as genes regulating plant architecture and development. The results obtained demonstrate the advantages and limitations of VIGS, alongside future perspectives for its integration with multi-omics technologies to accelerate breeding and advance functional genomics studies in pepper. Full article

Capsicum annuum (pepper) is a globally significant Solanaceous crop vulnerable to devastating pathogens such as Phytophthora capsici. Nucleotide-binding leucine-rich repeat (NLRs) proteins are crucial intracellular immune receptors mediating effector-triggered immunity (ETI). This study presents the comprehensive genome-wide identification and analysis of the NLR gene family in pepper using the high-quality ‘Zhangshugang’ reference genome. We identified 288 high-confidence canonical NLR genes. Chromosomal distribution analysis showed significant clustering, particularly near telomeric regions, with Chr09 harboring the highest density (63 NLRs). Evolutionary analysis demonstrated that tandem duplication is the primary driver of NLR family expansion, accounting for 18.4% of NLR genes (53/288), predominantly on Chr08 and Chr09. Analysis of promoter cis-regulatory elements (CREs) revealed enrichment in defense-related motifs, with 82.6% of promoters (238 genes) containing binding sites for salicylic acid (SA) and/or jasmonic acid (JA) signaling. Transcriptome profiling of Phytophthora capsici-infected resistant (C. annuum cv. CM334) and susceptible (C. annuum cv. NMCA10399) cultivars identified 44 significantly differentially expressed NLR genes, and protein–protein interaction (PPI) network analysis predicted key interactions among them, with Caz01g22900 and Caz09g03820 as potential hubs. This study elucidates the tandem-duplication-driven expansion, domain-specific functional implications, and expression dynamics of the pepper NLR family. It identifies conserved and lineage-specific candidate NLR genes, including Caz03g40070, Caz09g03770, Caz10g20900, and Caz10g21150. These findings provide valuable candidate gene targets for the development of molecular markers for pepper resistance to Phytophthora capsici. Full article

Bacterial leaf spot, particularly in chili peppers, is major concern worldwide, particularly in chili peppers. Enhancing pepper resistance to bacterial leaf spot addresses a key agricultural challenge while minimizing chemical usage. In this study, the efficacy of plant resistance inducers (PRIs) in controlling bacterial leaf spot in peppers was evaluated through molecular and secondary metabolite analyses. Pepper plant seedlings were treated with salicylic acid (SA), acibenzolar-S-methyl, β-aminobutyric acid, chitosan, Bacillus subtilis B01, and B. velezensis CH6 and inoculated with Xanthomonas euvesicatoria pv. euvesicatoria. Disease severity was assessed, and the expression level of genes (PR-1, PR-2, PR-4, and CAT) and the abundance of secondary metabolites were analyzed via quantitative PCR (qPCR) and gas chromatography-mass spectrometry (GC-MS), respectively. Soil drenching with B. subtilis B01 produced the best effects, reducing the disease severity by 80% and significantly inducing PR-1 expression 24–48 h post-treatment. SA was similarly effective in inducing systemic acquired resistance (SAR), while β-aminobutyric acid primed antioxidative defenses through sustained catalase (CAT) expression, and chitosan induced PR-4. GC-MS analysis revealed secondary metabolites associated with systemic resistance pathways including SAR and induced systemic resistance (ISR). Herein, B. subtilis B01 and SA were identified as potent resistance inducers that reduce the disease severity of bacterial leaf spot and activate key defense pathways in pepper plants. These findings contribute to the development of sustainable, integrated disease management strategies. Full article