Pathogen Interactions Research Articles

Comparative transcriptome analysis of Aspergillus niger revealed its biocontrol mechanisms in response to the guava wilt pathogen Fusarium oxysporum f. sp. psidii.

Wilt is one of the major destructive diseases in guava cultivation worldwide. Biocontrol agent Aspergillus niger has been recognized for its efficacy against various plant pathogens including guava wilt disease. This biocontrol fungus has been widely studied for its mycoparasitic and antibiosis mechanisms. Still, a notable gap exists in the literature regarding the molecular mechanisms and biosynthetic pathways underlying biocontrol activity when challenged with guava wilt pathogen. In this investigation, we conducted comprehensive global RNA sequencing, which generated a total of 35.16 GB data, comprising 18–22 million reads having 52-54% GC content. Over 55,464 transcripts displayed differential expression profiles during the interaction of biocontrol and the pathogen, out of that 5,285 transcripts were expressed at FC2 and Pval 0.05. They were mainly associated with catalytic activity (48.45%), protein or DNA binding activity (44.9%), transporter activity (8.2%), and transcription regulator activity (5.5%). In the biological process category, 36.5% and 34.7% of transcripts were linked to "metabolic" and "cellular processes," respectively. The upregulated DEGs were predominantly linked to hydrolytic activity and secondary metabolite production, encompassing AB hydrolases, cyanate hydratase, Isochorismatase hydrolase, galacturan 1,4-alpha-galacturonidase B, Esterase/Lipase, MFS monosaccharide transporter, ATP-binding cassette transporter, polyamine transporter 3, endoglucanase A, and non-ribosomal siderophore peptide synthase (SidC). Our investigation highlighted that the biocontrol mechanism primarily involves the active participation of hydrolytic enzymes, transporters, transcription factors, and secondary metabolites. Additionally, the data were validated using RT-qPCR, affirming the consistency of RNA-seq findings. This study represents the inaugural effort to elucidate the biocontrol mechanism of A. niger against F. oxysporum f. sp. psidii using the RNA-seq approach. The findings shed light on the antagonistic mechanisms of A. niger at the molecular level, enhancing our comprehension of A. niger as a biocontrol agent and deepening our exploration of biocontrol and pathogen interactions.

The chosen few: Mycobacterium tuberculosis isolates for IMPAc-TB

The three programs that make up the Immune Mechanisms of Protection Against Mycobacterium tuberculosis Centers (IMPAc-TB) had to prioritize and select strains to be leveraged for this work. The CASCADE team based at Seattle Children’s Research Institute are leveraging M.tb H37Rv, M.tb CDC1551, and M.tb SA161. The HI-IMPACT team based at Harvard T.H. Chan School of Public Health, Boston, have selected M.tb Erdman as well as a novel clinical isolate recently characterized during a longitudinal study in Peru. The PHOENIX team also based at Seattle Children’s Research Institute have selected M.tb HN878 and M.tb Erdman as their isolates of choice. Here, we describe original source isolation, genomic references, key virulence characteristics, and relevant tools that make these isolates attractive for use. The global context for M.tb lineage 2 and 4 selection is reviewed including what is known about their relative abundance and acquisition of drug resistance. Host–pathogen interactions seem driven by genomic differences on each side, and these play an important role in pathogenesis and immunity. The few M.tb strains chosen for this work do not reflect the vast genomic diversity within this species. They do, however, provide specific virulence, pathology, and growth kinetics of interest to the consortium. The strains selected should not be considered as “representative” of the growing available array of M.tb isolates, but rather tools that are being used to address key outstanding questions in the field.

Strategic genetic insights and integrated approaches for successful management of blackleg in canola/rapeseed farming

AbstractThis review describes a triumphant narrative in the battle against the devastating plant pathogen complex, Leptosphaeria maculans and L. biglobosa, and the success of the world's second‐largest oilseed crop, canola/oilseed rape. Emphasizing global collaborations, the article explores successfully mitigating this destructive disease in canola/rapeseed production across Australia, Canada and Europe. It highlights how strategies may vary between continents to adapt to specific contexts. While initial resistance (R) genes proved effective, the evolution of the pathogen under crop‐induced disease pressure led to the breakdown of these genes. Now, growers in these regions have been equipped with new tools, allowing them to make informed decisions that help to keep the disease at generally low levels. A pivotal factor in this success has been a deepened understanding of the intricate science underlying the host–pathogen interaction. Concerted efforts of individual laboratories and collaborative initiatives have played an essential role in this success, including novel methods for disease control based on extensive research that has translated into developing highly resistant varieties, enhanced pathogen monitoring, improved cultivar recommendation and integrated management strategies. The review showcases many milestone advancements, including the cloning of numerous avirulence genes within the pathogen, characterization of specific R genes, the development of various molecular tools for monitoring both pathogen and host, the introduction of groundbreaking disease management strategies such as R gene labelling, rotation and stacking, and establishment of a universal pathogen isolate collection that facilitates the exchange of information among multiple laboratories and adds a new dimension to this triumph.

Phosphonates of Pectobacterium atrosepticum: Discovery and Role in Plant–Pathogen Interactions

Many phytopathogens’ gene products that contribute to plant–pathogen interactions remain unexplored. In one of the most harmful phytopathogenic bacterium Pectobacterium atrosepticum (Pba), phosphonate-related genes have been previously shown to be among the most upregulated following host plant colonization. However, phosphonates, compounds characterized by a carbon–phosphorus bond in their composition, have not been described in Pectobacterium species and other phytopathogenic bacteria, with the exception of Pseudomonas syringae and Pantoea ananatis. Our study aimed to determine whether Pba synthesizes extracellular phosphonates and, if so, to analyze their physiological functions. We demonstrated that Pba produces two types of extracellular phosphonates: 2-diethoxyphosphorylethanamine and phenylphosphonic acid. Notably, such structures have not been previously described among natural phosphonates. The production of Pba phosphonates was shown to be positively regulated by quorum sensing and in the presence of pectic compounds. Pba phosphonates were found to have a positive effect on Pba stress resistance and a negative effect on Pba virulence. The discovered Pba phosphonates are discussed as metabolites that enable Pba to control its “harmful properties”, thereby maintaining its ecological niche (the host plant) in a relatively functional state for an extended period.

An overview of symbiotic and pathogenic interactions at the fungi-plant interface under environmental constraints

The complex and dynamic interactions between fungi and plants constitute a critical arena in ecological science. In this comprehensive review paper, we explore the multifaceted relationships at the fungi-plant interface, encompassing both mutualistic and antagonistic interactions, and the environmental factors influencing these associations. Mutualistic associations, notably mycorrhizal relationships, play a pivotal role in enhancing plant health and ecological balance. On the contrary, fungal diseases pose a significant threat to plant health, agriculture, and natural ecosystems, such as rusts, smuts, powdery mildews, downy mildews, and wilts, which can cause extensive damage and lead to substantial economic losses. Environmental constraints encompassing abiotic and biotic factors are elucidated to understand their role in shaping the fungi-plant interface. Temperature, moisture, and soil conditions, along with the presence of other microbes, herbivores, and competing plants, significantly influence the outcome of these interactions. The interplay between mutualism and antagonism is emphasised as a key determinant of ecosystem health and stability. The implications of these interactions extend to overall ecosystem productivity, agriculture, and conservation efforts. The potential applications of this knowledge in bioremediation, biotechnology, and biocontrol strategies emphasise the importance of adapting to climate change. However, challenges and future directions in this field include the impacts of climate change, emerging fungal pathogens, genomic insights, and the role of the fungi-plant interface in restoration ecology. Hence, this review paper provides a comprehensive overview of fungi-plant interactions, their environmental influences, and their applications in agriculture, conservation, and ecological restoration.

Genomic characterization of Pantoea dispersa A003 isolated from a clinical patient

IntroductionPantoea dispersa is a Gram-negative bacterium generally considered as a plant pathogen and rarely causes human infections. To date, there have been 13 studies that have documented clinical infections linked to P. dispersa, with a primary emphasis on the initial identification of this pathogen. The genomic features and the mechanisms underlying the pathogenesis of P. dispersa remain largely uninvestigated. In the present study, we describe a clinical infection caused by P. dispersa and provide the first genomic analysis of this bacterium.MethodsThe bacterial strain designated A003 was isolated from blood samples. Preliminary identification of strain A003 was conducted using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) technology (VITEK® MS, bioMérieux, France). Biochemical and antimicrobial susceptibility assessments were carried out utilizing the VITEK-2 compact automated microbial analysis system (bioMérieux, France). Additionally, whole genome sequencing and subsequent analysis were performed to further elucidate the potential pathogenicity.ResultsThe bacterial isolate was cultured overnight at 35°C in a CO2-enriched environment on Columbia blood agar, resulting in the appearance of a white, smooth, Gram-negative rod-shaped bacterium with diameters ranging from 1 to 2 mm. Identification of strain A003 was achieved with a high confidence level of 99.9% as P. dispersa using MALDI-TOF mass spectrometry. The average nucleotide identity (ANI) value between strain A003 and the reference strain P. dispersa DSM 30073T was 98.08%, while the DNA–DNA hybridization (DDH) value was 84.10% (Formula 2) based on genome sequencing data, which further confirmed that A003 belonged to the P. dispersa species. Comprehensive analysis revealed the presence of 372 virulence factors, 15 antibiotic resistance genes, 222 carbohydrate-active enzymes, and 666 genes related to Type III secretion system (T3SS) effector proteins, as identified through the core databases of VFDB (Virulence Factors of Pathogenic Bacteria), CARD (Comprehensive Antibiotic Resistance Database), CAZY (Carbohydrate-Active enZYmes Database), and T3SS. The virulence factors included type IV pili (TFP), type VI secretion system, flagella, iron uptake system, and ompA, which are implicated in bacterial pathogenicity. The antibiotic resistance profile indicated resistance to fluoroquinolones, cephalosporins, penams, macrolides, and aminoglycosides, as annotated by the CARD database.ConclusionThe draft genome sequenced represents the inaugural genomic sequence of P. dispersa derived from clinical sources. This advancement may enhance clinical practitioners’ comprehension of the organism’s clinical attributes and serve as a foundational resource for future research into its virulence, antibiotic resistance, and host–pathogen interactions.

Characterization, expressional and evolutionary analysis of five fish-specific CCRs (CCR4La, CCR4Lc, CCR12a1, CCR12a2, and CCR12b) in largemouth bass (Micropterus salmoides)

CC chemokine receptors (CCRs), the numbers of the G protein-coupled receptor (GPCR) superfamily, had crucial roles in treating infection, inflammation, and tissue damage by binding to their ligands. In this study, five fish-specific CCRs, namely CCR4La, CCR4Lc, CCR12a1, CCR12a2, and CCR12b, were identified in largemouth bass (Micropterus salmoides). The correction of nomenclatures of these CCRs were confirmed by phylogenetic analysis, structural analysis and genomic synteny analysis. Following 1×106 CFU/mL and 1×107 CFU/mL Edwardsiella piscicida infection, these five CCRs were significantly induced in spleen of largemouth bass, indicating their important roles in the immune response against bacterial infection. Selection pressure analysis revealed that CCR4La, CCR4Lc, CCR12a1, and CCR12a2 underwent negative selection pressure, whereas CCR12b experienced positive selection pressure. Robust selection site detection methods identified that positive selected sites of CCR4La, CCR4Lc, CCR12a1, and CCR12a2 mainly distributed in their extracellular regions, which involved in ligand binding and pathogen interaction. Similarly, the positive selected sites of CCR12b were also located in its extracellular regions. The accuracy of the pressure selected sites were also validated by molecular docking analysis. The potential ligands for these five CCRs were identified by molecular docking analysis, with finding that CCL3 and CCL5 might be the ligands of largemouth bass CCR4La/Lc, and CCL5, CCL8, CCL7, CCL13 and CCL26 might be that of largemouth bass CCR12a1/a2/b. Our results provided basis for elucidating the functions of chemokine-receptor complex in largemouth bass.

Metabolite profiling and transcriptome analyses reveal defense regulatory network against pink tea mite invasion in tea plant

BackgroundThe tea plant Camellia sinensis (L.) O. Kuntze is a perennial crop, invaded by diversity of insect pest species, and pink tea mite is one of the most devastating pests for sustainable tea production. However, molecular mechanism of defense responses against pink tea mites in tea is still unknown. In this study, metabolomics and transcriptome profiles of susceptible and resistant tea varieties were compared before and after pink tea mite infestation.ResultsMetabolomics analysis revealed that abundance levels of polyphenol-related compounds changed significantly before and after infestation. At the transcript level, nearly 8 GB of clean reads were obtained from each sequenced library, and a comparison of infested plants of resistant and susceptible tea varieties revealed 9402 genes with significant differential expression. An array of genes enriched in plant pathogen interaction and biosynthetic pathways of phenylpropanoids showed significant differential regulation in response to pink tea mite invasion. In particular, the functional network linkage of disease resistant proteins, phenylalanine ammonia lyase, flavanone -3-hydroxylase, hydroxycinnamoyl-CoA shikimate transferase, brassinosteroid-6-oxidase 1, and gibberellin 2 beta-dioxygenase induced dynamic defense signals to suppress prolonged pink tea mite attacks. Further integrated analyses identified a complex network of transcripts and metabolites interlinked with precursors of various flavonoids that are likely modulate resistance against to pink tea mite.ConclusionsOur results characterized the profiles of insect induced metabolic and transcript reprogramming and identified a defense regulatory network that can potentially be used to fend off pink tea mites damage.

Weighted Gene Co-Expression Network Analysis Uncovers Critical Genes and Pathways Involved in Soybean Response to Soybean Mosaic Virus

Background: Soybean mosaic virus (SMV) is a globally prevalent and detrimental virus that belongs to the Potyvirus genus. Pathogenic viruses of this genus are typically linear in shape, with dimensions ranging between 630 and 750 nm, and are composed of single-stranded RNA and proteins. We have developed an SMV-resistant soybean line, Dongnong 93-046, which has no significant changes in disease resistance identification in the adult plants and has neat grains with no obvious brown or black markings. To explore the defense mechanisms of soybean against SMV, we performed comparative transcriptomic sequencing of the leaves between the Dongnong 93-046 inoculated with SMV at 8 h (T) and the non-inoculated control (C) on the HiSeq2000 platform. In addition, we performed non-targeted metabolomic sequencing of leaves from the treatment and control groups. Results: We identified a total of 41,189 differentially expressed genes (DEGs). A total of 9809 differentially expressed genes (DEGs) met the criteria of |Log2FC (Fold Change)| ≥ 1 and adjusted p-value ≤ 0.001. Among the 41,189 DEGs identified, 9196 exhibited FPKM values greater than 10. KEGG pathway enrichment analysis of the 9809 DEGs revealed significant enrichment of genes involved in resistance-related pathways such as plant–pathogen interaction, linoleic acid metabolism, mitogen-activated protein kinase (MAPK) signaling pathway, and plant hormone signaling transduction. Functional analysis using MapMan software identified multiple DEGs that were associated with pathways such as jasmonate synthesis and phenylpropanoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) using the differential metabolites and the 9196 DEGs revealed a strong correlation between gene clusters within the Turquoise module and the content of jasmonate-related metabolites. Further functional enrichment analysis of the 894 genes within the gene clusters showed a significant and repeated enrichment of pathways related to plant–pathogen interaction, linoleic acid metabolism, and plant hormone signaling transduction. Subsequent focused pathway analysis identified key genes involved in plant hormone signaling transduction pathways, such as the jasmonate ZIM domain protein Glyma.16G010000, the gene Glyma.01G235600 encoding the essential diterpene reductase required for jasmonate synthesis in the jasmonate biosynthesis pathway, and the transcription factor Glyma.02G232600 involved in the plant–pathogen interaction pathway, among others. This study provides a theoretical framework for understanding the resistance mechanism of soybean cultivar Dongnong 93-046 against the SMV N1 strain, offers potential gene resources for breeding soybean varieties with resistance to SMV, and paves the way for new strategies to control SMV infection, enhance resistance, and improve crop yield and quality.

A comprehensive review of integrated management strategies for damping-off disease in chili

Damping-off disease in chili (Capsicum annum L.) cultivation is a significant global issue, severely affecting seeds, seedlings, and young plants, regardless of the location of cultivation, whether in greenhouses or open fields. Despite chili being a widely popular vegetable used in various cuisines globally, farmers face challenges in meeting the growing demand due to the extensive damage caused by this disease, ranging from 20 to 85%. The shelf life and quality of mature pods are also severely affected. Damping-off disease is mainly caused by soil-borne fungus from the Pythium species, with additional contributions from Phytophthora, Fusarium, and Rhizoctonia species. These pathogens’ adaptability to diverse environmental conditions and resistance to synthetic fungicides make controlling damping-off on a commercial scale challenging. However, integrated disease management has shown promising results as a remedial approach. In this review, we discuss the current state of chili diseases, the nature of the pathogens causing damping-off, the epidemiology of the disease, and various control mechanisms. In this review, we broadly discuss the current state of chili diseases, the nature of the pathogens causing damping-off, the epidemiology of the disease, and various control mechanisms. Furthermore, we highlight the importance and efficacy of integrated disease management techniques, along with future prospects in unexplored areas, such as host–pathogen interaction and sustainable disease control measures. The information in this review aims to assist chili growers in understanding the epidemiology and management of damping-off in chili cultivation.

The Influence of Climate Change on Vector-Borne Diseases in a Wilderness Medicine Context.

The imminent climate crisis has been labeled as the biggest health threat humanity must deal with. Vector-borne disease distribution and transmission as well as the population at risk are influenced to a great degree by environmental and climactic factors affecting both the vectors themselves and the causative pathogens. Paired with an increase in worldwide travel, urbanization, and globalization, along with population displacements and migration, elucidating the effects of anthropogenic climate change on these illnesses is therefore of the essence to stave off potential negative sequelae. Outcomes on different vector-borne diseases will be diverse, but for many of them, these developments will result in a distribution shift or expansion with the possibility of (re-)introduction of vector and pathogen species in previously nonendemic areas. The consequence will be a growing likelihood for novel human, vector, and pathogen interactions with an increased risk for infection, morbidity, and mortality. Wilderness medicine professionals commonly work in close relationship to the natural environment and therefore will experience these alterations most strongly in their practice. Hence, this article attempts to bring awareness to the subject at hand in a wilderness medicine context, with a focus on malaria, the most burdensome of arthropod-borne diseases. For prevention of the potentially dire consequences on human health induced by climate change, concerted and intensified efforts to reduce the burning of fossil fuels and thus greenhouse gas emissions will be imperative on a global scale.

Comparative transcriptome and hormone analyses of roots in apple among three rootstocks with different rooting abilities

Background Root plays an important role in the growth and development of fruit trees; however, the molecular mechanisms behind the differences among rootstock varie-ties remain unclear. Methods This study examined the effects of different rootstocks on root structure and the endogenous hormone content of 1-year old apple seedlings in combinations of Tianhong 2 (T2)/Malus robusta (HT), T2/G935, and T2/Jizhen 2 (J2). Results The results showed that the T2/HT treatment had greater root length, surface area, volume, average diameter, tips and forks, followed by G935 and J2. In T2/HT leaves and roots, the indole-3-acetic acid (IAA) and gibberellins (GA3) levels were highest, and the abscisic acid (ABA) levels were the lowest. A root transcriptome analysis detected 10,064, 10,511, and 8,719 differentially expressed genes in T2/HT vs. T2/G935, T2/HT vs. T2/J2, and T2/J2 vs. T2/G935, respectively. The analysis of Gene Ontology (GO) terms indicated a significant enrichment in biological processes, cellular components, and molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that plant hormone signaling, MAPK signaling pathway–plant, and plant–pathogen interaction played important roles in differences in the rooting ability of different rootstocks. In addition, some key differential genes were associated with root growth and development and were involved in these metabolic pathways. This study is important for enriching theoretical studies of fruit tree roots.

Genetic Diversity and Pathogenicity of Phytophthora infestans Isolates on Four Solanum tuberosum (Potato) Cultivars in Nariño, Colombia

Phytophthora infestans remains a major threat to global potato production. This study focused on characterizing and assessing the pathogenicity of P. infestans isolates on detached potato leaves and in greenhouse trials across four cultivars. Seven isolates were obtained from high potato-producing regions in the department of Nariño, Colombia. The isolates were analyzed using 12 microsatellite markers to determine genetic distances. Two genetically distinct isolates showed markedly different pathogenicity on detached leaves: isolate P00921 caused complete infection by day five, whereas P00321 showed no symptoms. These two isolates (P00921 and P00321) selected for having the greatest genetic distance and highest pathogenicity among the seven analyzed were further tested in a greenhouse setup on four potato cultivars using a randomized block design. Disease progression was monitored over nine days. The results indicated significant variations in pathogenicity linked to genetic diversity among isolates. Notably, Capiro and Margarita cultivars were more prone to severe disease than Suprema and Única. These findings highlight the complex nature of host–pathogen interactions and suggest the need for tailored approaches in disease management and cultivar selection.

Time-Resolved Multiomics Illustrates Host and Gut Microbe Interactions during Salmonella Infection.

Salmonella infection, also known as Salmonellosis, is one of the most common food-borne illnesses. Salmonella infection can trigger host defensive functions, including an inflammatory response. The provoked-host inflammatory response has a significant impact on the bacterial population in the gut. In addition, Salmonella competes with other gut microorganisms for survival and growth within the host. Compositional and functional alterations in gut bacteria occur because of the host immunological response and competition between Salmonella and the gut microbiome. Host variation and the inherent complexity of the gut microbial community make understanding commensal and pathogen interactions particularly difficult during a Salmonella infection. Here, we present metabolomics and lipidomics analyses along with the 16S rRNA sequence analysis, revealing a comprehensive view of the metabolic interactions between the host and gut microbiota during Salmonella infection in a CBA/J mouse model. We found that different metabolic pathways were altered over the four investigated time points of Salmonella infection (days -2, +2, +6, and +13). Furthermore, metatranscriptomics analysis integrated with metabolomics and lipidomics analysis facilitated an understanding of the heterogeneous response of mice, depending on the degree of dysbiosis.

Interactions between Pseudomonas aeruginosa and six opportunistic pathogens cover a broad spectrum from mutualism to antagonism.

Bacterial infections often involve more than one pathogen. While it is well established that polymicrobial infections can impact disease outcomes, we know little about how pathogens interact and affect each other's behaviour and fitness. Here, we used a microscopy approach to explore interactions between Pseudomonas aeruginosa and six human opportunistic pathogens that often co-occur in polymicrobial infections: Acinetobacter baumannii, Burkholderia cenocepacia, Escherichia coli, Enterococcus faecium, Klebsiella pneumoniae, and Staphylococcus aureus. When following growing microcolonies on agarose pads over time, we observed a broad spectrum of species-specific ecological interactions, ranging from mutualism to antagonism. For example, P. aeruginosa engaged in a mutually beneficial interaction with E. faecium but suffered from antagonism by E. coli. While we found little evidence for active directional growth towards or away from cohabitants, we observed that some pathogens increased growth in double layers in response to competition and that physical forces due to fast colony expansion had a major impact on fitness. Overall, our work provides an atlas of pathogen interactions, highlighting the diversity of potential species dynamics that may occur in polymicrobial infections. We discuss possible mechanisms driving pathogen interactions and offer predictions of how the different ecological interactions could affect virulence.

First person – Cecilia Alejandra Vazquez

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Cecilia Alejandra Vazquez is first author on ‘ Intracellular lipid droplets are exploited by Junín virus in a nucleoprotein-dependent process’, published in JCS. Cecilia Alejandra is a postdoc in the lab of Dr Sandra M. Cordo and Dr Cybele C. García at Universidad de Buenos Aires Int, Buenos Aires, Argentina, where she is interested in all things regarding the ‘One Health’ concept of optimizing the health of people, animals and ecosystems. In particular, I am passionate about host–pathogen interactions, how they can be affected by the environment and how understanding them can lead to the development of new therapies.

Genomic insights into codon usage bias in Cannabis sativa and pathogenic interactions

This study delves into codon usage bias (CUB) across Cannabis sativa and its associated pathogens (Meloidogyne incognita, Alternaria alternata, Aspergillus flavus, Aspergillus niger, and Fusarium oxysporum). It finds an AT-bias in C. sativa and M. incognita, favouring AT ending codons, while fungal pathogens lean towards GC-ending codons. Analysis suggests weak codon bias overall, with host and nematode showing similar preferences, and fungal pathogens preferring GC-ending codons. In ENC/GC3 plot, parity plot analyses both natural selection and mutational pressure influence CUB, slightly favouring T-ending codons.Neutrality plot analysis demonstrated varying degrees of mutational pressure and selection across the organisms. Correspondence analysis revealed indistinguishable CUB effective in all pathogens, despite differences in evolutionary forces. Correlation analysis illustrated the impact of nucleotide composition, mutational pressure, and natural selection on CUB. Additionally, amino acid composition analysis indicated differential usage of amino acids across organisms. Codon context analysis unveiled common trends in codon pairing, emphasizing the prevalence of preferred codons in C. sativa and M. incognita. This comprehensive analysis provides insights into the factors shaping CUB and the evolutionary forces influencing the genomes of the host plant and its associated pathogens, contributing to a deeper understanding of molecular interactions in host-pathogen systems. This data informs conservation for Cannabis sativa by identifying pathogen-resistant genetic traits, guiding breeding and management for biodiversity preservation.

Combined Analysis of Transcriptome and Metabolome Provides Insights in Response Mechanism under Heat Stress in Avocado (Persea americana Mill.)

Plants generate a range of physiological and molecular responses to sustain their growth and development when suffering heat stress. Avocado is a type of tropical fruit tree with high economic value. Most avocado cultivars delete, wither, or even die when exposed to heat stress for a long time, which seriously restricts the introduction and cultivation of avocados. In this study, samples of a heat-intolerant variety (‘Hass’) were treated under heat stress, and the transcriptomics and metabolomics were analyzed, with the expectation of providing information on the variety improvement and domestication of avocados. The differentially expressed genes identified using transcriptome analysis mainly involved metabolic pathways such as plant hormone signal transduction, plant–pathogen interaction, and protein processing in the endoplasmic reticulum. Combined transcriptome and metabolome analysis indicated that the down-regulation of Hass.g03.10206 and Hass.g03.10205 in heat shock-like proteins may result in the reduced Trehalose and Sinapoyl aldehyde content. Metabolomics analysis results indicated that the decrease in Trehalose and Sinapoyl aldehyde content may be an important factor for heat intolerance. These results provide important clues for understanding the physiological mechanisms of adaptation to heat stress in avocados.

Transcriptome Profiling Revealed ABA Signaling Pathway-Related Genes and Major Transcription Factors Involved in the Response to Water Shock and Rehydration in Ginkgo biloba

To assess the regulatory mechanisms involved in the transcriptomic response of Ginkgo biloba to water shock and rehydration, ginkgo seedlings were subjected to dehydration for 0, 3, 6, 12, and 24 h, followed by rehydration for 12 h (Re12 h). A total of 1388, 1802, 2267, 2667, and 3352 genes were upregulated, whereas 1604, 1839, 1934, 2435, and 3035 genes were downregulated, at 3, 6, 12, 24, and Re12 h, respectively, compared to 0 h. Two KEGG pathways—the plant pathogen interaction pathway and mitogen-activated protein kinase (MAPK) signaling pathway—were enriched under water shock but not under rehydration. Moreover, plant hormone signal transduction was enriched under both water shock and rehydration. Differentially expressed genes (DEGs) involved in the ABA signaling pathway (PYR/PYLs, PP2Cs, and SnRK2s) and major differentially expressed transcription factors (MYB, bHLH, AP2/ERF, NAC, WRKY, and bZIP TFs) were identified. qRT-PCR analysis further revealed GbWRKY3 as a negative regulator of the water shock response in G. biloba. The subcellular localization results revealed GbWRKY3 as a nuclear protein. These phenotype-related DEGs, pathways, and TFs provide valuable insight into the water shock and rehydration response in G. biloba.

Transcriptome Profiling Identifies Plant Hormone Signaling Pathway-Related Genes and Transcription Factors in the Drought and Re-Watering Response of Ginkgo biloba

Ginkgo biloba, usually referred to as a “living fossil,” is widely planted in many countries because of its medicinal value and beautiful appearance. Owing to ginkgo’s high resistance to drought stress, ginkgo seedlings can even survive withholding water for several days without exhibiting leaf wilting and desiccation. To assess the physiological and transcriptomic mechanisms involved in the drought stress and re-watering responses of Ginkgo biloba, ginkgo seedlings were subjected to drought treatment for 15 d (D_15 d) and 22 d (D_22 d) until they had severely wilted, followed by re-watering for 3 d (D_Re3 d) to restore normal growth. Variations in physiological characteristics (relative water content, malondialdehyde (MDA) content, stomatal aperture, and antioxidant enzyme activity) during drought and re-watering were assessed. In total, 1692, 2031, and 1038 differentially expressed genes (DEGs) were upregulated, while 1691, 2820, and 1910 were downregulated in D_15 d, D_22 d, and D_Re3 d, respectively, relative to the control. Three pathways, namely, plant hormone signal transduction, plant–pathogen interaction, and the plant MAPK signaling pathway, were enriched during drought stress and re-watering. The DEGs involved in plant hormone signal transduction pathways (those of IAA, CTK, GA, ABA, ETH, BR, SA, and JA) and the major differentially expressed transcription factors (TFs; MYB, bHLH, AP2/ERF, NAC, WRKY, and bZIP) were identified. Quantitative real-time PCR revealed six TFs as positive or negative regulators of drought stress response. These phenotype-related physiological characteristics, DEGs, pathways, and TFs provide valuable insights into the drought stress and re-watering responses in G. biloba.