Plant-pathogen Interaction Pathway Research Articles

Combined transcriptome and metabolome analysis identifies triterpenoid-induced defense responses in Myzus persicae Sülzer-infested peach.

The defense response of peach (Prunus persica) to insect attack involves changes in gene expression and metabolites. Piercing/sucking insects such as green peach aphid cause direct damage by obtaining phloem nutrients and indirect damage by spreading plant viruses. To investigate the response of peach trees to aphids, the leaf transcriptome and metabolome of two genotypes with different sensitivities to green peach aphid (GPA, Myzus persicae) were studied. The transcriptome analysis of infected peach leaves showed two different response patterns. The gene expression of aphid-susceptible peach plants infected by aphids was more similar to that of the control plants, while the gene expression of aphid-resistant peach plants infected by aphids showed strongly induced changes in gene expression compared with the response in the control plants. Furthermore, gene transcripts in defense-related pathways, including plant-pathogen interaction, MAPK signaling, and several metabolic pathways, were more strongly enriched upon aphid infestation. Untargeted secondary metabolite profiling confirmed that aphid treatment induced larger changes in aphid-resistant peaches than in aphid-susceptible peaches. Consistent with transcriptomic alterations, nine triterpenoids showed extremely significant GPA-induced accumulation in aphid-resistant peaches, whereas triterpenoid abundance remained predominantly unchanged or undetected in aphid- susceptible peaches. Furthermore, some types of transcription factors (including WRKYs, ERFs, NACs, etc.) were more strongly induced upon GPA infestation in aphid-resistant peaches but not in aphid-susceptible peaches. Aphid feeding-dependent transcriptome and metabolite profiles provide the foundation for understanding the molecular mechanisms underlying the response of peach to aphid infestation. These results suggested that accumulation of specialized triterpenoids and the corresponding pathway transcripts may play a key role in peach GPA resistance.

Microscopic observation and transcriptome analysis provide insights into mechanisms of hybrid incompatibility in Rhododendron

Hybridization across species has been widely utilized to improve agriculturally important traits in Rhododendron. These interspecific hybridizations are often inhibited by reproductive barriers at the prezygotic and postzygotic stages. Thus, in order to character the barriers and reveal the underlying regulation mechanism of interspecific hybrid incompatibility in Rhododendron, we compared the pollen germination and pollen tube growth, fruit growth, seed number and germination rate between intraspecific (Rhododendron ‘XXL’ × R. ‘XXL’) and interspecific (R. ‘XXL’ × R. delavayi) hybridizations. After pollination, the pollen germination rate and pollen tube growth rate of interspecific hybridization (Inter) were always higher than that of intraspecific hybridization (Intra) during the whole observation period. Conversely, the fruits and ovules of Intra grew faster than that of Inter after 20 DAP. The ratio of shrunken embryos of Inter was 73.27 ± 10.19 %, which was significantly higher than that of Intra with 28.41 ± 8.33 % at 40 DAP. Moreover, the fruit setting rate, the average number of seeds per fruit and seed germination rate of Intra were significantly higher than that of Inter at 150 DAP. These results indicated that the barriers of interspecific incompatibility between R. ‘XXL’ × R. delavayi could be mainly ascribed to post-fertilization isolation. Consequently, RNA-Seq analysis on ovaries at three developmental stages from two hybridizations indicated that plant hormone signal transduction, flavonoid biosynthesis, MAPK signaling pathway and plant-pathogen interaction pathways might play important roles in regulation of hybrid incompatibility between R. ‘XXL’ × R. delavayi. The results can provide a basis for the study of the hybrid incompatibility mechanism of Rhododendron, and provide useful information for the breeding and conservation of genetic resources of Rhododendron.

Joint analysis of transcriptome and hormone metabolome on the mechanism of pruning effect on tea tree (Camellia sinensis) growth

Pruning is a vital agronomic strategy in the cultivation and management of tea trees, greatly affecting the growth of tea trees. In this study, the effect of pruning on tea tree growth was analyzed from transcriptome and hormone metabolome perspectives. The study concluded that pruned (SX) tea trees showed significant increases in leaf area, hundred bud weight, and yield, which were 31.82 %, 36.05 %, and 72.73 %, respectively, compared to unpruned (SC) tea trees. Analysis of gene differential expression and KEGG pathway enrichment showed that 1246 genes characterized by significant differences between SC and SX were significantly enriched in seven pathways, namely plant hormone signal transduction (ko04075), MAPK signaling pathway-plant (ko04016), biosynthesis of secondary metabolites (ko01110), plant-pathogen interaction (ko04626), alpha-linolenic acid metabolism (ko00592), metabolic pathways (ko01100), and ABC transporters (ko02010). Where all of the above pathways were significantly higher in SX than in SC, except for plant-pathogen interaction pathway. Analysis of hormone content showed that SX (21.53 ppm) had significantly higher hormone content than SC (18.85 ppm). Further analysis showed that six characteristic hormones differed significantly in SX, including significantly increased contents of L-phenylalanine and N-6-iso-pentenyladenosine-5′-monophosphate (iPAMP), and significantly decreased contents of indole, abscisic acid, jasmonoyl-L-isoleucine, and 12-hydroxyjasmonic acid in SX. In conclusion, the results showed that pruning stimulated gene expression of the ko04016 pathway, enhanced the strength of the ko01100 and ko01110 pathways, and increased the metabolism of the ko04075, ko00592, and ko02010 pathways, which then led to the increase of L-phenylalanine and iPAMP contents, and promoted tea tree growth. This study provides valuable insight into the importance of cultivating and managing tea trees, particularly those that have undergone pruning procedures.

Transcriptomics and metabolomics of the molecular mechanisms of ginseng's response to the continuous cropping obstacle

Ginseng is a plant with a long history of use in traditional Chinese medicine. However, large-scale cultivation of ginseng is limited by widespread issues with continuous cropping. To explore the physiological and molecular mechanisms behind ginseng crop disorders, transcriptomics and metabolomics were combined in this study to analyze the effects of continuous cropping on changes in ginseng metabolites, differential gene expression, and regulation of root secretions. The results showed that 106 metabolites and 1175 genes were significantly altered at the metabolic and transcriptional levels in ginseng from continuous cropping compared with the control group. More organic acids, alkaloids, flavonoids, and phenolics accumulated in the ginseng from continuous cropping than the control ginseng. Furthermore, significant differences were found in the expression of genes involved in phytohormone signaling, phenylpropanoid biosynthesis, and plant–pathogen interaction pathways. The results provide information on the regulation of expression of genes associated with continuous cropping disorders, and suggest that continuous cropping disorders may lead to severe damage to ginseng roots by pathogens and result in slow growth. Our research provides new insight into the response of ginseng to crop disorders, and reveals potential molecular mechanisms of the ginseng response to crop disorders.

Sugarcane ScOPR1 gene enhances plant disease resistance through the modulation of hormonal signaling pathways.

Transgenic plants stably overexpressing ScOPR1 gene enhanced disease resistance by increasing the accumulation of JA, SA, and GST, as well as up-regulating the expression of genes related to signaling pathways. 12-Oxo-phytodienoate reductase (OPR) is an oxidoreductase that depends on flavin mononucleotide (FMN) and catalyzes the conversion of 12-oxophytodienoate (12-OPDA) into jasmonic acid (JA). It plays a key role in plant growth and development, and resistance to adverse stresses. In our previous study, we have obtained an OPR gene (ScOPR1, GenBank Accession Number: MG755745) from sugarcane. This gene showed positive responses to methyl jasmonate (MeJA), salicylic acid (SA), abscisic acid (ABA), and Sporisorium scitamineum, suggesting its potential for pathogen resistance. Here, in our study, we observed that Nicotiana benthamiana leaves transiently overexpressing ScOPR1 exhibited weaker disease symptoms, darker 3,3-diaminobenzidine (DAB) staining, higher accumulation of reactive oxygen species (ROS), and higher expression of hypersensitive response (HR) and SA pathway-related genes after inoculation with Ralstonia solanacearum and Fusarium solanacearum var. coeruleum. Furthermore, the transgenic N. benthamiana plants stably overexpressing the ScOPR1 gene showed enhanced resistance to pathogen infection by increasing the accumulation of JA, SA, and glutathione S-transferase (GST), as well as up-regulating genes related to HR, JA, SA, and ROS signaling pathways. Transcriptome analysis revealed that the specific differentially expressed genes (DEGs) in ScOPR1-OE were significantly enriched in hormone transduction signaling and plant-pathogen interaction pathways. Finally, a functional mechanism model of the ScOPR1 gene in response to pathogen infection was depicted. This study provides insights into the molecular mechanism of ScOPR1 and presents compelling evidence supporting its positive involvement in enhancing plant disease resistance.

Influence of polyethylene microplastics on Brassica rapa: Toxicity mechanism investigation

Polyethylene microplastics (PE-MPs) have toxicity to ecological environment, including animals and plants. This study investigated the toxicity of photodegraded PE-MPs on Brassica rapa, which is a typical model plant and only have around a 30-day life cycle. It is noted that the presence of photodegraded PE-MPs inhibited Brassica rapa growth since the stem length decreased by 11.94%–51.11 % while the fresh weight and dry weight decreased by 18.56%–27.46 % and 1.90 %–6.91 % respectively, compared to the blank group. PE-MPs receiving more light radiation became more hydrophobic. This inhibited PE-MPs entering the plant body along with the process of plant absorbing water. Furthermore, when PE-MPs were located in the lower soil layers, Brassica rapa reaching them needs a longer time, hence showing lower toxicity effect than the case of PE-MPs located in the upper soil layer. The research outcomes also indicated that malondialdehyde (MDA) contents in photodegraded PE-MPs exposure group increased by 1.37%–7.28 % while the catalase activity (CAT) increased by 60.11 %. This means that PE-MPs caused oxidative stress response in plants, inducing plants to resist external stress. Transcriptomic analysis results showed that Brassica rapa, which was affected by PE-MPs, significantly up-regulated genes related to the plant-pathogen interaction pathway while the ribosome pathway genes were significantly down-regulated. This led to a decrease in growth rate and a decrease in the homeostatic level of the ribosomal subunit and hence resulting in abnormal leaf vein development. These conclusions indicated the toxic effect and damage mechanism of photodegraded PE-MPs on Brassica rapa. The novelty of this study was to use both univariate analysis and transcriptomic analysis to investigate how photodegraded PE-MPs exert toxicity on Brassica rapa. The results can provide a theoretical basis for revealing the influence of MPs on plant growth.

Comparison of the Effect of Pruning on Plant Growth and Transcriptome Profiles in Different Tea Varieties

Although pruning contributes to the growth and development of new shoots, it is important to note that the growth potential and yield of tea varieties may differ after pruning due to genetic and environmental factors. In this experiment, 20 different varieties of tea plants were used to observe their potential for growth, shoot development, and other phenotypic indexes after pruning. The study aimed to determine the suitability of each variety for heavy pruning. It was concluded that there were obvious differences in tree strength and new growth after pruning of the different varieties, with ‘Zhongcha 302’ exhibiting the strongest growth and ‘Emei Wenchun’ showing the weakest growth. In order to understand the molecular mechanisms involved, a transcriptomic analysis was carried out on the two tea varieties. The results of the data indicate that the expression of CYP450 family was high in ‘Zhongcha 302’. In ‘Emei Wenchun’, the expression of NCED was higher than that in ‘Zhongcha 302’. The KEGG results indicate that pruning stimulates the expression of genes involved in phytohormone signalling and plant–pathogen interaction pathways in tea plants. The study offered scientific guidance for tea plant pruning suitability and preliminarily revealed the regulatory mechanism of new shoot growth in different tea plant varieties at the transcriptome level.

Pinus thunbergii Parl. Somatic Plants' Resistance to Bursaphelenchus xylophilus Depends on Pathogen-Induced Differential Transcriptomic Responses.

Pinus thunbergii Parl. is an economically and medicinally important plant, as well as a world-renowned horticultural species of the Pinus genus. Pine wilt disease is a dangerous condition that affects P. thunbergii. However, understanding of the genetics underlying resistance to this disease is poor. Our findings reveal that P. thunbergii's resistance mechanism is based on differential transcriptome responses generated by the early presence of the pathogen Bursaphelenchus xylophilus, also known as the pine wood nematode. A transcriptome analysis (RNA-seq) was performed to examine gene expression in shoot tissues from resistant and susceptible P. thunbergii trees. RNA samples were collected from the shoots of inoculated pines throughout the infection phases by the virulent Bursaphelenchus xylophilus AMA3 strain. The photosynthesis and plant-pathogen interaction pathways were significantly enriched in the first and third days after infection. Flavonoid biosynthesis was induced in response to late infestation (7 and 14 days post-infestation). Calmodulin, RBOH, HLC protein, RPS, PR1, and genes implicated in phytohormone crosstalk (e.g., SGT1, MYC2, PP2C, and ERF1) showed significant alterations between resistant and susceptible trees. Furthermore, salicylic acid was found to aid pine wood nematodes tolerate adverse conditions and boost reproduction, which may be significant for pine wood nematode colonization within pines. These findings provide new insights into how host defenses overcame pine wood nematode infection in the early stage, which could potentially contribute to the development of novel strategies for the control of pine wilt disease.

Comparative transcriptome analysis between two different cadmium-accumulating genotypes of soybean (Glycine max) in response to cadmium stress

BackgroundCadmium (Cd) is extremely toxic and non-essential for plants. Different soybean varieties differ greatly in their Cd accumulation ability, but little is known about the underlying molecular mechanisms.ResultsHere, we performed transcriptomic analysis using Illumina pair-end sequencing on root tissues from two soybean varieties (su8, high-Cd-accumulating (HAS) and su7, low Cd-accumulating (LAS)) grown with 0 or 50 μM CdSO4. A total of 18.76 million clean reads from the soybean root samples were obtained after quality assessment and data filtering. After Cd treatment, 739 differentially expressed genes (DEGs; 265 up and 474 down) were found in HAS; however, only 259 DEGs (88 up and 171 down) were found in LAS, and 64 genes were same between the two varieties. Pathway enrichment analysis suggested that after cadmium treatment, the DEGs between LAS and HAS were mainly enriched in glutathione metabolism and plant-pathogen interaction pathways. KEGG analysis showed that phenylalanine metabolism responding to cadmium stress in LAS, while ABC transporters responding to cadmium stress in HAS. Besides we found more differential expressed heavy metal transporters such as ABC transporters and zinc transporters in HAS than LAS, and there were more transcription factors differently expressed in HAS than LAS after cadmium treatment in two soybean varieties, eg. bHLH transcription factor, WRKY transcription factor and ZIP transcription factor.ConclusionsFindings from this study will shed new insights on the underlying molecular mechanisms behind the Cd accumulation in soybean.

WGCNA Reveals Hub Genes and Key Gene Regulatory Pathways of the Response of Soybean to Infection by Soybean mosaic virus.

Soybean mosaic virus (SMV) is one of the main pathogens that can negatively affect soybean production and quality. To study the gene regulatory network of soybeans in response to SMV SC15, the resistant line X149 and susceptible line X97 were subjected to transcriptome analysis at 0, 2, 8, 12, 24, and 48 h post-inoculation (hpi). Differential expression analysis revealed that 10,190 differentially expressed genes (DEGs) responded to SC15 infection. Weighted gene co-expression network analysis (WGCNA) was performed to identify highly related resistance gene modules; in total, eight modules, including 2256 DEGs, were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of 2256 DEGs revealed that the genes significantly clustered into resistance-related pathways, such as the plant-pathogen interaction pathway, mitogen-activated protein kinases (MAPK) signaling pathway, and plant hormone signal transduction pathway. Among these pathways, we found that the flg22, Ca2+, hydrogen peroxide (H2O2), and abscisic acid (ABA) regulatory pathways were fully covered by 36 DEGs. Among the 36 DEGs, the gene Glyma.01G225100 (protein phosphatase 2C, PP2C) in the ABA regulatory pathway, the gene Glyma.16G031900 (WRKY transcription factor 22, WRKY22) in Ca2+ and H2O2 regulatory pathways, and the gene Glyma.04G175300 (calcium-dependent protein kinase, CDPK) in Ca2+ regulatory pathways were highly connected hub genes. These results indicate that the resistance of X149 to SC15 may depend on the positive regulation of flg22, Ca2+, H2O2, and ABA regulatory pathways. Our study further showed that superoxide dismutase (SOD) activity, H2O2 content, and catalase (CAT) and peroxidase (POD) activities were significantly up-regulated in the resistant line X149 compared with those in 0 hpi. This finding indicates that the H2O2 regulatory pathway might be dependent on flg22- and Ca2+-pathway-induced ROS generation. In addition, two hub genes, Glyma.07G190100 (encoding F-box protein) and Glyma.12G185400 (encoding calmodulin-like proteins, CMLs), were also identified and they could positively regulate X149 resistance. This study provides pathways for further investigation of SMV resistance mechanisms in soybean.

Comparative physiological and transcriptomic analysis reveals an improved biological control efficacy of Sporidiobolus pararoseus Y16 enhanced with ascorbic acid against the oxidative stress tolerance caused by Penicillium expansum in pears

Sporidiobolus pararoseus Y16, a species of significant ecological importance, has distinctive physiological and biological regulatory systems that aid in its survival and environmental adaptation. The goal of this investigation was to understand the complex interactions between physiological and molecular mechanisms in pear fruits as induced by S. pararoseus Y16. The study investigated the use of S. pararoseus Y16 and ascorbic acid (VC) in combination in controlling blue mold decay in pears via physiological and transcriptomic approach. The study results showed that treatment of S. pararoseus Y16 with 150 μg/mL VC reduced pears blue mold disease incidence from 43% to 11%. Furthermore, the combination of S. pararoseus Y16 and VC significantly inhibited mycelia growth and spore germination of Penicillium expansum in the pear's wounds. The pre-treatment did not impair post-harvest qualities of pear fruit but increased antioxidant enzyme activity specifically polyphenol oxidase (PPO), peroxidase (POD), catalase (CAT) activities as well as phenylalanine ammonia-lyase (PAL) enzyme activity. The transcriptome analysis further uncovered 395 differentially expressed genes (DEGs) and pathways involved in defense mechanisms and disease resistance. Notable pathways of the DEGs include plant-pathogen interaction, tyrosine metabolism, and hormone signal transduction pathways. The integrative approach with both physiological and transcriptomic tools to investigate postharvest pathology in pear fruits with clarification on how S. pararoseus Y16 enhanced with VC, improved gene expression for disease defense, and create alternative controls strategies for managing postharvest diseases.

Transcriptomic analysis – Transient expression of CYP714C2 improves resistance in pears

Postharvest pear fruit is highly susceptible to infection by pathogens, particularly by Penicillium expansum. The cytochrome P450 family plays a crucial role in the plant's defense response against pathogen invasion. However, the mechanism underlying CYP714C2 defense in pear fruit remains unclear. In this study, we investigated the molecular and physiological changes in pears after overexpressing CYP714C2 using transient expression technology and transcriptomics analysis. Our findings demonstrate that the up-regulation of CYP714C2 significantly enhances the expression of genes related to pear resistance, including CDPK, CNGC, FLS2, WRKY22, WRKY29, PYL1, ETR, ERS, EIL3, ERF1, NPR, GST, BGLU and others. Moreover, CYP714C2 overexpression altered starch and sucrose metabolism, pentose and glucuronate interconversions, glutathione metabolism, plant hormone signal transduction, MAPK signaling pathway - Plant, plant-pathogen interaction and other resistance-related pathways. Meanwhile, SOD, POD and GST activities of pear were increased. The transient expression of CYP714C2 also resulted in reduced incidence and severity of pathogen infection in pears. It was also found that CYP714C2 protein can interact with GA2ox1 which is a key protein in gibberellin metabolic pathway. As a result, the research showed that CYP714C2 played a role in enhancing resistance in pear fruit and detailed its molecular mechanism for enhancing fruit resistance. This provides a theoretical foundation for future exploration of fruit disease resistance.

Transcriptome analysis reveals various genes involved in the regulation of potato to late blight

BackgroundPotato (Solanum tuberosum L.) production is seriously threatened by the oomycete Phytophthora infestans (P. infestans). However, it remains unclear how the two potato cultivars, Q9 (moderately resistant) and Atl (susceptible), initiate distinct defense responses after inoculation with P. infestans. To uncover the underlying process, we investigated the dynamic gene expression profiles and the functions of the differentially expressed genes (DEGs).ResultsThe results showed that the numbers of up-regulated DEGs were 1345, 1063 and 1694 in Q9 and 272, 603 and 2554 in Atl at 1 day post inoculation (dpi), 3 dpi and 5 dpi, respectively. Meanwhile, the down-regulated DEGs were 1557, 1417 and 389 in Q9 and 114, 364 and 2528 in Atl simultaneously. KEGG enrichment analysis revealed that plant-pathogen interaction, phenylpropanoid biosynthesis and MAPK signaling pathway were significantly enriched in Q9 at the later stage. Furthermore, DEGs associated with plant-pathogen interaction and phenylpropanoid biosynthesis showed higher expression levels in Q9 compared to Atl, especially at the later stage. The expressions of eight DEGs were validated by quantitative real-time PCR (qRT-PCR), which further verified the accuracy of the transcriptomics analysis. In addition, DEGs that were exclusively up-regulated and down-regulated in Q9 were analyzed, which may contribute to the resistance of Q9. Transient expression analysis revealed that four DEGs, including StHP1, StMYB2, StHSP3 and StNAC5, exhibited increased tolerance to P. infestans, indicating a positive role in enhancing the resistance of Q9.ConclusionTherefore, the DEGs associated with plant-pathogen interaction, phenylpropanoid biosynthesis and MAPK signaling pathway were involved in regulating late blight, and the expression level of the related genes significantly increased in Q9. In addition, StHP1, StHSP3 and the transcription factors, including StMYB2 and StNAC5, played positive roles in improving the resistance of potato Q9 to P. infestans. These findings provide useful information for further understanding the molecular mechanism of potato resistance to late blight. Furthermore, our study identified novel resistance genes that can be used in resistance breeding and functional research.Graphical abstract

Transcriptome-Wide N6-Methyladenosine (m6A) Methylation Analyses in a Compatible Wheat-Puccinia striiformis f. sp. tritici Interaction.

N6-methyladenosine (m6A) is a prevalent internal modification in eukaryotic mRNA, tRNA, miRNA, and long non-coding RNA. It is also known for its role in plant responses to biotic and abiotic stresses. However, a comprehensive m6A transcriptome-wide map for Puccinia striiformis f. sp. tritici (Pst) infections in wheat (Triticum aestivum) is currently unavailable. Our study is the first to profile m6A modifications in wheat infected with a virulent Pst race. Analysis of RNA-seq and MeRIP-seq data revealed that the majority of differentially expressed genes are up-regulated and hyper-methylated. Some of these genes are enriched in the plant-pathogen interaction pathway. Notably, genes related to photosynthesis showed significant down-regulation and hypo-methylation, suggesting a potential mechanism facilitating successful Pst invasion by impairing photosynthetic function. The crucial genes, epitomizing the core molecular constituents that fortify plants against pathogenic assaults, were detected with varying expression and methylation levels, together with a newly identified methylation motif. Additionally, m6A regulator genes were also influenced by m6A modification, and their expression patterns varied at different time points of post-inoculation, with lower expression at early stages of infection. This study provides insights into the role of m6A modification regulation in wheat's response to Pst infection, establishing a foundation for understanding the potential function of m6A RNA methylation in plant resistance or susceptibility to pathogens.

Transcriptome sequencing and expression analysis in peanut reveal the potential mechanism response to Ralstonia solanacearum infection

BackgroundBacterial wilt caused by Ralstonia solanacearum severely affects peanut (Arachis hypogaea L.) yields. The breeding of resistant cultivars is an efficient means of controlling plant diseases. Therefore, identification of resistance genes effective against bacterial wilt is a matter of urgency. The lack of a reference genome for a resistant genotype severely hinders the process of identification of resistance genes in peanut. In addition, limited information is available on disease resistance-related pathways in peanut.ResultsFull-length transcriptome data were used to generate wilt-resistant and -susceptible transcript pools. In total, 253,869 transcripts were retained to form a reference transcriptome for RNA-sequencing data analysis. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes revealed the plant-pathogen interaction pathway to be the main resistance-related pathway for peanut to prevent bacterial invasion and calcium plays an important role in this pathway. Glutathione metabolism was enriched in wilt-susceptible genotypes, which would promote glutathione synthesis in the early stages of pathogen invasion. Based on our previous quantitative trait locus (QTL) mapping results, the genes arahy.V6I7WA and arahy.MXY2PU, which encode nucleotide-binding site-leucine-rich repeat receptor proteins, were indicated to be associated with resistance to bacterial wilt.ConclusionsThis study identified several pathways associated with resistance to bacterial wilt and identified candidate genes for bacterial wilt resistance in a major QTL region. These findings lay a foundation for investigation of the mechanism of resistance to bacterial wilt in peanut.

Transcriptome analysis of genes involved in the pathogenesis mechanism of potato virus Y in potato cultivar YouJin.

Potatoes (Solanum tuberosum L.) can be infected by various viruses, but out of all of viruses, the potato virus Y (PVY) is the most detrimental. Research shows that the potato cultivar YouJin is especially vulnerable to PVY and displays severe symptoms, including leaf vein chlorosis, curled leaf margins, large necrotic spots on the leaf blades, and the growth of small new leaves. PVY infection in potato cultivar YouJin was confirmed through symptom observation, RT-PCR, and Western blot analysis. Transcriptome sequencing was used to analyze the genes associated with PVY pathogenesis in this cultivar. Transcriptome analysis of differential genes was conducted in this study to examine the pathogenesis of PVY on YouJin. The results showed that 1,949 genes were differentially regulated, including 853 upregulated genes and 1,096 downregulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that carbohydrate synthesis and metabolism pathways were suppressed, and electron transferase and hydrolase activities were reduced. Moreover, there were increased expression levels of protein kinase genes. By focusing on plant-pathogen interaction pathways, six core genes all upregulating the WARK family of transcription factors were obtained. Additionally, a constructed PPI network revealed the identification of key modular differential genes, such as downregulated photosynthesis-related protein genes and upregulated AP2/ERF-ERF transcription factors. Functional network enrichment analysis revealed that PVY infection limited RNA metabolism, glutathionylation, and peroxiredoxin activity while triggering the expression of associated defense genes in YouJin. After analyzing the above, 26 DEGs were screened and 12 DEGs were confirmed via RT-qPCR. These results establish a hypothetical framework for clarifying the pathogenesis of PVY in the YouJin variety of potatoes, which will help design the disease resistance of YouJin.

Functional verification of GhAFP8 in upland cotton under verticillium wilt stress

Verticillium wilt, caused by Verticillium dahliae, poses a severe threat to cotton growth and yield as a soil-borne disease. The ABI five binding protein (AFP) family, characterized by alkaline leucine zip-like transcription factors, responds to ABA signals, and its expression is induced by ABA as well as various biological and abiotic stresses. In this study, we identified 23 members of the four cotton AFP families, revealing high conservation in both gene and protein structures. Collinearity analysis indicated a closer relationship between GhAFPs and AtAFPs than rice. Cis-element analysis of the cotton AFP promoters unveiled elements associated with plant hormones, abscisic acid, abiotic stress, and light response. To unravel the role of the cotton AFP family in verticillium wilt resistance, we pinpointed a highly expressed gene, GhAFP8, from a resistant variety by monitoring expression levels pre- and post-inoculation for each family gene. Subcellular localization confirmed nuclear localization for GhAFP8. Overexpression of GhAFP8 in tobacco demonstrated enhanced resistance to Verticillium dahliae compared to wild-type plants. Further functional exploration utilizing the VIGs system in cotton revealed that silencing the GhAFP8 gene compromised cotton's resistance to Verticillium dahliae. Transcriptome analysis 72 hours post-inoculation in TRV::00 plants and TRV::GhAFP8-silenced plants showed that GhAFP8 silencing primarily impacts the abscisic acid-activated signaling pathway, MAPK signaling pathway, plant hormone signal transduction, and the activation of plant-pathogen interaction pathway. Additionally, GhAFP8 exhibited responsiveness to signals from jasmonic acid (JA), abscisic acid (ABA), and salicylic acid (SA). In summary, we demonstrated the active role of the GhAFP8 gene in conferring resistance to Verticillium dahliae, positioning it as a promising candidate for cotton breeding against verticillium wilt.

Molecular warfare between pathogenic Fusarium oxysporum R1 and host Crocus sativus L. unraveled by dual transcriptomics.

Phenylpropanoid biosynthesis and plant-pathogen interaction pathways in saffron and cell wall degrading enzymes in Fusarium oxysporum R1 are key players involved in the interaction. Fusarium oxysporum causes corm rot in saffron (Crocus sativus L.), which is one of the most devastating fungal diseases impacting saffron yield globally. Though the corm rot agent and its symptoms are known widely, little is known about the defense mechanism of saffron in response to Fusarium oxysporum infection at molecular level. Therefore, the current study reports saffron-Fusarium oxysporum R1 (Fox R1) interaction at the molecular level using dual a transcriptomics approach. The results indicated the activation of various defense related pathways such as the mitogen activated protein kinase pathway (MAPK), plant-hormone signaling pathways, plant-pathogen interaction pathway, phenylpropanoid biosynthesis pathway and PR protein synthesis in the host during the interaction. The activation of pathways is involved in the hypersensitive response, production of various secondary metabolites, strengthening of the host cell wall, systemic acquired resistance etc. Concurrently, in the pathogen, 60 genes reported to be linked to pathogenicity and virulence has been identified during the invasion. The expression of genes encoding plant cell wall degrading enzymes, various transcription factors and effector proteins indicated the strong pathogenicity of Fusarium oxysporum R1. Based on the results obtained, the putative molecular mechanism of the saffron-Fox R1 interaction was identified. As saffron is a male sterile plant, and can only be improved by genetic manipulation, this work will serve as a foundation for identifying genes that can be used to create saffron varieties, resistant to Fusarium oxysporum infection.

Transcriptome analysis reveals cadmium exposure enhanced the isoquinoline alkaloid biosynthesis and disease resistance in Coptis chinensis

Coptis chinensis Franch is a perennial herb from the Ranunculaceae family with a long history of medicinal use. As the medicinal part, the rhizome of coptis often accumulates excessive cadmium (Cd) even at low concentrations in the soil, which not only compromises its medicinal safety but also raises concerns about adverse effects on human health. Therefore, effective strategies are needed to mitigate this accumulation and ensure its safe use in traditional medicine. This study utilized transcriptome profiling and physiological analysis to explore molecular mechanisms associated with ecological significance and the active accumulation of Cd in C. chinensis. The response to Cd in C. chinensis was assessed through RNA sequencing, Cd determination and isoquinoline alkaloid measurement using its roots, stems, and leaves. The transcriptome revealed, a total of 2667, 2998, or 2815 up-regulated deferentially expressed genes in roots, stems or leaves in response to Cd exposure. Furthermore, we identified phenylpropanoid and isoquinoline alkaloid biosynthesis as the key pathways response to Cd exposure, which suggests that C. chinensis may improve its tolerance to Cd through regulating the phenylpropanoid biosynthesis pathway. Under Cd exposure, plant-pathogen interaction in leaves was identified as the key pathway, which indicates that upregulation of genes involved in plant-pathogen interaction could enhance disease resistance in C. chinensis. WGCNA analysis identified WRKY8 (Cluster-55763.31419) and WRKY47 (Cluster-55763.221590) as potential regulators of secondary metabolic synthesis and plant-pathogen interaction pathway in C. chinensis triggered by Cd. The measurement of berberine, coptisine, palmatine, and epiberberine also demonstrated that Cd simulated the four isoquinoline alkaloids in roots. Therefore, our study not only presented a transcriptome expression profiles that revealed significant upregulation of genes involved in metal transport and detoxification pathways but also suggested a possible mechanism to cope with Cd accumulation. This knowledge provides a new insight into gene manipulation for controlling Cd accumulation, enhancing resistance and promoting synthesis of secondary metabolites with potential medicinal properties in other medicinal plant species.

Transcriptomic-Proteomic Analysis Revealed the Regulatory Mechanism of Peanut in Response to Fusarium oxysporum.

Peanut Fusarium rot, which is widely observed in the main peanut-producing areas in China, has become a significant factor that has limited the yield and quality in recent years. It is highly urgent and significant to clarify the regulatory mechanism of peanuts in response to Fusarium oxysporum. In this study, transcriptome and proteome profiling were combined to provide new insights into the molecular mechanisms of peanut stems after F. oxysporums infection. A total of 3746 differentially expressed genes (DEGs) and 305 differentially expressed proteins (DEPs) were screened. The upregulated DEGs and DEPs were primarily enriched in flavonoid biosynthesis, circadian rhythm-plant, and plant-pathogen interaction pathways. Then, qRT-PCR analysis revealed that the expression levels of phenylalanine ammonia-lyase (PAL), chalcone isomerase (CHI), and cinnamic acid-4-hydroxylase (C4H) genes increased after F. oxysporums infection. Moreover, the expressions of these genes varied in different peanut tissues. All the results revealed that many metabolic pathways in peanut were activated by improving key gene expressions and the contents of key enzymes, which play critical roles in preventing fungi infection. Importantly, this research provides the foundation of biological and chemical analysis for peanut disease resistance mechanisms.