Transcriptome profiling in susceptible and tolerant rubber tree clones in response to cassiicolin Cas1, a necrotrophic effector from Corynespora cassiicola

Corynespora cassiicola, a fungal plant pathogen with a large host range, causes important damages in rubber tree (Hevea brasiliensis), in Asia and Africa. A small secreted protein named cassiicolin was previously identified as a necrotrophic effector required for the virulence of C. cassiicola in specific rubber tree clones. The objective of this study was to decipher the cassiicolin-mediated molecular mechanisms involved in this compatible interaction. We comparatively analyzed the RNA-Seq transcriptomic profiles of leaves treated or not with the purified cassiicolin Cas1, in two rubber clones: PB260 (susceptible) and RRIM600 (tolerant). The reads were mapped against a synthetic transcriptome composed of all available transcriptomic references from the two clones. Genes differentially expressed in response to cassiicolin Cas1 were identified, in each clone, at two different time-points. After de novo annotation of the synthetic transcriptome, we analyzed GO enrichment of the differentially expressed genes in order to elucidate the main functional pathways impacted by cassiicolin. Cassiicolin induced qualitatively similar transcriptional modifications in both the susceptible and the tolerant clones, with a strong negative impact on photosynthesis, and the activation of defense responses via redox signaling, production of pathogenesis-related protein, or activation of the secondary metabolism. In the tolerant clone, transcriptional reprogramming occurred earlier but remained moderate. By contrast, the susceptible clone displayed a late but huge transcriptional burst, characterized by massive induction of phosphorylation events and all the features of a hypersensitive response. These results confirm that cassiicolin Cas1 is a necrotrophic effector triggering a hypersensitive response in susceptible rubber clones, in agreement with the necrotrophic-effector-triggered susceptibility model.

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Altered miRNA and mRNA Expression in Sika Deer Skeletal Muscle with Age

Genes ◽

10.3390/genes11020172 ◽

2020 ◽

Vol 11 (2) ◽

pp. 172

Author(s):

Boyin Jia ◽

Yuan Liu ◽

Qining Li ◽

Jiali Zhang ◽

Chenxia Ge ◽

...

Keyword(s):

Skeletal Muscle ◽

Growth And Development ◽

Molecular Mechanisms ◽

Muscle Development ◽

Sika Deer ◽

De Novo ◽

Expression Profiles ◽

Differentially Expressed ◽

Growth Development ◽

Development And Aging

Studies of the gene and miRNA expression profiles associated with the postnatal late growth, development, and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA sequencing (RNA-seq) and microRNA sequencing (miRNA-seq) analyses to determine the differentially expressed (DE) unigenes and miRNAs from skeletal muscle tissues at 1, 3, 5, and 10 years in sika deer. A total of 51,716 unigenes, 171 known miRNAs, and 60 novel miRNAs were identified based on four mRNA and small RNA libraries. A total of 2,044 unigenes and 11 miRNAs were differentially expressed between adolescence and juvenile sika deer, 1,946 unigenes and 4 miRNAs were differentially expressed between adult and adolescent sika deer, and 2,209 unigenes and 1 miRNAs were differentially expressed between aged and adult sika deer. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that DE unigenes and miRNA were mainly related to energy and substance metabolism, processes that are closely associate with the growth, development, and aging of skeletal muscle. We also constructed mRNA–mRNA and miRNA–mRNA interaction networks related to the growth, development, and aging of skeletal muscle. The results show that mRNA (Myh1, Myh2, Myh7, ACTN3, etc.) and miRNAs (miR-133a, miR-133c, miR-192, miR-151-3p, etc.) may play important roles in muscle growth and development, and mRNA (WWP1, DEK, UCP3, FUS, etc.) and miRNAs (miR-17-5p, miR-378b, miR-199a-5p, miR-7, etc.) may have key roles in muscle aging. In this study, we determined the dynamic miRNA and unigenes transcriptome in muscle tissue for the first time in sika deer. The age-dependent miRNAs and unigenes identified will offer insights into the molecular mechanism underlying muscle development, growth, and maintenance and will also provide valuable information for sika deer genetic breeding.

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Comparative phosphoproteomic analysis of blast resistant and susceptible rice cultivars in response to salicylic acid

BMC Plant Biology ◽

10.1186/s12870-019-2075-5 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Ranran Sun ◽

Shiwen Qin ◽

Tong Zhang ◽

Zhenzhong Wang ◽

Huaping Li ◽

...

Keyword(s):

Salicylic Acid ◽

Molecular Mechanisms ◽

Defense Responses ◽

Differentially Expressed ◽

Phosphoglycerate Mutase ◽

Regulatory Function ◽

Rice Cultivars ◽

Resistance Response ◽

Basal Resistance ◽

Pathogen Invasion

Abstract Background Salicylic acid (SA) is a significant signaling molecule that induces rice resistance against pathogen invasion. Protein phosphorylation carries out an important regulatory function in plant defense responses, while the global phosphoproteome changes in rice response to SA-mediated defense response has not been reported. In this study, a comparative phosphoproteomic profiling was conducted by two-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS) analysis, with two near-isogenic rice cultivars after SA treatment. Results Thirty-seven phosphoprotein spots were differentially expressed after SA treatment, twenty-nine of which were identified by MALDI-TOF/TOF MS, belonging to nine functional categories. Phosphoproteins involved in photosynthesis, antioxidative enzymes, molecular chaperones were similarly expressed in the two cultivars, suggesting SA might alleviate decreases in plant photosynthesis, regulate the antioxidant defense activities, thus improving basal resistance response in both cultivars. Meanwhile, phosphoproteins related to defense, carbohydrate metabolism, protein synthesis and degradation were differentially expressed, suggesting phosphorylation regulation mediated by SA may coordinate complex cellular activities in the two cultivars. Furthermore, the phosphorylation sites of four identified phosphoproteins were verified by NanoLC-MS/MS, and phosphorylated regulation of three enzymes (cinnamoyl-CoA reductase, phosphoglycerate mutase and ascorbate peroxidase) was validated by activity determination. Conclusions Our study suggested that phosphorylation regulation mediated by SA may contribute to the different resistance response of the two cultivars. To our knowledge, this is the first report to measure rice phosphoproteomic changes in response to SA, which provides new insights into molecular mechanisms of SA-induced rice defense.

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Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages

Journal of Insect Science ◽

10.1093/jisesa/iew053 ◽

2016 ◽

Vol 16 (1) ◽

Cited By ~ 7

Author(s):

Juan Ma ◽

Rongyan Wang ◽

Xiuhua Li ◽

Bo Gao ◽

Shulong Chen

Keyword(s):

Sweet Potato ◽

Molecular Mechanisms ◽

Developmental Stages ◽

De Novo ◽

Average Length ◽

Expression Profiles ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Cylas Formicarius ◽

Important Pest

Abstract The sweet potato weevil, Cylas formicarius (F.) (Coleoptera: Brentidae), is an important pest of sweet potato worldwide. However, there is limited knowledge on the molecular mechanisms underlying growth and differentiation of C. formicarius. The transcriptomes of the eggs, second instar larvae, third instar larvae (L3), pupae, females, and males of C. formicarius were sequenced using Illumina sequencing technology for obtaining global insights into developing transcriptome characteristics and elucidating the relative functional genes. A total of 54,255,544 high-quality reads were produced, trimmed, and de novo assembled into 115,281 contigs. 61,686 unigenes were obtained, with an average length of 1,009 nt. Among these unigenes, 17,348 were annotated into 59 Gene Ontology (GO) terms and 12,660 were assigned to 25 Cluster of Orthologous Groups classes, whereas 24,796 unigenes were mapped to 258 pathways. Differentially expressed unigenes between various developmental stages of C. formicarius were detected. Higher numbers of differentially expressed genes (DEGs) were recorded in the eggs versus L3 and eggs versus male samples (2,141 and 2,058 unigenes, respectively) than the others. Genes preferentially expressed in each stage were also identified. GO and pathway-based enrichment analysis were used to further investigate the functions of the DEGs. In addition, the expression profiles of ten DEGs were validated by quantitative real-time PCR. The transcriptome profiles presented in this study and these DEGs detected by comparative analysis of different developed stages of C. formicarius will facilitate the understanding of the molecular mechanism of various living process and will contribute to further genome-wide research.

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Transcriptome analysis reveals ethylene-mediated defense responses to Fusarium oxysporum f. sp. cucumerinum infection in Cucumis sativus

10.21203/rs.2.21765/v1 ◽

2020 ◽

Author(s):

Jingping Dong ◽

Yuean Wang ◽

Qianqian Xian ◽

Xuehao Chen ◽

Jun Xu

Keyword(s):

Fusarium Oxysporum ◽

Cucumis Sativus ◽

Fusarium Wilt ◽

Defense Mechanisms ◽

Molecular Mechanisms ◽

Severe Disease ◽

Defense Responses ◽

Differentially Expressed ◽

Pcr Analysis ◽

Positive Role

Abstract Background: Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum (Foc), is a severe disease affecting cucumber (Cucumis sativus L.) production worldwide, but the molecular mechanisms underlying Fusarium wilt resistance in cucumber remain unknown. To gain an improved understanding of the defense mechanisms elicited in response to Foc inoculation, RNA sequencing-based transcriptomic profiling of responses of the Fusarium wilt-resistant cucumber line ‘Rijiecheng’ at 0, 24, 48, 96, and 192 h after Foc inoculation was performed.Results: We identified 4116 genes that were differentially expressed between 0 h and other time points after inoculation. All ethylene-related and pathogenesis-related genes from among the differentially expressed genes were filtered out. Real-time PCR analysis showed that ethylene-related genes were induced in response to Foc infection. Importantly, after Foc infection and exogenous application of ethephon, a donor of ethylene, these genes were highly expressed. In response to exogenous ethephon treatment in conjunction with Foc inoculation, the infection resistance of cucumber seedlings was enhanced and endogenous ethylene biosynthesis increased dramatically. Conclusion: Collectively, ethylene signaling pathways play a positive role in regulating the defense response of cucumber to Foc infection. The results provide insight into the cucumber Fusarium wilt defense mechanisms and provide valuable information for breeding new cucumber cultivars with enhanced Fusarium wilt tolerance.

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Identification and Molecular Mechanisms of Key Nucleotides Causing Attenuation in Pathogenicity of Dahlia Isolate of Potato Spindle Tuber Viroid

International Journal of Molecular Sciences ◽

10.3390/ijms21197352 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7352

Author(s):

Shoya Kitabayashi ◽

Daiki Tsushima ◽

Charith Raj Adkar-Purushothama ◽

Teruo Sano

Keyword(s):

Symptom Severity ◽

Molecular Mechanisms ◽

Infected Plant ◽

Potato Spindle Tuber Viroid ◽

Defense Responses ◽

Tomato Cultivar ◽

Qpcr Analysis ◽

Pathogenesis Related Protein ◽

Pathogenesis Related ◽

Chalcone Synthase Genes

While the potato spindle tuber viroid (PSTVd) variant, PSTVd-Dahlia (PSTVd-D or PSTVd-Dwt) induces very mild symptoms in tomato cultivar ‘Rutgers’, PSTVd-Intermediate (PSTVd-I or PSTVd-Iwt) induces severe symptoms. These two variants differ by nine nucleotides, of which six mutations are located in the terminal left (TL) to the pathogenicity (P) domains. To evaluate the importance of mutations located in the TL to the P domains, ten types of point mutants were created by swapping the nucleotides between the two viroid variants. Bioassay in tomato plants demonstrated that two mutants created on PSTVd-Iwt at positions 42 and 64 resulted in symptom attenuation. Phenotypic and RT-qPCR analysis revealed that mutation at position 42 of PSTVd-Iwt significantly reduced disease severity and accumulation of the viroid, whereas mutation at position 64 showed a significant reduction in stunting when compared to the PSTVd-Iwt infected plant. RT-qPCR analysis on pathogenesis-related protein 1b1 and chalcone synthase genes showed a direct correlation with symptom severity whereas the expansin genes were down-regulated irrespective of the symptom severity. These results indicate that the nucleotides at positions 42 and 64 are in concert with the ones at positions 43, 310, and 311/312, which determines the slower and stable accumulation of PSTVd-D without eliciting excessive host defense responses thus contributing in the attenuation of disease symptom.

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Transcriptomic Analysis Identifies New Non-Target Site Glyphosate-Resistance Genes in Conyza bonariensis

Plants ◽

10.3390/plants8060157 ◽

2019 ◽

Vol 8 (6) ◽

pp. 157 ◽

Cited By ~ 7

Author(s):

Cristiano Piasecki ◽

Yongil Yang ◽

Daiane P. Benemann ◽

Frederico S. Kremer ◽

Vanessa Galli ◽

...

Keyword(s):

Molecular Mechanisms ◽

Target Genes ◽

De Novo ◽

Average Length ◽

Transcriptome Assembly ◽

Glyphosate Resistance ◽

Target Site ◽

Differentially Expressed ◽

Irreversible Damage ◽

Conyza Bonariensis

Conyza bonariensis (hairy fleabane) is one of the most problematic and widespread glyphosate-resistant weeds in the world. This highly competitive weed species significantly interferes with crop growth and substantially decreases crop yield. Despite its agricultural importance, the molecular mechanisms of glyphosate resistance are still unknown. The present RNA-Seq study was performed with the goal of identifying differentially expressed candidate transcripts (genes) related to metabolism-based non-target site glyphosate resistance in C. bonariensis. The whole-transcriptome was de novo assembled from glyphosate-resistant and -sensitive biotypes of C. bonariensis from Southern Brazil. The RNA was extracted from untreated and glyphosate-treated plants at several timepoints up to 288 h after treatment in both biotypes. The transcriptome assembly produced 90,124 contigs with an average length of 777 bp and N50 of 1118 bp. In response to glyphosate treatment, differential gene expression analysis was performed on glyphosate-resistant and -sensitive biotypes. A total of 9622 genes were differentially expressed as a response to glyphosate treatment in both biotypes, 4297 (44.6%) being up- and 5325 (55.4%) down-regulated. The resistant biotype presented 1770 up- and 2333 down-regulated genes while the sensitive biotype had 2335 and 2800 up- and down-regulated genes, respectively. Among them, 974 up- and 1290 down-regulated genes were co-expressed in both biotypes. In the present work, we identified 41 new candidate target genes from five families related to herbicide transport and metabolism: 19 ABC transporters, 10 CYP450s, one glutathione S-transferase (GST), five glycosyltransferases (GT), and six genes related to antioxidant enzyme catalase (CAT), peroxidase (POD), and superoxide dismutase (SOD). The candidate genes may participate in metabolic-based glyphosate resistance via oxidation, conjugation, transport, and degradation, plus antioxidation. One or more of these genes might ‘rescue’ resistant plants from irreversible damage after glyphosate treatment. The 41 target genes we report in the present study may inform further functional genomics studies, including gene editing approaches to elucidate glyphosate-resistance mechanisms in C. bonariensis.

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Transcriptional profiling reveals conserved and species-specific plant defense responses during the interaction of the early divergent plant Physcomitrium patens with Botrytis cinerea

10.1101/2020.10.29.361329 ◽

2020 ◽

Author(s):

Guillermo Reboledo ◽

Astrid Agorio ◽

Lucía Vignale ◽

Ramón Alberto Batista-García ◽

Inés Ponce De León

Keyword(s):

Immune Response ◽

Botrytis Cinerea ◽

Defense Mechanisms ◽

Molecular Mechanisms ◽

Defense Responses ◽

Land Plants ◽

Differentially Expressed ◽

Microbial Pathogens ◽

Limited Information ◽

Pathogen Invasion

AbstractBryophytes were among the first plants that colonized earth and they evolved key defense mechanisms to counteract microbial pathogens present in the new environment. Although great advances have been made on pathogen perception and subsequent defense activation in angiosperms, limited information is available in early divergent land plants. In this study, a transcriptomic approach uncovered the molecular mechanisms underlying the defense response of the bryophyte Physcomitrium patens against the important plant pathogen Botrytis cinerea. A total of 3.072 differentially expressed genes were significantly affected during B. cinerea infection, including genes encoding proteins with known function in angiosperm immunity and involved in pathogen perception, signaling, transcription, hormonal signaling, metabolic pathways such as shikimate and phenylpropanoid, and proteins with diverse role in defense against biotic stress. Similarly as in other plants, B. cinerea infection leads to downregulation of genes involved in photosynthesis and cell cycle progression. These results highlight the existence of evolutionary conserved defense responses to pathogens throughout the green plant lineage, suggesting that they were probably present in the common ancestors of land plants. Moreover, several genes acquired by horizontal transfer from prokaryotes and fungi, and a high number of P. patens-specific orphan genes were differentially expressed during B. cinerea infection, indicating that they are part of the moss immune response and probably played an ancestral role related to effective adaptation mechanisms to cope with pathogen invasion during the conquest of land.Key MessageEvolutionary conserved defense mechanisms present in extant bryophytes and angiosperms, as well as moss-specific defenses are part of the immune response of the early divergent land plant Physcomitrium patens.

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Comparative Transcriptome Analysis Identified Differentially Expressed Genes between Male and Female Flowers of Zanthoxylum armatum var. novemfolius

Agronomy ◽

10.3390/agronomy10020283 ◽

2020 ◽

Vol 10 (2) ◽

pp. 283 ◽

Cited By ~ 2

Author(s):

Xian Zhang ◽

Ning Tang ◽

Xiaomeng Liu ◽

Jiabao Ye ◽

Jingyi Zhang ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Flower Development ◽

Molecular Mechanisms ◽

De Novo ◽

Transcriptome Assembly ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Zanthoxylum Armatum ◽

Medicinal Value ◽

Male Flowers

As a traditional spicy condiment, Zanthoxylum armatum var. novemfolius is of high economical and medicinal value. Despite the long history of human cultivation, the molecular mechanisms underlying flower development are still poorly understood in Z. armatum. In this study, we performed de novo transcriptome assembly and comparative analysis of female and male flowers in Z. armatum. A total of 94,771 unigenes were obtained, and 50,605 unigenes were successfully annotated against the public database. Transcriptome data showed that 20,431 annotated unigenes were differentially expressed genes. KEGG enrichment analysis revealed that the most representative pathway was plant hormone signal transduction. Among them, 41, 16, 41, 27, 95, and 40 unigenes were involved in the biosynthesis and signaling of abscisic acid, ethylene, cytokinin, gibberellin, auxin, and jasmonic acid, respectively. Transcription factors also played crucial roles in flower development, such as AGL11, PMADS2, and NAC. These results provided an important basis for characterizing the potential mechanism of flower development and enriching the knowledge of reproduction genetics in Z. armatum.

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Stress-Activated Protein Kinase OsSAPK9 Regulates Tolerance to Salt Stress and Resistance to Bacterial Blight in Rice

Rice ◽

10.1186/s12284-019-0338-2 ◽

2019 ◽

Vol 12 (1) ◽

Author(s):

Fan Zhang ◽

Dan Zeng ◽

Liyu Huang ◽

Yingyao Shi ◽

Tengjun Chen ◽

...

Keyword(s):

Salt Stress ◽

Disease Resistance ◽

Protein Kinase ◽

Stress Responses ◽

Bacterial Blight ◽

Molecular Mechanisms ◽

Defense Responses ◽

Stress Conditions ◽

Differentially Expressed ◽

Limiting Factors

Abstract Background Salt stress and bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) are key limiting factors of rice (Oryza sativa L.) yields. Members of sucrose non-fermenting 1 (SNF1)-related protein kinase 2 (SnRK2), which is a family of plant-specific Ser/Thr kinases, are important components of signaling pathways involved in plant developmental processes and responses to stresses. There are 10 members of the SnRK2 family in rice; however, their functions are poorly understood, as are the underlying molecular mechanisms. Results In this study, we found that OsSAPK9, which belongs to the SnRK2 family, positively regulated salt-stress tolerance and strain-specific resistance to bacterial blight in rice. RNA sequencing revealed that there were 404 and 1324 genes differentially expressed in OsSAPK9-RNAi in comparison with wild-type plants under salt-stress conditions and after Xoo inoculation, respectively, which participate in basic metabolic processes. In total, 65 common differentially expressed genes involved mainly in defense responses were detected both under salt-stress conditions and after Xoo inoculation. Moreover, in vivo and in vitro experiments demonstrated that OsSAPK9 forms a protein complex with the molecular chaperones OsSGT1 and OsHsp90, and transgenic plants overexpressing OsSGT1 exhibited decreased tolerances to salt stress and significantly increased resistance levels to bacterial blight. Thus, OsSAPK9 may function as a center node regulator of salt-stress responses and disease-resistance pathways through its interaction with OsSGT1 in rice. Conclusion This study confirms that OsSAPK9 functions as a positive regulator of salt-stress responses and disease resistance through its interaction with OsSGT1 in rice.

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De novo Comparative Transcriptome Analysis of Genes Differentially Expressed in the Scion of Homografted and Heterografted Tomato Seedlings

Scientific Reports ◽

10.1038/s41598-019-56563-z ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 6

Author(s):

Hui Wang ◽

Peng Zhou ◽

Wenying Zhu ◽

Fu Wang

Keyword(s):

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

De Novo ◽

Healing Process ◽

Differentially Expressed ◽

Mitogen Activated Protein Kinase ◽

Graft Union ◽

Tomato Production ◽

Tomato Seedlings ◽

Hormone Signalling

AbstractTomato is an important vegetable crop grown worldwide. Grafting is an agricultural technique that is used to improve growth, yield, and resistance to diverse stresses in tomato production. Here, we examined the differences between the scion of heterografted (‘Provence’/‘Haomei’) and homografted (‘Provence’/‘Provence’) tomato seedlings. We observed anatomical changes during the graft-union healing process in heterografted and homografted tomato seedlings and conducted transcriptome analyses of the ‘Provence’ scion from both graft combinations. With the development of calli from both graft partners, the isolation layer became thinner at 16 d after grafting (DAG). Compared with that of homografts, the healing in heterografts was slightly delayed, but the graft union had completely healed at 21 DAG. In total, 858 significantly differentially expressed genes were detected between the transcriptomes of heterografts and homografts at 16 DAG. Functional pathways identified by GO and KEGG enrichment analyses were associated with primary and secondary metabolism, hormone signalling, transcription factor regulation, transport, and responses to stimuli. Many differentially expressed genes were involved in pathways associated with mitogen-activated protein kinase signalling, plant hormone signalling, and oxidative stress. A number of transcription factors were up-regulated in the scion of heterografted seedlings. The results provide a valuable resource for the elucidation of the molecular mechanisms, and candidate genes for functional analyses, of heterograft and homograft systems.

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