scholarly journals Comparative Transcriptome Profiling of Resistant and Susceptible Sugarcane Cultivars in Response to Infection by Xanthomonas albilineans

2019 ◽  
Vol 20 (24) ◽  
pp. 6138 ◽  
Author(s):  
Mbuya Sylvain Ntambo ◽  
Jian-Yu Meng ◽  
Philippe C. Rott ◽  
Robert J. Henry ◽  
Hui-Li Zhang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Molecular Mechanisms ◽  
Plant Hormone ◽  
Glutathione Metabolism ◽  
Bacterial Disease ◽  
Post Inoculation ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Leaf Scald ◽  
Xanthomonas Albilineans

Sugarcane (Saccharum spp. hybrids) is a major source of sugar and renewable bioenergy crop worldwide and suffers serious yield losses due to many pathogen infections. Leaf scald caused by Xanthomonas albilineans is a major bacterial disease of sugarcane in most sugarcane-planting countries. The molecular mechanisms of resistance to leaf scald in this plant are, however, still unclear. We performed a comparative transcriptome analysis between resistant (LCP 85-384) and susceptible (ROC20) sugarcane cultivars infected by X. albilineans using the RNA-seq platform. 24 cDNA libraries were generated with RNA isolated at four time points (0, 24, 48, and 72 h post inoculation) from the two cultivars with three biological replicates. A total of 105,783 differentially expressed genes (DEGs) were identified in both cultivars and the most upregulated and downregulated DEGs were annotated for the processes of the metabolic and single-organism categories, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the 7612 DEGs showed that plant–pathogen interaction, spliceosome, glutathione metabolism, protein processing in endoplasmic reticulum, and plant hormone signal transduction contributed to sugarcane’s response to X. albilineans infection. Subsequently, relative expression levels of ten DEGs determined by quantitative reverse transcription-PCR (qRT-PCR), in addition to RNA-Seq data, indicated that different plant hormone (auxin and ethylene) signal transduction pathways play essential roles in sugarcane infected by X. albilineans. In conclusion, our results provide, for the first time, valuable information regarding the transcriptome changes in sugarcane in response to infection by X. albilineans, which contribute to the understanding of the molecular mechanisms underlying the interactions between sugarcane and this pathogen and provide important clues for further characterization of leaf scald resistance in sugarcane.

scholarly journals Comparative Transcriptome Analysis of Early- and Late-Bolting Traits in Chinese Cabbage (Brassica rapa)

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiaochun Wei ◽  
Md. Abdur Rahim ◽  
Yanyan Zhao ◽  
Shuangjuan Yang ◽  
Zhiyong Wang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Molecular Mechanisms ◽  
Plant Hormone ◽  
Transcriptome Profiling ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Heading Chinese Cabbage ◽  
Dh Lines

Chinese cabbage is one of the most important and widely consumed vegetables in China. The developmental transition from the vegetative to reproductive phase is a crucial process in the life cycle of flowering plants. In spring-sown Chinese cabbage, late bolting is desirable over early bolting. In this study, we analyzed double haploid (DH) lines of late bolting (“Y410-1” and “SY2004”) heading Chinese cabbage (Brassica rapa var. pekinensis) and early-bolting Chinese cabbage (“CX14-1”) (B. rapa ssp. chinensis var. parachinensis) by comparative transcriptome profiling using the Illumina RNA-seq platform. We assembled 721.49 million clean high-quality paired-end reads into 47,363 transcripts and 47,363 genes, including 3,144 novel unigenes. There were 12,932, 4,732, and 4,732 differentially expressed genes (DEGs) in pairwise comparisons of Y410-1 vs. CX14-1, SY2004 vs. CX14-1, and Y410-1 vs. SY2004, respectively. The RNA-seq results were confirmed by reverse transcription quantitative real-time PCR (RT-qPCR). A Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of DEGs revealed significant enrichment for plant hormone and signal transduction as well as starch and sucrose metabolism pathways. Among DEGs related to plant hormone and signal transduction, six unigenes encoding the indole-3-acetic acid-induced protein ARG7 (BraA02g009130), auxin-responsive protein SAUR41 (BraA09g058230), serine/threonine-protein kinase BSK11 (BraA07g032960), auxin-induced protein 15A (BraA10g019860), and abscisic acid receptor PYR1 (BraA08g012630 and BraA01g009450), were upregulated in both late bolting Chinese cabbage lines (Y410-1 and SY2004) and were identified as putative candidates for the trait. These results improve our understanding of the molecular mechanisms underlying flowering in Chinese cabbage and provide a foundation for studies of this key trait in related species.

scholarly journals Identification of Differentially Expressed Proteins in Sugarcane in Response to Infection by Xanthomonas albilineans Using iTRAQ Quantitative Proteomics

2020 ◽  
Vol 8 (1) ◽  
pp. 76
Author(s):  
Jian-Yu Meng ◽  
Mbuya Sylvain Ntambo ◽  
Philippe C. Rott ◽  
Hua-Ying Fu ◽  
Mei-Ting Huang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Vascular System ◽  
Lipid Transfer Protein ◽  
Differentially Expressed ◽  
Post Inoculation ◽  
Differentially Expressed Proteins ◽  
Lipid Transfer ◽  
Leaf Scald ◽  
Improvement Programs ◽  
Xanthomonas Albilineans

Sugarcane can suffer severe yield losses when affected by leaf scald, a disease caused by Xanthomonas albilineans. This bacterial pathogen colonizes the vascular system of sugarcane, which can result in reduced plant growth and plant death. In order to better understand the molecular mechanisms involved in the resistance of sugarcane to leaf scald, a comparative proteomic study was performed with two sugarcane cultivars inoculated with X. albilineans: one resistant (LCP 85-384) and one susceptible (ROC20) to leaf scald. The iTRAQ (isobaric tags for relative and absolute quantification) approach at 0 and 48 h post-inoculation (hpi) was used to identify and annotate differentially expressed proteins (DEPs). A total of 4295 proteins were associated with 1099 gene ontology (GO) terms by GO analysis. Among those, 285 were DEPs during X. albilineans infection in cultivars LCP 85-384 and ROC20. One hundred seventy-two DEPs were identified in resistant cultivar LCP 85-384, and 113 of these proteins were upregulated and 59 were downregulated. One hundred ninety-two DEPs were found in susceptible cultivar ROC20 and half of these (92) were upregulated, whereas the other half corresponded to downregulated proteins. The significantly upregulated DEPs in LCP 85-384 were involved in metabolic pathways, the biosynthesis of secondary metabolites, and the phenylpropanoid biosynthesis pathway. Additionally, the expression of seven candidate genes related to photosynthesis and glycolytic pathways, plant innate immune system, glycosylation process, plant cytochrome P450, and non-specific lipid transfer protein was verified based on transcription levels in sugarcane during infection by X. albilineans. Our findings shed new light on the differential expression of proteins in sugarcane cultivars in response to infection by X. albilineans. The identification of these genes provides important information for sugarcane variety improvement programs using molecular breeding strategies.

scholarly journals Global Gene Responses of Resistant and Susceptible Sugarcane Cultivars to Acidovorax avenae subsp. avenae Identified Using Comparative Transcriptome Analysis

2019 ◽  
Vol 8 (1) ◽  
pp. 10 ◽  
Author(s):  
Na Chu ◽  
Jing-Ru Zhou ◽  
Hua-Ying Fu ◽  
Mei-Ting Huang ◽  
Hui-Li Zhang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Defense Responses ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Post Inoculation ◽  
Rna Seq ◽  
Mitogen Activated Protein

Red stripe disease in sugarcane caused by Acidovorax avenae subsp. avenae (Aaa) is related to serious global losses in yield. However, the underlying molecular mechanisms associated with responses of sugarcane plants to infection by this pathogen remain largely unknown. Here, we used Illumina RNA-sequencing (RNA-seq) to perform large-scale transcriptome sequencing of two sugarcane cultivars to contrast gene expression patterns of plants between Aaa and mock inoculations, and identify key genes and pathways involved in sugarcane defense responses to Aaa infection. At 0–72 hours post-inoculation (hpi) of the red stripe disease-resistant cultivar ROC22, a total of 18,689 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples. Of these, 8498 and 10,196 genes were up- and downregulated, respectively. In MT11-610, which is susceptible to red stripe disease, 15,782 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples and 8807 and 6984 genes were up- and downregulated, respectively. The genes that were differentially expressed following Aaa inoculation were mainly involved in photosynthesis and carbon metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and plant–pathogen interaction pathways. Further, qRT-PCR and RNA-seq used for additional validation of 12 differentially expressed genes (DEGs) showed that eight genes in particular were highly expressed in ROC22. These eight genes participated in the biosynthesis of lignin and coumarin, as well as signal transduction by salicylic acid, jasmonic acid, ethylene, and mitogen-activated protein kinase (MAPK), suggesting that they play essential roles in sugarcane resistance to Aaa. Collectively, our results characterized the sugarcane transcriptome during early infection with Aaa, thereby providing insights into the molecular mechanisms responsible for bacterial tolerance.

scholarly journals Transcriptome Analysis Reveals Key Seed-Development Genes in Common Buckwheat (Fagopyrum esculentum)

2019 ◽  
Vol 20 (17) ◽  
pp. 4303 ◽  
Author(s):  
Hongyou Li ◽  
Qiuyu Lv ◽  
Jiao Deng ◽  
Juan Huang ◽  
Fang Cai ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Seed Development ◽  
Seed Size ◽  
Molecular Mechanisms ◽  
Signal Transduction Pathway ◽  
Fagopyrum Esculentum ◽  
Rna Seq ◽  
Common Buckwheat ◽  
Size Change ◽  
Key Genes

Seed development is an essential and complex process, which is involved in seed size change and various nutrients accumulation, and determines crop yield and quality. Common buckwheat (Fagopyrum esculentum Moench) is a widely cultivated minor crop with excellent economic and nutritional value in temperate zones. However, little is known about the molecular mechanisms of seed development in common buckwheat (Fagopyrum esculentum). In this study, we performed RNA-Seq to investigate the transcriptional dynamics and identify the key genes involved in common buckwheat seed development at three different developmental stages. A total of 4619 differentially expressed genes (DEGs) were identified. Based on the results of Gene Ontology (GO) and KEGG analysis of DEGs, many key genes involved in the seed development, including the Ca2+ signal transduction pathway, the hormone signal transduction pathways, transcription factors (TFs), and starch biosynthesis-related genes, were identified. More importantly, 18 DEGs were identified as the key candidate genes for seed size through homologous query using the known seed size-related genes from different seed plants. Furthermore, 15 DEGs from these identified as the key genes of seed development were selected to confirm the validity of the data by using quantitative real-time PCR (qRT-PCR), and the results show high consistency with the RNA-Seq results. Taken together, our results revealed the underlying molecular mechanisms of common buckwheat seed development and could provide valuable information for further studies, especially for common buckwheat seed improvement.

Comparative transcriptome profiling in human bicuspid aortic valve disease using RNA sequencing

2015 ◽  
Vol 47 (3) ◽  
pp. 75-87 ◽  
Author(s):  
Ratnasari Padang ◽  
Richard D. Bagnall ◽  
Tatiana Tsoutsman ◽  
Paul G. Bannon ◽  
Christopher Semsarian
Keyword(s):  
Aortic Valve ◽  
Rna Sequencing ◽  
Bicuspid Aortic Valve ◽  
Molecular Mechanisms ◽  
Transcriptome Profiling ◽  
Common Complication ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Calcific Aortic Stenosis ◽  
Phenotype Heterogeneity

Intrinsic valvular degeneration and dysfunction is the most common complication of bicuspid aortic valve (BAV) disease. Phenotypically, it ranges from calcific aortic stenosis to redundant or prolapsing regurgitant leaflets. The underlying molecular mechanism underpinning phenotype heterogeneity of valvular degeneration in BAV is poorly understood. We used RNA sequencing (RNA-seq) to identify genes and pathways responsible for the development of valvular degeneration in BAV, compared with tricuspid aortic valve (TAV). Comparative transcriptome analysis was performed on total RNA of aortic valve tissues of patients with diseased BAV ( n = 5) and calcified TAV ( n = 3). RNA-seq findings were validated by RT-qPCR. A total of 59 and 177 genes were significantly up- and downregulated, respectively, in BAV compared with TAV. Hierarchical clustering indicated heterogeneity within the BAV group, separating those with heavy calcification (BAVc) from those with redundant leaflets and/or minimal calcification (BAVr). Interestingly, the gene expression profile of the BAVc group closely resembled the TAV, with shared up- and downregulation of inflammatory and NOTCH1 signaling pathways, respectively. Downregulation of matrix protease ADAMTS9 and protein aggrecan were observed in BAVr compared with TAV. Dysregulation of fetal gene programs were also present, with notable downregulation of SEMA6B and SEMA3F in BAVr and BAVc compared with TAV, respectively. Upregulation of TBX20 was observed exclusively in BAVr compared with BAVc. In conclusion, diverging molecular mechanisms underpin phenotype heterogeneity of valvular degeneration in BAV and data from the present study suggest that there may be shared mechanisms leading to calcification in BAV and TAV. Recognition of these pathways is fundamental to improve our understanding of the molecular basis of human BAV disease.

Molecular detection and quantification of Xanthomonas albilineans in juice from symptomless sugarcane stalks using a real-time quantitative PCR assay

Plant Disease ◽  
2021 ◽  
Author(s):  
Yang Shi ◽  
Jian-Ying Zhao ◽  
Jing-Ru Zhou ◽  
Mbuya Sylvain Ntambo ◽  
Peng-Yuan Xu ◽  
...  
Keyword(s):  
Qpcr Assay ◽  
Taqman Probe ◽  
Bacterial Suspension ◽  
Bacterial Disease ◽  
Conventional Pcr ◽  
Pcr Assay ◽  
Leaf Scald ◽  
Sugarcane Production ◽  
Xanthomonas Albilineans ◽  
Detection And Quantification

Leaf scald, a bacterial disease caused by Xanthomonas albilineans (Ashby) Dowson, is a major limiting factor for sugarcane production worldwide. Accurate identification and quantification of X. albilineans is a prerequisite for successful management of this disease. A very sensitive and robust qPCR assay was developed in this study for detection and quantification of X. albilineans using TaqMan probe and primers targeting a putative adenosine triphosphate-binding cassette (ABC) transporter gene (abc). The novel qPCR assay was highly specific to the 43 tested X. albilineans strains belonging to different pulsed-field gel electrophoresis (PFGE) groups. The detection thresholds were 100 copies/µL of plasmid DNA, 100 fg/µL of bacterial genomic DNA, and 100 CFU/ml of bacterial suspension prepared from pure culture. This qPCR assay was 100 times more sensitive than a conventional PCR assay. The pathogen was detected by qPCR in 75.1% (410/546) symptomless stalk samples, whereas only 28.4% (155/546) samples tested positive by conventional PCR. Based on qPCR data, population densities of X. albilineans in symptomless stalks of the same varieties differed between two sugarcane production areas in China, Beihai (Guangxi province) and Zhanjiang (Guangdong province), and no significant correlation between these populations was identified. Furthermore, no relationship was found between these populations of the pathogen in asymptomatic stalks and the resistance level of the sugarcane varieties to leaf scald. The newly developed qPCR assay proved to be highly sensitive and reliable for the detection and quantification of X. albilineans in sugarcane stalks.

scholarly journals Comparative transcriptome analyses of adzuki bean weevil (Callosobruchus chinensis) response to hypoxia and hypoxia/hypercapnia

2018 ◽  
Vol 109 (2) ◽  
pp. 266-277 ◽  
Author(s):  
S.F. Cui ◽  
L. Wang ◽  
L. Ma ◽  
Y.L. Wang ◽  
J.P. Qiu ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Immune System ◽  
Underlying Mechanism ◽  
Genomic Research ◽  
Callosobruchus Chinensis ◽  
Adzuki Bean ◽  
Comparative Transcriptome ◽  
Rna Seq ◽  
Bean Weevil ◽  
Significant Difference

AbstractStored product insects show high adaption to hypoxia and hypercapnia, but the underlying mechanism is still unclear. Herein, a comparative transcriptome on 4th adzuki bean weevil (Callosobruchus chinensis) instar larvae was studied to clarify the response mechanisms to hypoxia (HA) and hypoxia/hypercapnia (HHA) using NextSeq500 RNA-Seq. Transcript profiling showed a significant difference in HA or HHA exposure both quantitatively and qualitatively. Compared with control, 631 and 253 genes were significantly changed in HHA and HA, respectively. Comparing HHA with HA, 1135 differentially expressed genes (DEGs) were identified. The addition of hypercapnia made a complex alteration on the hypoxia response of bean weevil transcriptome, carbohydrate, energy, lipid and amino acid metabolism were the most highly enriched pathways for genes significantly changed. In addition, some biological processes that were not significantly enriched but important were also discussed, such as immune system and signal transduction. Most of the DEGs related to metabolism both in HHA and HA were up-regulated, while the DEGs related to the immune system, stress response or signal transduction were significantly down-regulated or suppressed. This research reveals a comparatively full-scale result in adzuki bean weevil hypoxia and hypoxia/hypercapnia tolerance mechanism at transcription level, which might provide new insights into the genomic research of this species.

scholarly journals TMT-based quantitative proteomic analysis reveals defense mechanism of wheat against the crown rot pathogen Fusarium pseudograminearum

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Fangfang Qiao ◽  
Xiwen Yang ◽  
Fengdan Xu ◽  
Yuan Huang ◽  
Jiemei Zhang ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Defense Mechanism ◽  
Quantitative Polymerase Chain Reaction ◽  
Mapk Signaling ◽  
Crown Rot ◽  
Glutathione Metabolism ◽  
Post Inoculation ◽  
Root Tips ◽  
Fusarium Pseudograminearum

Abstract Background Fusarium crown rot is major disease in wheat. However, the wheat defense mechanisms against this disease remain poorly understood. Results Using tandem mass tag (TMT) quantitative proteomics, we evaluated a disease-susceptible (UC1110) and a disease-tolerant (PI610750) wheat cultivar inoculated with Fusarium pseudograminearum WZ-8A. The morphological and physiological results showed that the average root diameter and malondialdehyde content in the roots of PI610750 decreased 3 days post-inoculation (dpi), while the average number of root tips increased. Root vigor was significantly increased in both cultivars, indicating that the morphological, physiological, and biochemical responses of the roots to disease differed between the two cultivars. TMT analysis showed that 366 differentially expressed proteins (DEPs) were identified by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment in the two comparison groups, UC1110_3dpi/UC1110_0dpi (163) and PI610750_3dpi/PI610750_0dpi (203). It may be concluded that phenylpropanoid biosynthesis (8), secondary metabolite biosynthesis (12), linolenic acid metabolites (5), glutathione metabolism (8), plant hormone signal transduction (3), MAPK signaling pathway-plant (4), and photosynthesis (12) contributed to the defense mechanisms in wheat. Protein-protein interaction network analysis showed that the DEPs interacted in both sugar metabolism and photosynthesis pathways. Sixteen genes were validated by real-time quantitative polymerase chain reaction and were found to be consistent with the proteomics data. Conclusion The results provided insight into the molecular mechanisms of the interaction between wheat and F. pseudograminearum.

scholarly journals Comparative transcriptome analysis by Tilletia horrida infection in resistant and susceptible rice (Oryza sativa L.) male sterile lines reveals candidate genes and resistant mechanisms

2019 ◽  
Author(s):  
Aijun Wang ◽  
Desuo Yin ◽  
Xinyue Shu ◽  
Linxia Wang ◽  
Ping Li ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Unsaturated Fatty Acids ◽  
Oryza Sativa L ◽  
Resistance Breeding ◽  
Glutathione Metabolism ◽  
Comparative Transcriptome ◽  
Male Sterile ◽  
Comparative Transcriptome Analysis

Abstract Background Rice kernel smut (RKS), caused by the basidiomycete fungus Tilletia horrida , is one of the most devastating diseases affecting the production of male sterile lines of rice ( Oryza sativa ) worldwide. However, molecular mechanisms of resistance to T. horrida have not yet been explored.Results In the present study, analysis of the amount of T. horrida biomass in rice kernels and RNA sequencing (RNA-Seq) analysis of rice male sterile lines resistant and susceptible to RKS (Jiangcheng 3A and 9311A, respectively) were conducted after T. horrida infection. Transcriptomic analysis showed that 9, 840 and 7, 902 differentially expressed genes (DEGs) were observed in Jiangcheng3A and 9311A, respectively, after T. horrida inoculation, compared with the control. KEGG analyses of DEGs revealed that cutin, suberine and wax biosynthesis, flavonoid biosynthesis, glutathione metabolism, tyrosine metabolism, and biosynthesis of unsaturated fatty acids were enriched by T. horrida inoculation in Jiangcheng 3A; however, not significantly enriched in 9311A. Furthermore, the DEGs related to plant-pathogen interaction, plant hormone signal transduction, and transcriptional factor genes were identified in both rice male sterile lines.Conclusions This is the first comparative transcriptome analysis of two rice genotypes with different responses to T. horrida infection, revealing DEGs with potentially important roles in defense against T. horrida infection. Ours results will serve as a strong foundation for developing effective strategies for T. horrida -resistance breeding.

scholarly journals Key Cannabis Salt-Responsive Genes and Pathways Revealed by Comparative Transcriptome and Physiological Analyses of Contrasting Varieties

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2338
Author(s):  
Jiangjiang Zhang ◽  
Cuiping Zhang ◽  
Siqi Huang ◽  
Li Chang ◽  
Jianjun Li ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Salt Stress ◽  
Plant Hormone ◽  
Signal Transduction Pathway ◽  
Mapk Signaling ◽  
Molecular Networks ◽  
Molecular Response ◽  
Rna Seq ◽  
Physiological Diversity ◽  
Phenylpropanoid Biosynthesis

For the dissection and identification of the molecular response mechanisms to salt stress in cannabis, an experiment was conducted surveying the diversity of physiological characteristics. RNA-seq profiling was carried out to identify differential expression genes and pathway which respond to salt stress in different cannabis materials. The result of physiological diversity analyses showed that it is more sensitive to proline contents in K94 than in W20; 6 h was needed to reach the maximum in K94, compared to 12 h in W20. For profiling 0–72 h after treatment, a total of 10,149 differentially expressed genes were identified, and 249 genes exhibited significantly diverse expression levels in K94, which were clustered in plant hormone signal transduction and the MAPK signaling pathway. A total of 371 genes showed significant diversity expression variations in W20, which were clustered in the phenylpropanoid biosynthesis and plant hormone signal transduction pathway. The pathway enrichment by genes which were identified in K94 and W20 showed a similar trend to those clustered in plant hormone signal transduction pathways and MAPK signaling. Otherwise, there were 85 genes which identified overlaps between the two materials, indicating that these may be underlying genes related to salt stress in cannabis. The 86.67% agreement of the RNA-seq and qRT-PCR indicated the accuracy and reliability of the RNA-seq technique. Additionally, the result of physiological diversity was consistent with the predicted RNA-seq-based findings. This research may offer new insights into the molecular networks mediating cannabis to respond to salt stress.

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