scholarly journals Comprehensive transcriptome analysis of grafting onto Artemisia scoparia to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium)

2019 ◽  
Author(s):  
Xueying Zhang ◽  
Xianzhi Sun ◽  
Sheng Zhang ◽  
Fangfang Liu ◽  
Jinghui Yang ◽  
...  
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Enrichment Analysis ◽  
Chrysanthemum Morifolium ◽  
Aphid Infestation ◽  
A Genome ◽  
Artemisia Scoparia ◽  
Grafting Onto

Abstract Aphid stress drastically influences the yield and quality of chrysanthemum, and thus grafting has been widely used to improve tolerance to biotic and abiotic stresses. But how grafting affects chrysanthemum resistance to aphid the mechanism remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the selfrooted grafted chrysanthemum (Chrysanthemum morifolium Ramat. 'Hangbaiju') and the grafted Artermisia-chrysanthemum (grafting onto Artemisia scoparia) transcription response to aphid stress. The results showed that there were 1337 differently expressed genes (DEGs), among which 680 were up-regulated, and 667 were down-regulated in Cm/As in comparison to Cm/Cm. These genes were mainly involved in glycometabolism, biosynthesis of secondary metabolites, phytohormone signaling and plant-to-pathogen pathway, and so on. KEGG and GO enrichment analysis revealed the coordinated up-regulation of these genes from numerous functional categories related to aphid stress responses. In addition, we performed the determination of physiological indicators of chrysanthemum treated under aphid stress, and the results were basically consistent with molecular sequencing results. All evidence indicated that grafting onto Artemisia scoparia upregulated aphid stress responses in chrysanthemum. In summary, our study presents a genome-wide transcript profile of the selfrooted grafted chrysanthemum and the grafted Artermisia-chrysanthemum and provides insights into the molecular mechanisms of C.morifolium in response to aphid infestation. These data contributes to our deeper relevant researches on aphid tolerance and further exploring new candidate genes for chrysanthemum molecular breeding.

scholarly journals Comprehensive transcriptome analysis of grafting onto Artemisia scoparia  W. to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium T. )

2019 ◽  
Author(s):  
Xue-ying Zhang ◽  
Xian-zhi Sun ◽  
Sheng Zhang ◽  
Jing-hui Yang ◽  
Fang-fang Liu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Chrysanthemum Morifolium ◽  
The Self ◽  
Rna Seq ◽  
Aphid Infestation ◽  
A Genome ◽  
Artemisia Scoparia

Abstract Abstract Background: Aphid ( Macrosiphoniella sanbourni ) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the self-rooted grafted chrysanthemum ( Chrysanthemum morifolium T. 'Hangbaiju') and the grafted Artermisia-chrysanthemum (grafted onto Artemisia scoparia W.) transcription response to aphid stress. Results : The results showed that there were 1337 differentially expressed genes (DEGs), among which 680 were upregulated and 667 were downregulated, in the grafted Artemisia-chrysanthemum compared to the self-rooted grafted chrysanthemum. These genes were mainly involved in sucrose metabolism, the biosynthesis of secondary metabolites, the plant hormone signaling pathway and the plant-to-pathogen pathway. KEGG and GO enrichment analyses revealed the coordinated upregulation of these genes from numerous functional categories related to aphid stress responses. In addition, we determined the physiological indicators of chrysanthemum under aphid stress, and the results were consistent with the molecular sequencing results. All evidence indicated that grafting chrysanthemum onto A. scoparia W. upregulated aphid stress responses in chrysanthemum. Conclusion: In summary, our study presents a genome-wide transcript profile of the self-rooted grafted chrysanthemum and the grafted Artemisia-chrysanthemum and provides insights into the molecular mechanisms of C. morifolium T. in response to aphid infestation. These data will contribute to further studies of aphid tolerance and the exploration of new candidate genes for chrysanthemum molecular breeding. Key words : Chrysanthemum, Grafting, Aphid stress, Gene expression, RNA-Seq

scholarly journals Comprehensive transcriptome analysis of grafting onto Artemisia scoparia  W. to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium T. )

2019 ◽  
Author(s):  
Xue-ying Zhang ◽  
Xian-zhi Sun ◽  
Sheng Zhang ◽  
Jing-hui Yang ◽  
Fang-fang Liu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Chrysanthemum Morifolium ◽  
The Self ◽  
Rna Seq ◽  
Aphid Infestation ◽  
A Genome ◽  
Artemisia Scoparia

Abstract Abstract Background: Aphid ( Macrosiphoniella sanbourni ) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the self-rooted grafted chrysanthemum ( Chrysanthemum morifolium T. 'Hangbaiju') and the grafted Artermisia-chrysanthemum (grafted onto Artemisia scoparia W.) transcription response to aphid stress. Results : The results showed that there were 1337 differentially expressed genes (DEGs), among which 680 were upregulated and 667 were downregulated, in the grafted Artemisia-chrysanthemum compared to the self-rooted grafted chrysanthemum. These genes were mainly involved in sucrose metabolism, the biosynthesis of secondary metabolites, the plant hormone signaling pathway and the plant-to-pathogen pathway. KEGG and GO enrichment analyses revealed the coordinated upregulation of these genes from numerous functional categories related to aphid stress responses. In addition, we determined the physiological indicators of chrysanthemum under aphid stress, and the results were consistent with the molecular sequencing results. All evidence indicated that grafting chrysanthemum onto A. scoparia W. upregulated aphid stress responses in chrysanthemum. Conclusion: In summary, our study presents a genome-wide transcript profile of the self-rooted grafted chrysanthemum and the grafted Artemisia-chrysanthemum and provides insights into the molecular mechanisms of C. morifolium T. in response to aphid infestation. These data will contribute to further studies of aphid tolerance and the exploration of new candidate genes for chrysanthemum molecular breeding. Key words : Chrysanthemum, Grafting, Aphid stress, Gene expression, RNA-Seq

scholarly journals Comprehensive transcriptome analysis of grafting onto Artemisia scoparia W. to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium T.)

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Xue-ying Zhang ◽  
Xian-zhi Sun ◽  
Sheng Zhang ◽  
Jing-hui Yang ◽  
Fang-fang Liu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Chrysanthemum Morifolium ◽  
The Self ◽  
Aphid Infestation ◽  
Physiological Indicators ◽  
A Genome ◽  
Artemisia Scoparia

Abstract Background Aphid (Macrosiphoniella sanbourni) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the self-rooted grafted chrysanthemum (Chrysanthemum morifolium T. ‘Hangbaiju’) and the grafted Artermisia-chrysanthemum (grafted onto Artemisia scoparia W.) transcription response to aphid stress. Results The results showed that there were 1337 differentially expressed genes (DEGs), among which 680 were upregulated and 667 were downregulated, in the grafted Artemisia-chrysanthemum compared to the self-rooted grafted chrysanthemum. These genes were mainly involved in sucrose metabolism, the biosynthesis of secondary metabolites, the plant hormone signaling pathway and the plant-to-pathogen pathway. KEGG and GO enrichment analyses revealed the coordinated upregulation of these genes from numerous functional categories related to aphid stress responses. In addition, we determined the physiological indicators of chrysanthemum under aphid stress, and the results were consistent with the molecular sequencing results. All evidence indicated that grafting chrysanthemum onto A. scoparia W. upregulated aphid stress responses in chrysanthemum. Conclusion In summary, our study presents a genome-wide transcript profile of the self-rooted grafted chrysanthemum and the grafted Artemisia-chrysanthemum and provides insights into the molecular mechanisms of C. morifolium T. in response to aphid infestation. These data will contribute to further studies of aphid tolerance and the exploration of new candidate genes for chrysanthemum molecular breeding.

scholarly journals Comprehensive transcriptome analysis of grafting onto Artemisia scoparia  W. to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium T. )

2019 ◽  
Author(s):  
Xue-ying Zhang ◽  
Xian-zhi Sun ◽  
Sheng Zhang ◽  
Jing-hui Yang ◽  
Fang-fang Liu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Chrysanthemum Morifolium ◽  
The Self ◽  
Rna Seq ◽  
Aphid Infestation ◽  
A Genome ◽  
Artemisia Scoparia

Abstract Abstract Background: Aphid ( Macrosiphoniella sanbourni ) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the self-rooted grafted chrysanthemum ( Chrysanthemum morifolium T. 'Hangbaiju') and the grafted Artermisia-chrysanthemum (grafted onto Artemisia scoparia W.) transcription response to aphid stress. Results : The results showed that there were 1337 differentially expressed genes (DEGs), among which 680 were upregulated and 667 were downregulated, in the grafted Artemisia-chrysanthemum compared to the self-rooted grafted chrysanthemum. These genes were mainly involved in sucrose metabolism, the biosynthesis of secondary metabolites, the plant hormone signaling pathway and the plant-to-pathogen pathway. KEGG and GO enrichment analyses revealed the coordinated upregulation of these genes from numerous functional categories related to aphid stress responses. In addition, we determined the physiological indicators of chrysanthemum under aphid stress, and the results were consistent with the molecular sequencing results. All evidence indicated that grafting chrysanthemum onto A. scoparia W. upregulated aphid stress responses in chrysanthemum. Conclusion: In summary, our study presents a genome-wide transcript profile of the self-rooted grafted chrysanthemum and the grafted Artemisia-chrysanthemum and provides insights into the molecular mechanisms of C. morifolium T. in response to aphid infestation. These data will contribute to further studies of aphid tolerance and the exploration of new candidate genes for chrysanthemum molecular breeding. Key words : Chrysanthemum, Grafting, Aphid stress, Gene expression, RNA-Seq

scholarly journals Comparative Analysis of Transcriptome Responses to Cold Stress in Galeruca daurica (Coleoptera: Chrysomelidae)

2019 ◽  
Vol 19 (6) ◽  
Author(s):  
Xiao-Rong Zhou ◽  
Yan-Min Shan ◽  
Yao Tan ◽  
Zhuo-Ran Zhang ◽  
Bao-Ping Pang
Keyword(s):  
Cold Stress ◽  
Stress Responses ◽  
Low Temperatures ◽  
Fatty Acid Synthase ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Glucose Dehydrogenase ◽  
Insect Pest ◽  
Cuticle Protein

Abstract Galeruca daurica (Joannis) has become a new insect pest in the Inner Mongolia grasslands since 2009, and its larvae and eggs have strong cold tolerance. To get a deeper insight into its molecular mechanisms of cold stress responses, we performed de novo transcriptome assembly for G. daurica by RNA-Seq and compared the transcriptomes of its larvae exposed to five different temperature treatments (−10, −5, 0, 5, and 25°C for 1 h and then recovered at 25°C for 1 h), respectively. Compared with the control (25°C), the numbers of differentially expressed genes (DEGs) decreased from 1,821 to 882, with the temperature declining from 5 to −10°C. Moreover, we obtained 323 coregulated DEGs under different low temperatures. Under four low temperatures (−10, −5, 0, and 5°C), a large number of genes were commonly upregulated during recovery from cold stresses, including those related to cuticle protein, followed by cytochrome P450, clock protein, fatty acid synthase, and fatty acyl-CoA reductase; meanwhile, lots of genes encoding cuticle protein, RNA replication protein, RNA-directed DNA polymerase, and glucose dehydrogenase were commonly downregulated. Our findings provide important clues for further investigations of key genes and molecular mechanisms involved in the adaptation of G. daurica to harsh environments.

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

Agronomy ◽  
2020 ◽  
Vol 10 (2) ◽  
pp. 283 ◽  
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.

scholarly journals Comprehensive transcriptome analysis of grafting onto Artemisia scoparia  W. to affect the aphid resistance of chrysanthemum (Chrysanthemum morifolium T. )

2019 ◽  
Author(s):  
Xue-ying Zhang(Former Corresponding Author) ◽  
Xian-zhi Sun(New Corresponding Author) ◽  
Sheng Zhang ◽  
Fang-fang Liu ◽  
Jing-hui Yang ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Chrysanthemum Morifolium ◽  
De Novo Transcriptome Assembly ◽  
Rna Seq ◽  
De Novo Transcriptome ◽  
Biotic And Abiotic Stresses ◽  
Yield And Quality ◽  
Artemisia Scoparia

Abstract Aphid ( Macrosiphoniella sanbourni ) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the RNA-Seq platform to perform a de novo transcriptome assembly to analyze the self - rooted grafted chrysanthemum ( Chrysanthemum morifolium 'Hangbaiju') and the grafted Artermisia-chrysanthemum ( grafted onto Artemisia scoparia ) transcription response to aphid stress.

scholarly journals De Novo Transcriptome Assembly, Functional Annotation, and Transcriptome Dynamics Analyses Reveal Stress Tolerance Genes in Mangrove Tree (Bruguiera gymnorhiza)

2021 ◽  
Vol 22 (18) ◽  
pp. 9874
Author(s):  
Matin Miryeganeh ◽  
Hidetoshi Saze
Keyword(s):  
Stress Tolerance ◽  
Molecular Mechanisms ◽  
High Salinity ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Natural Habitats ◽  
Mangrove Species ◽  
Mangrove Tree ◽  
Bruguiera Gymnorhiza

Their high adaptability to difficult coastal conditions makes mangrove trees a valuable resource and an interesting model system for understanding the molecular mechanisms underlying stress tolerance and adaptation of plants to the stressful environmental conditions. In this study, we used RNA sequencing (RNA-Seq) for de novo assembling and characterizing the Bruguiera gymnorhiza (L.) Lamk leaf transcriptome. B. gymnorhiza is one of the most widely distributed mangrove species from the biggest family of mangroves; Rhizophoraceae. The de novo assembly was followed by functional annotations and identification of individual transcripts and gene families that are involved in abiotic stress response. We then compared the genome-wide expression profiles between two populations of B. gymnorhiza, growing under different levels of stress, in their natural habitats. One population living in high salinity environment, in the shore of the Pacific Ocean- Japan, and the other population living about one kilometre farther from the ocean, and next to the estuary of a river; in less saline and more brackish condition. Many genes involved in response to salt and osmotic stress, showed elevated expression levels in trees growing next to the ocean in high salinity condition. Validation of these genes may contribute to future salt-resistance research in mangroves and other woody plants. Furthermore, the sequences and transcriptome data provided in this study are valuable scientific resources for future comparative transcriptome research in plants growing under stressful conditions.

scholarly journals Genome-wide identification and analysis of cystatin family genes in Sorghum (Sorghum bicolor (L.) Moench)

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10617
Author(s):  
Jie Li ◽  
Xinhao Liu ◽  
Qingmei Wang ◽  
Junyan Sun ◽  
Dexian He
Keyword(s):  
Gene Family ◽  
Seed Development ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Expression Profiles ◽  
Seed Formation ◽  
Aphid Infestation ◽  
Genome Wide ◽  
A Genome ◽  
Cystatin Family

To set a systematic study of the Sorghum cystatins (SbCys) gene family, a genome-wide analysis of the SbCys family genes was performed by bioinformatics-based methods. In total, 18 SbCys genes were identified in Sorghum, which were distributed unevenly on chromosomes, and two genes were involved in a tandem duplication event. All SbCys genes had similar exon/intron structure and motifs, indicating their high evolutionary conservation. Transcriptome analysis showed that 16 SbCys genes were expressed in different tissues, and most genes displayed higher expression levels in reproductive tissues than in vegetative tissues, indicating that the SbCys genes participated in the regulation of seed formation. Furthermore, the expression profiles of the SbCys genes revealed that seven cystatin family genes were induced during Bipolaris sorghicola infection and only two genes were responsive to aphid infestation. In addition, quantitative real-time polymerase chain reaction (qRT-PCR) confirmed that 17 SbCys genes were induced by one or two abiotic stresses (dehydration, salt, and ABA stresses). The interaction network indicated that SbCys proteins were associated with several biological processes, including seed development and stress responses. Notably, the expression of SbCys4 was up-regulated under biotic and abiotic stresses, suggesting its potential roles in mediating the responses of Sorghum to adverse environmental impact. Our results provide new insights into the structural and functional characteristics of the SbCys gene family, which lay the foundation for better understanding the roles and regulatory mechanism of Sorghum cystatins in seed development and responses to different stress conditions.

scholarly journals Arkas: Rapid reproducible RNAseq analysis

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 586 ◽  
Author(s):  
Anthony R. Colombo ◽  
Timothy J. Triche Jr ◽  
Giridharan Ramsingh
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis ◽  
Special Focus ◽  
Gene Set Enrichment ◽  
Cloud Computing Environment ◽  
Gene Set ◽  
Structured Information ◽  
Computing Platforms

The recently introduced Kallisto pseudoaligner has radically simplified the quantification of transcripts in RNA-sequencing experiments.  We offer cloud-scale RNAseq pipelines Arkas-Quantification, which deploys Kallisto for parallel cloud computations, and Arkas-Analysis, which annotates the Kallisto results by extracting structured information directly from source FASTA files with per-contig metadata and calculates the differential expression and gene-set enrichment analysis on both coding genes and transcripts. The biologically informative downstream gene-set analysis maintains special focus on Reactome annotations while supporting ENSEMBL transcriptomes. The Arkas cloud quantification pipeline includes support for custom user-uploaded FASTA files, selection for bias correction and pseudoBAM output. The option to retain pseudoBAM output for structural variant detection and annotation provides a middle ground between de novo transcriptome assembly and routine quantification, while consuming a fraction of the resources used by popular fusion detection pipelines.  Illumina's BaseSpace cloud computing environment, where these two applications are hosted, offers a massively parallel distributive quantification step for users where investigators are better served by cloud-based computing platforms due to inherent efficiencies of scale.

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