Corynebacterium pseudotuberculosis RNA-seq data from abiotic stresses

Sesame is a source of a healthy vegetable oil, attracting a growing interest worldwide. Abiotic stresses have devastating effects on sesame yield; hence, studies have been performed to understand sesame molecular responses to abiotic stresses, but the core abiotic stress-responsive genes (CARG) that the plant reuses in response to an array of environmental stresses are unknown. We performed a meta-analysis of 72 RNA-Seq datasets from drought, waterlogging, salt and osmotic stresses and identified 543 genes constantly and differentially expressed in response to all stresses, representing the sesame CARG. Weighted gene co-expression network analysis of the CARG revealed three functional modules controlled by key transcription factors. Except for salt stress, the modules were positively correlated with the abiotic stresses. Network topology of the modules showed several hub genes predicted to play prominent functions. As proof of concept, we generated over-expressing Arabidopsis lines with hub and non-hub genes. Transgenic plants performed better under drought, waterlogging, and osmotic stresses than the wild-type plants but did not tolerate the salt treatment. As expected, the hub gene was significantly more potent than the non-hub gene. Overall, we discovered several novel candidate genes, which will fuel investigations on plant responses to multiple abiotic stresses.

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Differential transcriptional profile of Corynebacterium pseudotuberculosis in response to abiotic stresses

BMC Genomics ◽

10.1186/1471-2164-15-14 ◽

2014 ◽

Vol 15 (1) ◽

pp. 14 ◽

Cited By ~ 27

Author(s):

Anne Pinto ◽

Pablo Henrique Caracciolo Gomes de Sá ◽

Rommel T J Ramos ◽

Silvanira Barbosa ◽

Hivana P Melo Barbosa ◽

...

Keyword(s):

Abiotic Stresses ◽

Transcriptional Profile ◽

Corynebacterium Pseudotuberculosis

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Plant Co-expression Annotation Resource: a webserver for identifying targets for genetically modified crop breeding pipelines

10.1101/2020.05.22.110510 ◽

2020 ◽

Author(s):

Marcos José Andrade Viana ◽

Adhemar Zerlotini ◽

Mauricio de Alvarenga Mudadu

Keyword(s):

Abiotic Stresses ◽

Molecular Mechanisms ◽

Genetically Modified ◽

Genetically Modified Crops ◽

Gm Crops ◽

Rna Seq ◽

Web Interface ◽

Crop Breeding ◽

Web Resource ◽

Guilt By Association

ABSTRACTBackgroundThe development of genetically modified crops (GM) includes the discovery of candidate genes through bioinformatics analysis using genomics data, gene expression, and others. Proteins of unknown function (PUFs) are interesting targets for GM crops breeding pipelines for the novelty associated to such targets and also to avoid copyright protections. One method of inferring the putative function of PUFs is by relating them to factors of interest such as abiotic stresses using orthology and co-expression networks, in a guilt-by-association manner.ResultsIn this regard, we have downloaded, analyzed, and processed genomics data of 53 angiosperms, totaling 1,862,010 genes and 2,332,974 RNA. Diamond and InterproScan were used to discover 72,266 PUFs for all organisms. RNA-seq datasets related to abiotic stresses were downloaded from NCBI/GEO. The RNA-seq data was used as input to the LSTrAP software to construct co-expression networks. LSTrAP also created clusters of transcripts with correlated expression, whose members are more probably related to the molecular mechanisms associated to abiotic stresses in the plants. Orthologous groups were created (OrhtoMCL) using all 2,332,974 proteins in order to associate PUFs to abiotic stress related clusters of co-expression and therefore infer their function in a guilt-by-association manner.ConclusionA freely available web resource named “Plant Co-expression Annotation Resource” (https://www.machado.cnptia.embrapa.br/plantannot), Plantannot, was created to provide indexed queries to search for PUF putatively associated to abiotic stresses. The web interface also allows browsing, querying and retrieving of public genomics data from 53 plants. We hope Plantannot to be useful for researchers trying to obtain novel GM crops resistant to climate change hazards.

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Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses

BMC Plant Biology ◽

10.1186/s12870-021-03329-3 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Haitao Xing ◽

Yusong Jiang ◽

Yong Zou ◽

Xiaoling Long ◽

Xiaoli Wu ◽

...

Keyword(s):

Gene Structure ◽

Abiotic Stresses ◽

Growth And Development ◽

Expression Profiles ◽

Rna Seq ◽

Qrt Pcr ◽

Genome Wide ◽

Evolutionary Features ◽

Erf Family

Abstract Background AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis. Results A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger. Conclusion A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and qRT-PCR showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.

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Mining Fiskeby III and Mandarin (Ottawa) Expression Profiles to Understand Iron Stress Tolerant Responses in Soybean

International Journal of Molecular Sciences ◽

10.3390/ijms222011032 ◽

2021 ◽

Vol 22 (20) ◽

pp. 11032

Author(s):

Jamie A. O’Rourke ◽

Michael J. Morrisey ◽

Ryan Merry ◽

Mary Jane Espina ◽

Aaron J. Lorenz ◽

...

Keyword(s):

Abiotic Stress ◽

Iron Deficiency ◽

Gene Silencing ◽

Stress Tolerance ◽

Abiotic Stresses ◽

Yield Loss ◽

Abiotic Stress Tolerance ◽

Iron Stress ◽

Rna Seq ◽

Virus Induced Gene Silencing

The soybean (Glycine max L. merr) genotype Fiskeby III is highly resistant to a multitude of abiotic stresses, including iron deficiency, incurring only mild yield loss during stress conditions. Conversely, Mandarin (Ottawa) is highly susceptible to disease and suffers severe phenotypic damage and yield loss when exposed to abiotic stresses such as iron deficiency, a major challenge to soybean production in the northern Midwestern United States. Using RNA-seq, we characterize the transcriptional response to iron deficiency in both Fiskeby III and Mandarin (Ottawa) to better understand abiotic stress tolerance. Previous work by our group identified a quantitative trait locus (QTL) on chromosome 5 associated with Fiskeby III iron efficiency, indicating Fiskeby III utilizes iron deficiency stress mechanisms not previously characterized in soybean. We targeted 10 of the potential candidate genes in the Williams 82 genome sequence associated with the QTL using virus-induced gene silencing. Coupling virus-induced gene silencing with RNA-seq, we identified a single high priority candidate gene with a significant impact on iron deficiency response pathways. Characterization of the Fiskeby III responses to iron stress and the genes underlying the chromosome 5 QTL provides novel targets for improved abiotic stress tolerance in soybean.

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OXS2 is Required for Salt Tolerance Mainly through Associating with Salt Inducible Genes, CA1 and Araport11, in Arabidopsis

Scientific Reports ◽

10.1038/s41598-019-56456-1 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Ying Jing ◽

Lin Shi ◽

Xin Li ◽

Han Zheng ◽

Jianwei Gao ◽

...

Keyword(s):

Salt Stress ◽

Salt Tolerance ◽

Abiotic Stresses ◽

Growth And Yield ◽

Functional Screening ◽

Rna Seq ◽

Salt Tolerant ◽

Promoter Regions ◽

Inducible Genes ◽

Chip Analysis

AbstractSalt stress is one of the abiotic stresses affecting crop growth and yield. The functional screening and mechanism investigation of the genes in response to salt stress are essential for the development of salt-tolerant crops. Here, we found that OXIDATIVE STRESS 2 (OXS2) was a salinity-induced gene, and the mutant oxs2-1 was hypersensitive to salt stress during seed germination and root elongation processes. In the absence of stress, OXS2 was predominantly localized in the cytoplasm; when the plants were treated with salt, OXS2 entered the nuclear. Further RNA-seq analysis and qPCR identification showed that, in the presence of salt stress, a large number of differentially expressed genes (DEGs) were activated, which contain BOXS2 motifs previously identified as the binding element for AtOXS2. Further ChIP analysis revealed that, under salt stress, OXS2 associated with CA1 and Araport11 directly through binding the BOXS2 containing fragments in the promoter regions. In conclusion, our results indicate that OXS2 is required for salt tolerance in Arabidopsis mainly through associating with the downstream CA1 and Araport11 directly.

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Defining the function of SUMO system in pod development and abiotic stresses in Peanut

BMC Plant Biology ◽

10.1186/s12870-019-2136-9 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Yiyang Liu ◽

Jiao Zhu ◽

Sheng Sun ◽

Feng Cui ◽

Yan Han ◽

...

Keyword(s):

Abiotic Stresses ◽

Developmental Process ◽

Expression Patterns ◽

Rna Seq ◽

Specific Expression ◽

Genome Wide ◽

Pod Development ◽

Core Components ◽

Arachis Duranensis ◽

New Strategies

Abstract Background Posttranslational modification of proteins by small ubiquitin like modifier (SUMO) proteins play an important role during the developmental process and in response to abiotic stresses in plants. However, little is known about SUMOylation in peanut (Arachis hypogaea L.), one of the world’s major food legume crops. In this study, we characterized the SUMOylation system from the diploid progenitor genomes of peanut, Arachis duranensis (AA) and Arachis ipaensis (BB). Results Genome-wide analysis revealed the presence of 40 SUMO system genes in A. duranensis and A. ipaensis. Our results showed that peanut also encodes a novel class II isotype of the SCE1, which was previously reported to be uniquely present in cereals. RNA-seq data showed that the core components of the SUMOylation cascade SUMO1/2 and SCE1 genes exhibited pod-specific expression patterns, implying coordinated regulation during pod development. Furthermore, both transcripts and conjugate profiles revealed that SUMOylation has significant roles during the pod development. Moreover, dynamic changes in the SUMO conjugates were observed in response to abiotic stresses. Conclusions The identification and organization of peanut SUMO system revealed SUMOylation has important roles during stress defense and pod development. The present study will serve as a resource for providing new strategies to enhance agronomic yield and reveal the mechanism of peanut pod development.

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In Silico Analyses of Autophagy-Related Genes in Rapeseed (Brassica napus L.) under Different Abiotic Stresses and in Various Tissues

Plants ◽

10.3390/plants9101393 ◽

2020 ◽

Vol 9 (10) ◽

pp. 1393

Author(s):

Elham Mehri Eshkiki ◽

Zahra Hajiahmadi ◽

Amin Abedi ◽

Mojtaba Kordrostami ◽

Cédric Jacquard

Keyword(s):

Brassica Napus ◽

Abiotic Stresses ◽

Genetic Manipulation ◽

Expression Patterns ◽

Rna Seq ◽

Brassica Napus L ◽

Genome Wide ◽

A Genome ◽

Ssr Loci ◽

Post Transcriptional Regulation

The autophagy-related genes (ATGs) play important roles in plant growth and response to environmental stresses. Brassica napus (B. napus) is among the most important oilseed crops, but ATGs are largely unknown in this species. Therefore, a genome-wide analysis of the B. napus ATG gene family (BnATGs) was performed. One hundred and twenty-seven ATGs were determined due to the B. napus genome, which belongs to 20 main groups. Segmental duplication occurred more than the tandem duplication in BnATGs. Ka/Ks for the most duplicated pair genes were less than one, which indicated that the negative selection occurred to maintain their function during the evolution of B. napus plants. Based on the results, BnATGs are involved in various developmental processes and respond to biotic and abiotic stresses. One hundred and seven miRNA molecules are involved in the post-transcriptional regulation of 41 BnATGs. In general, 127 simple sequence repeat marker (SSR) loci were also detected in BnATGs. Based on the RNA-seq data, the highest expression in root and silique was related to BnVTI12e, while in shoot and seed, it was BnATG8p. The expression patterns of the most BnATGs were significantly up-regulated or down-regulated responding to dehydration, salinity, abscisic acid, and cold. This research provides information that can detect candidate genes for genetic manipulation in B. napus.

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