scholarly journals Time Series RNA-seq in Pigeonpea Revealed the Core Genes in Metabolic Pathways under Aluminum Stress

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 380 ◽  
Author(s):  
Zhaoxu Gao ◽  
Biying Dong ◽  
Hongyan Cao ◽  
Hang He ◽  
Qing Yang ◽  
...  
Keyword(s):  
Time Series ◽  
Metabolic Pathways ◽  
Expression Patterns ◽  
Plant Stress ◽  
Regulation Mechanism ◽  
Rna Seq ◽  
Aluminum Stress ◽  
Biological Regulation ◽  
Al Stress ◽  
The Impact

Pigeonpea is an important economic crop in the world and is mainly distributed in tropical and subtropical regions. In order to further expand the scope of planting, one of the problems that must be solved is the impact of soil acidity on plants in these areas. Based on our previous work, we constructed a time series RNA sequencing (RNA-seq) analysis under aluminum (Al) stress in pigeonpea. Through a comparison analysis, 11,425 genes were found to be differentially expressed among all the time points. After clustering these genes by their expression patterns, 12 clusters were generated. Many important functional pathways were identified by gene ontology (GO) analysis, such as biological regulation, localization, response to stimulus, metabolic process, detoxification, and so on. Further analysis showed that metabolic pathways played an important role in the response of Al stress. Thirteen out of the 23 selected genes related to flavonoids and phenols were downregulated in response to Al stress. In addition, we verified these key genes of flavonoid- and phenol-related metabolism pathways by qRT-PCR. Collectively, our findings not only revealed the regulation mechanism of pigeonpea under Al stress but also provided methodological support for further exploration of plant stress regulation mechanisms.

scholarly journals RNA-Seq Time Series of Vitis vinifera Bud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile

2020 ◽  
Author(s):  
Boas Pucker ◽  
Anna Schwandner ◽  
Sarah Becker ◽  
Ludger Hausmann ◽  
Prisca Viehöver ◽  
...  
Keyword(s):  
Time Series ◽  
Vitis Vinifera ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Families ◽  
Rna Seq ◽  
Data Set ◽  
Bud Development ◽  
Tf Gene ◽  
The Impact

AbstractPlants display sophisticated mechanisms to tolerate challenging environmental conditions and need to manage their ontogenesis in parallel. Here, we set out to generate an RNA-Seq time series dataset throughout grapevine (Vitis vinifera) early bud development. The expression of the developmental regulator VviAP1 served as an indicator for progress of development. We investigated the impact of changing temperatures on gene expression levels during the time series and detected a correlation between increased temperatures and a high expression level of genes encoding heat-shock proteins. The data set also allowed the exemplary investigation of expression patterns of genes from three transcription factor (TF) gene families, namely MADS-box, WRKY, and R2R3-MYB genes. Inspection of the expression profiles from all three TF gene families indicated that a switch in the developmental program takes place in July which coincides with increased expression of the bud dormancy marker gene VviDRM1.

scholarly journals RNA-Seq Time Series of Vitis vinifera Bud Development Reveals Correlation of Expression Patterns with the Local Temperature Profile

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1548
Author(s):  
Boas Pucker ◽  
Anna Schwandner ◽  
Sarah Becker ◽  
Ludger Hausmann ◽  
Prisca Viehöver ◽  
...  
Keyword(s):  
Time Series ◽  
Vitis Vinifera ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Marker Gene ◽  
Gene Families ◽  
Rna Seq ◽  
Bud Development ◽  
Tf Gene ◽  
The Impact

Plants display sophisticated mechanisms to tolerate challenging environmental conditions and need to manage their ontogenesis in parallel. Here, we set out to generate an RNA-Seq time series dataset throughout grapevine (Vitis vinifera) early bud development. The expression of the developmental regulator VviAP1 served as an indicator of the progression of development. We investigated the impact of changing temperatures on gene expression levels during the time series and detected a correlation between increased temperatures and a high expression level of genes encoding heat-shock proteins. The dataset also allowed the exemplary investigation of expression patterns of genes from three transcription factor (TF) gene families, namely MADS-box, WRKY, and R2R3-MYB genes. Inspection of the expression profiles from all three TF gene families indicated that a switch in the developmental program takes place in July which coincides with increased expression of the bud dormancy marker gene VviDRM1.

scholarly journals AtHB7/12 Regulate Root Growth in Response to Aluminum Stress

2020 ◽  
Vol 21 (11) ◽  
pp. 4080
Author(s):  
Yang Liu ◽  
Jiameng Xu ◽  
Siyi Guo ◽  
Xianzheng Yuan ◽  
Shan Zhao ◽  
...  
Keyword(s):  
Cell Wall ◽  
Transcription Factors ◽  
Root Growth ◽  
Crop Production ◽  
Expression Patterns ◽  
Acid Soils ◽  
Limiting Factor ◽  
Aluminum Stress ◽  
Al Stress

Aluminum (Al) stress is a major limiting factor for plant growth and crop production in acid soils. At present, only a few transcription factors involved in the regulation of Al resistance have been characterized. Here, we used reversed genetic approach through phenotype analysis of overexpressors and mutants to demonstrate that AtHB7 and AtHB12, two HD-Zip I transcription factors, participate in Al resistance. In response to Al stress, AtHB7 and AtHB12 displayed different dynamic expression patterns. Although both AtHB7 and AtHB12 positively regulate root growth in the absence of Al stress, our results showed that AtHB7 antagonizes with AtHB12 to control root growth in response to Al stress. The athb7/12 double mutant displayed a wild-type phenotype under Al stress. Consistently, our physiological analysis showed that AtHB7 and AtHB12 oppositely regulate the capacity of cell wall to bind Al. Yeast two hybrid assays showed that AtHB7 and AtHB12 could form homo-dimers and hetero-dimers in vitro, suggesting the interaction between AtHB7 and AtHB12 in the regulation of root growth. The conclusion was that AtHB7 and AtHB12 oppositely regulate Al resistance by affecting Al accumulation in root cell wall.

scholarly journals Time Series Expression Analyses Using RNA-seq: A Statistical Approach

2013 ◽  
Vol 2013 ◽  
pp. 1-16 ◽  
Author(s):  
Sunghee Oh ◽  
Seongho Song ◽  
Gregory Grabowski ◽  
Hongyu Zhao ◽  
James P. Noonan
Keyword(s):  
Time Series ◽  
Statistical Approach ◽  
Expression Patterns ◽  
Temporal Analysis ◽  
Rna Seq ◽  
Computationally Efficient ◽  
Evolutionary Trajectory ◽  
Dynamic Methods ◽  
Series Expression ◽  
Time Lagged

RNA-seq is becoming thede factostandard approach for transcriptome analysis with ever-reducing cost. It has considerable advantages over conventional technologies (microarrays) because it allows for direct identification and quantification of transcripts. Many time series RNA-seq datasets have been collected to study the dynamic regulations of transcripts. However, statistically rigorous and computationally efficient methods are needed to explore the time-dependent changes of gene expression in biological systems. These methods should explicitly account for the dependencies of expression patterns across time points. Here, we discuss several methods that can be applied to model timecourse RNA-seq data, including statistical evolutionary trajectory index (SETI), autoregressive time-lagged regression (AR(1)), and hidden Markov model (HMM) approaches. We use three real datasets and simulation studies to demonstrate the utility of these dynamic methods in temporal analysis.

scholarly journals MetaMap, an interactive webtool for the exploration of metatranscriptomic reads in human disease-related RNA-seq data

2018 ◽  
Author(s):  
LM Simon ◽  
G Tsitsiridis ◽  
P Angerer ◽  
FJ Theis
Keyword(s):  
Human Disease ◽  
Expression Patterns ◽  
Heterogeneous Data ◽  
Rna Seq ◽  
Web Tool ◽  
Differential Abundance ◽  
Downstream Analysis ◽  
User Friendly ◽  
Differential Abundance Analysis ◽  
The Impact

AbstractMotivationThe MetaMap resource contains metatranscriptomic expression data from screening >17,000 RNA-seq samples from >400 archived human disease-related studies for viral and microbial reads, so-called “metafeatures”. However, navigating this set of large and heterogeneous data is challenging, especially for researchers without bioinformatic expertise. Therefore, a user-friendly interface is needed that allows users to visualize and statistically analyse the data.ResultsWe developed an interactive frontend to facilitate the exploration of the MetaMap resource. The webtool allows users to query the resource by searching study abstracts for keywords or browsing expression patterns for specific metafeatures. Moreover, users can manually define sample groupings or use the existing annotation for downstream analysis. The web tool provides a large variety of analyses and visualizations including dimension reduction, differential abundance analysis and Krona visualizations. The MetaMap webtool represents a valuable resource for hypothesis generation regarding the impact of the microbiome in human disease.AvailabilityThe presented web tool can be accessed at https://github.com/theislab/MetaMap

scholarly journals Identification and visualisation of differential isoform expression in RNA-seq time series

2017 ◽  
Author(s):  
María José Nueda ◽  
Jordi Martorell-Marugan ◽  
Cristina Martí ◽  
Sonia Tarazona ◽  
Ana Conesa
Keyword(s):  
Time Series ◽  
Time Series Data ◽  
Expression Patterns ◽  
R Package ◽  
Series Data ◽  
Rna Seq ◽  
Sequencing Technologies ◽  
Isoform Expression ◽  
Time Series Data Analysis ◽  
Differential Isoform Expression

AbstractAs sequencing technologies improve their capacity to detect distinct transcripts of the same gene and to address complex experimental designs such as longitudinal studies, there is a need to develop statistical methods for the analysis of isoform expression changes in time series data. Iso-maSigPro is a new functionality of the R package maSigPro for transcriptomics time series data analysis. Iso-maSigPro identifies genes with a differential isoform usage across time. The package also includes new clustering and visualization functions that allow grouping of genes with similar expression patterns at the isoform level, as well as those genes with a shift in major expressed isoform. The package is freely available under the LGPL license from the Bioconductor web site (http://bioconductor.org).

scholarly journals Structure and expression analysis of seven salt-related ERF genes of Populus

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10206
Author(s):  
Juanjuan Huang ◽  
Shengji Wang ◽  
Xingdou Wang ◽  
Yan Fan ◽  
Youzhi Han
Keyword(s):  
Abiotic Stress ◽  
Stress Tolerance ◽  
Expression Pattern ◽  
Target Genes ◽  
Abiotic Stress Tolerance ◽  
Critical Role ◽  
Plant Stress ◽  
Regulation Mechanism ◽  
Rna Seq ◽  
Go Annotation

Ethylene response factors (ERFs) are plant-specific transcription factors (TFs) that play important roles in plant growth and stress defense and have received a great amount of attention in recent years. In this study, seven ERF genes related to abiotic stress tolerance and response were identified in plants of the Populus genus. Systematic bioinformatics, including sequence phylogeny, genome organisation, gene structure, gene ontology (GO) annotation, etc. were detected. Expression-pattern of these seven ERF genes were analyzed using RT-qPCR and cross validated using RNA-Seq. Data from a phylogenetic tree and multiple alignment of protein sequences indicated that these seven ERF TFs belong to three subfamilies and contain AP2, YRG, and RAYD conserved domains, which may interact with downstream target genes to regulate the plant stress response. An analysis of the structure and promoter region of these seven ERF genes showed that they have multiple stress-related motifs and cis-elements, which may play roles in the plant stress-tolerance process through a transcriptional regulation mechanism; moreover, the cellular_component and molecular_function terms associated with these ERFs determined by GO annotation supported this hypothesis. In addition, the spatio-temporal expression pattern of these seven ERFs, as detected using RT-qPCR and RNA-seq, suggested that they play a critical role in mediating the salt response and tolerance in a dynamic and tissue-specific manner. The results of this study provide a solid basis to explore the functions of the stress-related ERF TFs in Populus abiotic stress tolerance and development process.

scholarly journals In vitro rhizobia response and symbiosis process under aluminum stress

2018 ◽  
Vol 64 (8) ◽  
pp. 511-526 ◽  
Author(s):  
María D. Artigas Ramírez ◽  
Jéssica D. Silva ◽  
Naoko Ohkama-Ohtsu ◽  
Tadashi Yokoyama
Keyword(s):  
Metabolic Pathways ◽  
Al Toxicity ◽  
Plant Genotype ◽  
Al Tolerance ◽  
Aluminum Stress ◽  
Selective Force ◽  
Al Stress ◽  
Acidic Conditions ◽  
Ph Conditions

Aluminum (Al) toxicity is a major problem affecting soil fertility, microbial diversity, and nutrient uptake of plants. Rhizobia response and legume interaction under Al conditions are still unknown; it is important to understand how to develop and improve legume cultivation under Al stress. In this study, rhizobia response was recorded under different Al concentrations. Al effect on rhizobial cells was characterized by combination with different two pH conditions. Symbiosis process was compared between α- and β-rhizobia inoculated onto soybean varieties. Rhizobial cell numbers was decreased as Al concentration increased. However, induced Al tolerance considerably depended on rhizobia types and their origins. Accordingly, organic acid results were in correlation with growth rate and cell density which suggested that citric acid might be a positive selective force for Al tolerance and plant interaction on rhizobia. Al toxicity delayed and interrupted the plant–rhizobia interaction and the effect was more pronounced under acidic conditions. Burkholderia fungorum VTr35 significantly improved plant growth under acid–Al stress in combination with all soybean varieties. Moreover, plant genotype was an important factor to establish an effective nodulation and nitrogen fixation under Al stress. Additionally, tolerant rhizobia could be applied as an inoculant on stressful agroecosystems. Furthermore, metabolic pathways have still been unknown under Al stress.

scholarly journals Genome-wide identification and evolutionary analysis of RLKs involved in response to Aluminum stress in peanut

2020 ◽  
Author(s):  
Xin Wang ◽  
Ming-Hua Wu ◽  
Dong Xiao ◽  
Ruo-Lan Huang ◽  
Jie Zhan ◽  
...  
Keyword(s):  
Expression Pattern ◽  
Stress Responses ◽  
Expression Patterns ◽  
Tissue Expression ◽  
Segmental Duplications ◽  
Evolutionary Analysis ◽  
Aluminum Stress ◽  
Specific Expression ◽  
Al Stress ◽  
Peanut Genome

Abstract Background: As an important cash crop, the yield of peanut is influenced by soil acidification and pathogen infection. Receptor-like protein kinase plays important roles in plant growth, development and stress responses. However, little is known about the number, location, structure, molecular phylogenetic, and expression of the RLKs in peanut, and no comprehensive analysis of RLKs in Al stress response in peanut have been reported. Results: A total of 1311 AhRLKs were identified from the peanut genome. The AhLRR-RLKs and AhLec-RLKs were further divided into 24 subfamilies and 35 subfamilies, respectively. The AhRLKs are randomly distributed across all 20 chromosomes in peanut. Among them, 67.8% and 0.6% of the AhRLKs originated from tandem duplications and segmental duplications, respectively. The ka/ks ratios of 94.9% (1290/1360) of AhRLKs were less than 1. Moreover, totally 90 Al-responsive AhRLKs were identified by mining transcriptome data, and they were divided into 7 groups. Most of Al responsive AhRLKs clustered together had similar motifs and evolutionarily conserved structures. The gene expression patterns of these genes in different tissues were further analyzed, and tissue specific expression genes, including 14 root-specific Al responsive AhRLKs were found. Besides, all of the 90 Al responsive AhRLKs which distributed unevenly in the subfamilies of AhRLKs have different expression pattern between two peanut varieties (Al-sensitive and Al-tolerant) under Al stress.Conclusions: In this study, we analyzed the RLK gene family by the peanut genome. Tandem replication events were the main driving force for AhRLKs evolution, and most AhRLKs were selected for purification. A total of 90 genes were identified as Al responsive AhRLKs, and the classification, conservative motif, structure, tissue expression pattern and predicted function of Al responsive AhRLKs were further analyzed and discussed, revealing their putative roles. This study provides a better understanding of the structures and functions of AhRLKs as well as Al responsive AhRLKs.

scholarly journals Homoeologue expression insights into the basis of growth heterosis at the intersection of ploidy and hybridity in Cyprinidae (Carassius auratus red var. × Cyprinus carpio)

2015 ◽  
Author(s):  
Li Ren ◽  
Wuhui Li ◽  
Chenchen Tang ◽  
Jun Xiao ◽  
Xiaojun Tan ◽  
...  
Keyword(s):  
Cyprinus Carpio ◽  
Carassius Auratus ◽  
Driving Forces ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Regulation Mechanism ◽  
Rna Seq ◽  
Allopolyploid Speciation ◽  
Expression Bias ◽  
Changing Patterns

Hybridization and polyploidization are considered important driving forces that form new epigenetic regulations. To study the changing patterns of expression accompanying hybridization and polyploidization, we used RNA-seq and qPCR to investigate global expression and homoeologue expression in diploid and allotetraploid hybrids of Carassius auratus red var. (♀) (R) and Cyprinus carpio (♂) (C). By comparing the relative expression levels between the hybrids and their parents, we defined the expression level dominance (ELD) and homoeologue expression bias (HEB) in liver tissue. The results showed that polyploidization contributed to the conversion of homoeologue ELD. In addition, hybridization had more effect on the change in HEB than polyploidization, while polyploidization has been considered to have more effect on the change of global gene expression than hybridization. Meanwhile, similar expression patterns were found in growth-related genes. The results suggested that hybridization and polyploidization result in differential degrees of maternal HEB in the three tissues tested. The results of this study will increase our understanding of the underlying regulation mechanism of rapid growth in diploid hybrids and allotetraploids. The differential degrees of global expression and homoeologue expression contribute to growth heterosis in newly formed hybrids and allotetraploids, ensuring the on-going success of allopolyploid speciation.

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