scholarly journals Transcriptome Analysis of Banana (Musa acuminate L.) in Response to Low-Potassium Stress

Agronomy ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 169
Author(s):  
Min Xu ◽  
Can-Bin Zeng ◽  
Rui He ◽  
Zhen Yan ◽  
Zhao Qi ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Dry Weight ◽  
Phenotypic Traits ◽  
Rna Seq ◽  
Expression Of Genes ◽  
K Deficiency ◽  
Banana Leaves ◽  
Gene Functional Classification ◽  
Low K

Potassium (K+) is an abundant and important macronutrient for plants. It plays crucial roles in many growth and developmental processes, and growth is inhibited under low −K+ conditions. The molecular mechanisms operating under K+ starvation have been little reported in banana, which is a non-model plant. We conducted a transcriptome analysis of banana (Musa acuminata L. AAA group, cv. Cavendish) in response to low −K+ stress. The phenotypic traits and transcriptomic profiles of banana leaves and roots were compared between low −K+ (LK) and normal −K+ (NK) groups. The phenotypic parameters for the LK group, including fresh and dry weight, were lower than those for the NK group, which suggested that low −K+ stress may inhibit some important metabolic and biosynthetic processes. K+ content and biomass were both decreased in the LK group compared to the NK group. Following ribonucleic acid sequencing (RNA-Seq), a total of 26,796 expressed genes were detected in normal −K+ leaves (NKL), 27,014 were detected in low −K+ leaves (LKL), 29,158 were detected in normal −K+ roots (NKR), and 28,748 were detected in low −K+ roots (LKR). There were 797 up-regulated differentially expressed genes (DEGs) and 386 down-regulated DEGs in NKL versus LKL, while there were 1917 up-regulated DEGs and 2830 down-regulated DEGs in NKR versus LKR. This suggested that the roots were more sensitive to low −K+ stress than the leaves. DEGs related to K+ transport and uptake were analyzed in detail. Gene functional classification showed that the expression of genes regarding ABC transporters, protein kinases, transcription factors, and ion transporters were also detected, and may play important roles during K+ deficiency.

scholarly journals Differential Expression of Genes Related to the Formation of Giant Leaves in Triploid Poplar

Forests ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 920 ◽  
Author(s):  
Kang Du ◽  
Qiang Han ◽  
Ying Zhang ◽  
Xiangyang Kang
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Leaf Growth ◽  
Growth Hormones ◽  
Endogenous Hormones ◽  
Rna Seq ◽  
Hormone Metabolism ◽  
Expression Of Genes ◽  
Genes Expression ◽  
Differential Expression Of Genes

Plant polyploids tend to have large leaves, but their formation mechanism has not yet been well explained. Therefore, daily transcriptomic differences between triploids and diploids from a synthetic Populus sect. Tacamahaca three times a day (i.e., 04:00, 09:00, and 21:00) were investigated using high-throughput RNA-seq analysis. In this study, we identified several transcription factors associated with giant leaves. The combined effects included the high expression of several transcription factors (WRKY, MYB, etc.) and hormone-related genes (e.g., activates auxin, cytokine, and brassinosteroid synthesis-related genes) that accelerate the synthesis and accumulation of endogenous hormones. High levels of growth hormones were maintained by reducing the genes’ expression of hormone metabolism and degradation. The coordination of hormones accumulated sufficient materials and energy for leaf growth and development. Thereby, cell division and growth were accelerated which enhanced the photosynthesis of leaves, and the increased accumulation of photosynthetic products led to giant triploid leaves. This study lays the foundation for revealing the molecular mechanisms in the formation of giant leaves in polyploids.

scholarly journals Transcriptome Analysis Reveals the Molecular Mechanisms Underlying Adenosine Biosynthesis in Anamorph Strain of Caterpillar Fungus

2019 ◽  
Vol 2019 ◽  
pp. 1-12
Author(s):  
Shan Lin ◽  
Zhicheng Zou ◽  
Cuibing Zhou ◽  
Hancheng Zhang ◽  
Zhiming Cai
Keyword(s):  
Gene Expression ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Purine Metabolism ◽  
Expression Data ◽  
Rna Seq ◽  
Metabolism Pathway ◽  
Caterpillar Fungus ◽  
Regulated Gene Expression ◽  
Late Stages

Caterpillar fungus is a well-known fungal Chinese medicine. To reveal molecular changes during early and late stages of adenosine biosynthesis, transcriptome analysis was performed with the anamorph strain of caterpillar fungus. A total of 2,764 differentially expressed genes (DEGs) were identified (p≤0.05, |log2 Ratio| ≥ 1), of which 1,737 were up-regulated and 1,027 were down-regulated. Gene expression profiling on 4–10 d revealed a distinct shift in expression of the purine metabolism pathway. Differential expression of 17 selected DEGs which involved in purine metabolism (map00230) were validated by qPCR, and the expression trends were consistent with the RNA-Seq results. Subsequently, the predicted adenosine biosynthesis pathway combined with qPCR and gene expression data of RNA-Seq indicated that the increased adenosine accumulation is a result of down-regulation of ndk, ADK, and APRT genes combined with up-regulation of AK gene. This study will be valuable for understanding the molecular mechanisms of the adenosine biosynthesis in caterpillar fungus.

scholarly journals Age effects aggressive behavior: RNA-seq analysis in cattle with implications for studying neoteny under domestication

2020 ◽  
Author(s):  
Paulina G. Eusebi ◽  
Natalia Sevane ◽  
Thomas O’Rourke ◽  
Manuel Pizarro ◽  
Cedric Boeckx ◽  
...  
Keyword(s):  
Prefrontal Cortex ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Aggressive Behaviors ◽  
Intentional Actions ◽  
Expression Of Genes ◽  
Differential Gene ◽  
The Impact ◽  
The Brain ◽  
Novel Model

AbstractAggressiveness is one of the most basic behaviors, characterized by targeted intentional actions oriented to cause harm. The reactive type of aggression is regulated mostly by the brain’s prefrontal cortex; however, the molecular changes underlying aggressiveness in adults have not been fully characterized. Here we used an RNA-seq approach to investigate differential gene expression in the prefrontal cortex of bovines from the aggressive Lidia breed at different age stages: young three-year old and adult four-year-old bulls. A total of 50 up and 193 down-regulated genes in the adult group were identified. Furthermore, a cross-species comparative analysis retrieved 29 genes in common with previous studies on aggressive behaviors, representing an above-chance overlap with the differentially expressed genes in adult bulls.Particularly, we detected changes in the regulation of networks such as synaptogenesis, involved in maintenance and refinement of synapses, and the glutamate receptor pathway, which acts as excitatory driver in aggressive responses. Our results provide insights into candidate genes and networks involved in the molecular mechanisms leading to the maturation of the brain. The reduced reactive aggression typical of domestication has been proposed to form part of a retention of juvenile traits as adults (neoteny). The significant age-associated differential expression of genes implicated in aggressive behaviors and concomitant increase in Lidia cattle aggression validates this species as a novel model comparator to explore the impact of behavioral neoteny under domestication.

scholarly journals Transcriptome analysis and functional identification of GmMYB46 in soybean seedlings under salt stress

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12492
Author(s):  
Xun Liu ◽  
Xinxia Yang ◽  
Bin Zhang
Keyword(s):  
Salt Stress ◽  
Stress Response ◽  
Salt Tolerance ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Functional Identification ◽  
Salt Stress Response ◽  
Soybean Seedlings

Salinity is one of the major abiotic stress that limits crop growth and productivity. We investigated the transcriptomes of salt-treated soybean seedlings versus a control using RNA-seq to better understand the molecular mechanisms of the soybean (Glycine max L.) response to salt stress. Transcriptome analysis revealed 1,235 differentially expressed genes (DEGs) under salt stress. Several important pathways and key candidate genes were identified by KEGG enrichment. A total of 116 differentially expressed transcription factors (TFs) were identified, and 17 TFs were found to belong to MYB families. Phylogenetic analysis revealed that these TFs may be involved in salt stress adaptation. Further analysis revealed that GmMYB46 was up-regulated by salt and mannitol and was localized in the nucleus. The salt tolerance of transgenic Arabidopsis overexpressing GmMYB46 was significantly enhanced compared to wild-type (WT). GmMYB46 activates the expression of salt stress response genes (P5CS1, SOD, POD, NCED3) in Arabidopsis under salt stress, indicating that the GmMYB46 protein mediates the salt stress response through complex regulatory mechanisms. This study provides information with which to better understand the molecular mechanism of salt tolerance in soybeans and to genetically improve the crop.

An RNA-Seq transcriptome analysis revealing novel insights into fluorine absorption and transportation in the tea plant

Botany ◽  
2020 ◽  
Vol 98 (5) ◽  
pp. 249-259
Author(s):  
Xin Huang ◽  
Pu Wang ◽  
Siyi Liu ◽  
Yaru Du ◽  
Dejiang Ni ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Fluorine Content ◽  
Tea Plant ◽  
Glutathione Metabolism ◽  
Rna Seq ◽  
High Concentration ◽  
Systematic Analysis ◽  
Shock Proteins

The tea plant [Camellia sinensis (L.) O. Kuntze] is a species with a high concentration of fluorine in its leaves, especially in the mature leaves. The physiological mechanisms for fluorine absorption and accumulation have been well studied, but the related molecular mechanisms are poorly understood in the tea plant. In this study, transcriptome analysis by RNA-Seq following exposure to 16 mg/L of fluorine for 0, 3, 6, and 24 h was performed to identify the candidate genes involved in the transmembrane transportation of fluorine. More than 1.23 billion high-quality reads were generated, and 259.84 million unigenes were assembled de novo, with 518 216 of them being annotated in the seven databases used. Meanwhile, a large number of transporters, transcription factors, and heat-shock proteins with differential expression in response to high levels of fluorine (P ≤ 0.05) were identified. Comparative transcriptome analysis showed that the uptake of fluorine is related to photosynthesis, plant hormone signal transduction, and glutathione metabolism. Further systematic analysis of nitrate and potassium transporter genes revealed that many of these genes regulate fluorine transportation in roots and leaves. Gene expression and fluorine content analysis in different cultivars revealed CsNRT1/PTR 3.1 and CsPT 8 as the key genes regulating the transmembrane transportation of fluorine in the tea plant.

scholarly journals Transcriptomic Response in Pseudomonas aeruginosa towards Treatment with a Kaempferol Isolated from Melastoma malabathricum Linn Leaves

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Mourouge Saadi Alwash ◽  
Wan Syaidatul Aqma ◽  
Wan Yaacob Ahmad ◽  
Nazlina Ibrahim
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Iron Homeostasis ◽  
Molecular Mechanisms ◽  
Opportunistic Infections ◽  
Membrane Lipid ◽  
Rna Seq ◽  
Amino Acid Synthesis ◽  
Transcriptomic Response ◽  
Melastoma Malabathricum ◽  
Expression Of Genes

Pseudomonas aeruginosa is one of the main causes of nosocomial infections and is frequently associated with opportunistic infections among hospitalized patients. Kaempferol-3-O-(2′,6′-di-O-trans-p-coumaroyl)-β-D glucopyranoside (KF) is an antipseudomonal compound isolated from the leaves of the native medicinal plant Melastoma malabathricum. Herein, an RNA-seq transcriptomic approach was employed to study the effect of KF treatment on P. aeruginosa and to elucidate the molecular mechanisms underlying the response to KF at two time points (6 h and 24 h incubation). Quantitative real-time PCR (qRT-PCR) was performed for four genes (uvrD, sodM, fumC1, and rpsL) to assess the reliability of the RNA-seq results. The RNA-seq transcriptomic analysis revealed that KF increases the expression of genes involved in the electron transport chain (NADH-I), resulting in the induction of ATP synthesis. Furthermore, KF also increased the expression of genes associated with ATP-binding cassette transporters, flagella, type III secretion system proteins, and DNA replication and repair, which may further influence nutrient uptake, motility, and growth. The results also revealed that KF decreased the expression of a broad range of virulence factors associated with LPS biosynthesis, iron homeostasis, cytotoxic pigment pyocyanin production, and motility and adhesion that are representative of an acute P. aeruginosa infection profile. In addition, P. aeruginosa pathways for amino acid synthesis and membrane lipid composition were modified to adapt to KF treatment. Overall, the present research provides a detailed view of P. aeruginosa adaptation and behaviour in response to KF and highlights the possible therapeutic approach of using plants to combat P. aeruginosa infections.

scholarly journals 4353 The Role of BCL2 Mediated Calcium Signaling on Leukemia Stem Cell Metabolism

2020 ◽  
Vol 4 (s1) ◽  
pp. 19-19
Author(s):  
Anagha Inguva ◽  
Shanshan Pei ◽  
Maria Amaya ◽  
Brett Stevens ◽  
Courtney Jones ◽  
...  
Keyword(s):  
Stem Cells ◽  
Calcium Signaling ◽  
Intracellular Calcium ◽  
Metal Ion ◽  
Molecular Mechanisms ◽  
Calcium Influx ◽  
Survival Rates ◽  
Rna Seq ◽  
Expression Of Genes ◽  
Er Membrane

OBJECTIVES/GOALS: The objective of this study is to define the molecular mechanisms that control survival of malignant stem cells in acute myeloid leukemia (AML). Leukemia stem cells (LSCs) are not effectively eradicated by standard treatment and lead to resistance and relapse, which contribute to poor survival rates. METHODS/STUDY POPULATION: The recently FDA approved venetoclax, a BCL2 inhibitor, with azacitidine, a hypomethylating agent leads to a 70% response rate in AML patients. Analysis of patients treated with this regimen showed direct targeting of LSCs. BCL2 has a non-canonical function in regulation of intracellular calcium. To determine how BCL2 mediated calcium signaling plays a role in LSC biology, we used LSCs isolated from venetoclax/azacitidine (ven/aza) sensitive and resistant patient samples to measure expression of calcium channels via RNA seq. BIO-ID, siRNA, flow cytometry, seahorse assays, calcium measurements and colony assays were used to determine the effects of calcium channel perturbation on LSC biology. RESULTS/ANTICIPATED RESULTS: BCL2 inhibition leads to decreased OXPHOS activity in primary AML specimens. BIO-ID studies revealed cation/metal ion transporters, ER membrane proteins and ER membrane organization as top enriched pathways interacting with BCL2. RNA-seq data showed increased expression of genes involved in calcium influx into the ER in ven/aza sensitive LSCs and increased expression of genes involved in calcium efflux from the ER in ven/aza resistant samples. Ven/Aza resistant LSCs have increased mitochondrial calcium content, consistent with their increased OXPHOS activity as calcium is required for OXPHOS. Perturbation of these channels leads to decreased OXPHOS activity and decreased viability in LSCs. DISCUSSION/SIGNIFICANCE OF IMPACT: We postulate that a deeper understanding of the mechanisms behind ven/aza targeting of LSCs will lead to the development of novel therapies for patients who do not respond to ven/aza. Our data show targeting intracellular calcium signaling could be a viable therapeutic strategy for AML patients.

scholarly journals Metabolome and transcriptome analysis reveals the molecular profiles underlying the ginseng response to rusty root symptoms

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xingbo Bian ◽  
Yan Zhao ◽  
Shengyuan Xiao ◽  
He Yang ◽  
Yongzhong Han ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Plant Hormone ◽  
Soil Microbiology ◽  
Mechanism Model ◽  
Expression Of Genes ◽  
Phenylpropanoid Biosynthesis ◽  
Plant Pathogen Interaction ◽  
Molecular Profiles

Abstract Background Ginseng rusty root symptoms (GRS) is one of the primary diseases of ginseng. This disease leads to a severe decline in the quality of ginseng. It has been shown that the occurrence of GRS is associated with soil environmental degradation, which may involve changes in soil microbiology and physicochemical properties. Results In this study, GRS and healthy ginseng (HG) samples were used as experimental materials for comparative analysis of transcriptome and metabolome. Compared with those in HG samples, 949 metabolites and 9451 genes were significantly changed at the metabolic and transcriptional levels in diseased samples. The diseased tissues’ metabolic patterns changed, and the accumulation of various organic acids, alkaloids, alcohols and phenols in diseased tissues increased significantly. There were significant differences in the expression of genes involved in plant hormone signal transduction, phenylpropanoid biosynthesis, the peroxidase pathway, and the plant-pathogen interaction pathway. Conclusion The current study involved a comparative metabolome and transcriptome analysis of GRS and HG samples. Based on the findings at the transcriptional and metabolic levels, a mechanism model of the ginseng response to GRS was established. Our results provide new insights into ginseng’s response to GRS, which will reveal the potential molecular mechanisms of this disease in ginseng.

Transcriptome analysis of a Triticum aestivum landrace (Roshan) in response to salt stress conditions

2021 ◽  
pp. 1-14
Author(s):  
Jamshid Azimian ◽  
Eslam Majidi Hervan ◽  
Amin Azadi ◽  
Mohammad Reza Bakhtiarizadeh ◽  
Reza Azizinezhad
Keyword(s):  
Salt Stress ◽  
Transcriptome Analysis ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
Illumina Hiseq ◽  
Kegg Pathways ◽  
Go Enrichment ◽  
Meristem Maintenance ◽  
Polymerase Chain ◽  
Gene Expression Levels

Abstract In order to better understand the molecular mechanisms associated with salinity tolerance, transcriptome analysis of a local salt-tolerant wheat landrace (i.e. Roshan) was performed under salt stress. Transcriptome sequencing yielded 137,508,542 clean reads using the Illumina HiSeq 2000 platform. The results of two alignment programs, i.e. STAR and HISAT2, were used separately to perform the analysis of differentially expressed genes (DEGs) using DESeq2. Finally, a total of 17,897 DEGs were identified by DESeq2. Moreover, gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses identified 108 GO terms and 62 significant KEGG pathways, of which ‘metabolic process’ and ‘metabolic pathways’ were the most abundant enriched term and pathway, respectively. Additionally, key salinity-tolerant genes, including asparagine synthetase, were also identified in the present study. Out of 87 identified families of transcription factors, GAI‐RGA ‐ and ‐SCR (GRAS) was one of the most important, which participates in signal transduction, and meristem maintenance and development. Eventually, to validate the gene expression levels, six DEGs were selected for a quantitative real-time polymerase chain reaction, and the results were in line with those of RNA-Seq. The findings of the current study can guide future genetic and molecular studies and allow a better understanding and improvement of salt tolerance in wheat.

scholarly journals Transcriptome Analysis Unravels Key Factors Involved in Response to Potassium Deficiency and Feedback Regulation of K+ Uptake in Cotton Roots

2021 ◽  
Vol 22 (6) ◽  
pp. 3133
Author(s):  
Doudou Yang ◽  
Fangjun Li ◽  
Fei Yi ◽  
A. Egrinya Eneji ◽  
Xiaoli Tian ◽  
...  
Keyword(s):  
Root Growth ◽  
Molecular Mechanisms ◽  
Feedback Regulation ◽  
Virus Induced Gene Silencing ◽  
Key Factors ◽  
K Uptake ◽  
Response Factors ◽  
Interacting Protein ◽  
K Deficiency ◽  
Low K

To properly understand cotton responses to potassium (K+) deficiency and how its shoot feedback regulates K+ uptake and root growth, we analyzed the changes in root transcriptome induced by low K+ (0.03 mM K+, lasting three days) in self-grafts of a K+ inefficient cotton variety (CCRI41/CCRI41, scion/rootstock) and its reciprocal grafts with a K+ efficient variety (SCRC22/CCRI41). Compared with CCRI41/CCRI41, the SCRC22 scion enhanced the K+ uptake and root growth of CCRI41 rootstock. A total of 1968 and 2539 differently expressed genes (DEGs) were identified in the roots of CCRI41/CCRI41 and SCRC22/CCRI41 in response to K+ deficiency, respectively. The overlapped and similarly (both up- or both down-) regulated DEGs in the two grafts were considered the basic response to K+ deficiency in cotton roots, whereas the DEGs only found in SCRC22/CCRI41 (1954) and those oppositely (one up- and the other down-) regulated in the two grafts might be the key factors involved in the feedback regulation of K+ uptake and root growth. The expression level of four putative K+ transporter genes (three GhHAK5s and one GhKUP3) increased in both grafts under low K+, which could enable plants to cope with K+ deficiency. In addition, two ethylene response factors (ERFs), GhERF15 and GhESE3, both down-regulated in the roots of CCRI41/CCRI41 and SCRC22/CCRI41, may negatively regulate K+ uptake in cotton roots due to higher net K+ uptake rate in their virus-induced gene silencing (VIGS) plants. In terms of feedback regulation of K+ uptake and root growth, several up-regulated DEGs related to Ca2+ binding and CIPK (CBL-interacting protein kinases), one up-regulated GhKUP3 and several up-regulated GhNRT2.1s probably play important roles. In conclusion, these results provide a deeper insight into the molecular mechanisms involved in basic response to low K+ stress in cotton roots and feedback regulation of K+ uptake, and present several low K+ tolerance-associated genes that need to be further identified and characterized.

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