Transcriptome Characterization of Panax Quinquefolius L. seedlings in Response to Arbuscular Mycorrhizal Fungi using RNA-seq

2021 ◽  
Author(s):  
Zhifang Ran ◽  
Xiaotong Yang ◽  
Yongqing Zhang ◽  
Jie Zhou
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Stress Responses ◽  
Mycorrhizal Fungi ◽  
Differential Expression Analysis ◽  
Enrichment Analysis ◽  
Arbuscular Mycorrhizal ◽  
Transcriptome Profiling ◽  
Underlying Mechanism ◽  
Panax Quinquefolius ◽  
Rna Seq

Abstract Panax quinquefolius L. has been considered as an important traditional Chinese medicine with a history of more than 300 years in China. Ginsenoside is the main bioactive component. Our research group has found that the accumulation of ginsenoside could be affected by arbuscular mycorrhizal fungi (AMF). However the underlying mechanism how AMF affected the biosynthesis of ginsenoside in P. quinquefolius is still unclear. In this study, the RNA-seq analysis was used to evaluate the effects of AMF (Rhizophagus intraradices, R. intraradices) on the expression of ginsenoside synthesis related genes in P. quinquefolius root. The results indicated that a symbiotic relationship between R. intraradices and P. quinquefolius was established. RNA-seq achieved approximately 48.62 G reads of all samples. Assembly of all the reads involved in all samples produced 63420 transcripts and 24137 unigenes. Differential expression analysis was performed between the control and AMF group. A total of 111 differentially expressed genes (DEGs) in response to AMF vs control were identified, 78 and 33 transcripts were upregulated and downregulated, respectively. Based on the functional analysis, Gene ontology (GO) analysis revealed that most DEGs were related to stress responses and cellular metabolic processes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified transduction, plant hormone signal transduction and terpenoids and polyketides biosynthesis pathways. Furthermore, the expression of glycolysis-related genes and ginsenoside synthesis related genes was largely induced by AMF. In conclusion, our results comprehensively elucidated the molecular mechanism how AMF affected the biosynthesis of ginsenoside in P.quinquefolius by transcriptome profiling.

Genome-wide identification of citrus calmodulin-like genes and their expression in response to arbuscular mycorrhizal fungi colonization and drought

2021 ◽  
Author(s):  
Bo Shu ◽  
YaChao Xie ◽  
Fei Zhang ◽  
Dejian Zhang ◽  
Chunyan Liu ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Drought Stress ◽  
Arbuscular Mycorrhizal Fungi ◽  
Stress Responses ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Arbuscular Mycorrhizal ◽  
Biotic And Abiotic Stress ◽  
Genome Wide ◽  
A Genome

Calmodulin-like (CML) proteins represent a diverse family of protein in plants, and play significant roles in biotic and abiotic stress responses. However, the involvement of citrus CMLs in plant responses to drought stress (abiotic stress) and arbuscular mycorrhizal fungi (AMF) colonization remain relatively unknown. We characterized the citrus CML genes by analyzing the EF-hand domains and a genome-wide search, and identified a total of 38 such genes, distributed across at least nine chromosomes. Six tandem duplication clusters were observed in the CsCMLs, and 12 CsCMLs exhibited syntenic relationships with Arabidopsis thaliana CMLs. Gene expression analysis showed that 29 CsCMLs were expressed in the roots, and exhibited differential expression patterns. The regulation of CsCMLs expression was not consistent with the cis-elements identified in their promoters. CsCML2, 3, and 5 were upregulated in response to drought stress, and AMF colonization repressed the expression of CsCML7, 9, 12, 13,20, 27, 28, and 35,and induced that of CsCML1, 2, 3, 5, 8, 10, 11, 14, 15, 16, 18, 25, 30, 33, and 37. Furthermore, AMF colonization and drought stress exerted a synergistic effect, evident from the enhanced repression of CsCML7, 9, 12, 13, 27, 28, and 35 and enhanced expression of CsCML2, 3, and 5 under AMF colonization and drought stress. The present study provides valuable insights into the CsCML gene family and its responses to AMF colonization and drought stress.

scholarly journals Transcriptome Analysis of Wheat Roots Reveals a Differential Regulation of Stress Responses Related to Arbuscular Mycorrhizal Fungi and Soil Disturbance

Biology ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 93 ◽  
Author(s):  
Catarina Campos ◽  
Tânia Nobre ◽  
Michael J. Goss ◽  
Jorge Faria ◽  
Pedro Barrulas ◽  
...  
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Stress Responses ◽  
Mycorrhizal Fungi ◽  
Metal Ion ◽  
Arbuscular Mycorrhizal ◽  
Soil Disturbance ◽  
Cellular Division ◽  
Wheat Roots ◽  
New Host ◽  
Mn Toxicity

Symbioses with soil microorganisms are central in shaping the diversity and productivity of land plants and provide protection against a diversity of stresses, including metal toxicity. Arbuscular mycorrhizal fungi (AMF) can form extensive extraradical mycelial networks (ERM), which are very efficient in colonizing a new host. We quantified the responses of transcriptomes of wheat and one AMF partner, Rhizoglomus irregulare, to soil disturbance (Undisturbed vs. Disturbed) and to two different preceding mycotrophic species (Ornithopus compressus and Lolium rigidum). Soil disturbance and preceding plant species engender different AMF communities in wheat roots, resulting in a differential tolerance to soil manganese (Mn) toxicity. Soil disturbance negatively impacted wheat growth under manganese toxicity, probably due to the disruption of the ERM, and activated a large number of stress and starvation-related genes. The O. compressus treatment, which induces a greater Mn protection in wheat than L. rigidum, activated processes related to cellular division and growth, and very few related to stress. The L. rigidum treatment mostly induced genes that were related to oxidative stress, disease protection, and metal ion binding. R. irregulare cell division and molecular exchange between nucleus and cytoplasm were increased by O. compressus. These findings are highly relevant for sustainable agricultural systems, when considering a fit-for-purpose symbiosis.

scholarly journals Structure-specific regulation of nutrient absorption, metabolism and transfer in arbuscular mycorrhizal fungi

2018 ◽  
Author(s):  
Hiromu Kameoka ◽  
Taro Maeda ◽  
Nao Okuma ◽  
Masayoshi Kawaguchi
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Arbuscular Mycorrhizal ◽  
Nutrient Absorption ◽  
Rna Seq ◽  
Specific Expression ◽  
Symbiotic Relationships ◽  
Specific Regulation ◽  
Fungal Nutrition

AbstractArbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with most land plants, mainly for the purpose of nutrient exchange. Many studies have revealed the regulation of absorption, metabolism, and transfer of nutrients in AMF and the genes involved in these processes. However, the spatial regulation of the genes among the structures comprising each developmental stage are not well understood. Here, we demonstrate the structure-specific transcriptome of the model AMF species, Rhizophagus irregularis. We performed an ultra-low input RNA-seq analysis, SMART-seq2, comparing five extraradical structures, germ tubes, runner hyphae, branched absorbing structures, immature spores, and mature spores. In addition, we reanalyzed the recently reported RNA-seq data comparing intraradical hyphae and arbuscules. Our analyses captured the distinct features of each structure and revealed the structure-specific expression patterns of genes related to absorption, metabolism, and transfer of nutrients. Of note, the transcriptional profiles suggest the distinct functions of branched absorbing structures in nutrient absorption. These findings provide a comprehensive dataset to advance our understanding of the transcriptional dynamics of fungal nutrition in this symbiotic system.

scholarly journals Structure-Specific Regulation of Nutrient Transport and Metabolism in Arbuscular Mycorrhizal Fungi

2019 ◽  
Vol 60 (10) ◽  
pp. 2272-2281 ◽  
Author(s):  
Hiromu Kameoka ◽  
Taro Maeda ◽  
Nao Okuma ◽  
Masayoshi Kawaguchi
Keyword(s):  
Arbuscular Mycorrhizal Fungi ◽  
Mycorrhizal Fungi ◽  
Expression Patterns ◽  
Nutrient Transport ◽  
Arbuscular Mycorrhizal ◽  
Nutrient Absorption ◽  
Rna Seq ◽  
Specific Expression ◽  
Symbiotic Relationships ◽  
Specific Regulation

Abstract Arbuscular mycorrhizal fungi (AMF) establish symbiotic relationships with most land plants, mainly for the purpose of nutrient exchange. Many studies have revealed the regulation of processes in AMF, such as nutrient absorption from soil, metabolism and exchange with host plants, and the genes involved. However, the spatial regulation of the genes within the structures comprising each developmental stage is not well understood. Here, we demonstrate the structure-specific transcriptome of the model AMF species, Rhizophagus irregularis. We performed an ultra-low input RNA-seq analysis, SMART-seq2, comparing five extraradical structures, germ tubes, runner hyphae, branched absorbing structures (BAS), immature spores and mature spores. In addition, we reanalyzed the recently reported RNA-seq data comparing intraradical mycelium and arbuscule. Our analyses captured the distinct features of each structure and revealed the structure-specific expression patterns of genes related to nutrient transport and metabolism. Of note, the transcriptional profiles suggest distinct functions of BAS in nutrient absorption. These findings provide a comprehensive dataset to advance our understanding of the transcriptional dynamics of fungal nutrition in this symbiotic system.

scholarly journals Multiple Omics Integration Reveals Key Circular RNAs in Hepatocellular Carcinoma

2021 ◽  
Vol 11 ◽  
Author(s):  
Zi-Li Huang ◽  
Xiu-Yan Huang ◽  
Jin Huang ◽  
Xin-Yu Huang ◽  
Yong-Hua Xu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Target Genes ◽  
Differential Expression Analysis ◽  
Enrichment Analysis ◽  
Underlying Mechanism ◽  
Gene Set Enrichment Analysis ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Rna Seq ◽  
Highly Correlated

BackgroundHCC is one of the most common malignancies with an increasing incidence worldwide, especially in Asian countries. However, even though targeted cancer therapy drugs such as sorafenib and regorafenib are available, the overall outcome of HCC remains unsatisfactory. Thus, it is urgent to investigate the molecular mechanisms of HCC progression, so as to provide accurate diagnostic criteria and therapeutic targets.MethodsRNA-seq data was used to identify and quantify circular RNAs (circRNAs). DESeq2 was used to identify the differentially expressed circRNAs. miRNA binding sites within circRNAs were identified by miRanda. Gene set enrichment analysis (GSEA) was conducted to predict the biological function of circRNAs.ResultsThe differential expression analysis identified 107 upregulated and 95 downregulated circRNAs in HCC tissues. We observed that a differentially expressed circRNA (DE-circRNA), hsa_circ_0141900 was highly negatively correlated with its parental gene RAB1A (PCC < -0.6), which was also closely associated with mTOR signaling pathway. Moreover, we also constructed competing endogenous RNA (ceRNA) network to identify key circRNAs involved in HCC. Notably, hsa_circ_0002130 and hsa_circ_0008774 were highly correlated with the genes involved in gluconeogenesis and HNF3A pathway via the target genes, GOT2 and AR, suggesting that the two circRNAs might regulate these pathways, respectively. Survival analysis revealed that GOT2 was associated with favorable prognosis. Furthermore, high expression of hsa_circ_0002130 was found to inhibit tumor cell growth and promotes GOT2 expression.ConclusionIn summary, the circRNAs highlighted by the integrative analysis greatly improved our understanding of the underlying mechanism of circRNAs in HCC.

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