scholarly journals Integrated mRNA and miRNA expression profiling analyses of Pinus massoniana roots and shoots in response to phosphate deficiency

2020 ◽  
Author(s):  
Fuhua Fan ◽  
Xianwen Shang ◽  
Guijie Ding ◽  
Zijing Zhou ◽  
Jianhui Tan
Keyword(s):  
Differential Expression Analysis ◽  
Differentially Expressed Gene ◽  
Pinus Massoniana ◽  
Dynamic Responses ◽  
Differentially Expressed ◽  
Masson Pine ◽  
Pine Seedlings ◽  
Low Pi Stress ◽  
Pi Deficiency ◽  
Pi Stress

Abstract Background Masson pine ( Pinus massoniana ) is primarily present in subtropical and tropical areas of China, which are severely deficient in inorganic phosphate (Pi). Although some studies identified transcriptomic and proteomic responses to Pi deficiency in Masson pine seedlings, different tissues, especially the roots, that exhibit primary responses to low-Pi stress, have not been well studied. To shed further light on the complex responses of Masson pine to Pi deficiency, a spatiotemporal experiment was performed to identify differentially expressed mRNAs and miRNAs under Pi-deficient conditions. Results Spatiotemporal analyses of 72 RNA sequencing libraries provided a comprehensive overview of the dynamic responses of Masson pine to low-Pi stress. Differentially expressed gene analysis revealed several high-affinity phosphate transporters and nitrate transporters, reflecting the crosstalk between nitrate and Pi homeostasis in plants. The MYB family was the most abundant transcription factor family identified. miRNA differential expression analysis identified several families that were associated with Pi deficiency, such as miR399. In addition, some other families, including novel miRNA families in Masson pine, were dramatically changed in response to Pi starvation. GO and KEGG analyses of these mRNAs and targets of miRNAs indicated that metabolic processes were most enriched under Pi deficiency. Conclusions This study provided abundant spatiotemporal transcriptomic information to functionally dissect the response of Masson pine seedlings to Pi deficiency, which will aid in further elucidation of the biological regulatory mechanisms of pines in response to low-Pi stress.

scholarly journals Transcriptome analysis of low phosphate stress response in the roots of masson pine (Pinus massoniana) seedlings

2019 ◽  
Author(s):  
Xiaocheng Pan ◽  
Haibo Hu
Keyword(s):  
Pinus Massoniana ◽  
Ethylene Response Factor ◽  
Rna Seq ◽  
Metal Transporters ◽  
Masson Pine ◽  
Severe Deficiency ◽  
Tropical Areas ◽  
Low Pi Stress ◽  
Pi Deficiency ◽  
Pi Stress

Abstract Background: Masson pine (Pinus massoniana) is primarily present within subtropical and tropical areas in China, and a number of these regions have a severe deficiency in inorganic phosphate (Pi). As a macronutrient, phosphorus plays a crucial role in plant development. Although several studies have studied the responses of masson pine to Pi starvation at the global level using RNA-Seq and comparative proteomic analyses, the detailed features in the roots that primarily respond to low Pi stress have not yet been studied. Results: This study examined the masson pine of the response of masson pine roots to a deficiency in Pi. Approximately 1,117 unigenes were shown to respond to Pi-deficiency by differential expression when analyzed using RNA-Seq. A total of 819 and 298 of these transcripts were up- and down-regulated, respectively. The results identified several phosphate transporters (PHT1, PHO88), ABC transporters and metal transporters. In particular, the ethylene response factor (ERF) was the most abundant transcription factor. Analyses of these genes, including gene ontology enrichment and the KEGG pathway analysis, indicated that the metabolic processes are the most enriched under abiotic stresses, including Pi-deficiency. Conclusions: This study provided abundant transcriptomic information to functionally dissect the response of masson pine roots to a deficiency of Pi, which will provide additional aid to elucidate the biological regulatory mechanisms that the pines use to respond to low Pi stress.

scholarly journals Role of Suillus placidus in Improving the Drought Tolerance of Masson Pine (Pinus massoniana Lamb.) Seedlings

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 332
Author(s):  
Min Li ◽  
Haoyun Wang ◽  
Xizhou Zhao ◽  
Zhongke Lu ◽  
Xueguang Sun ◽  
...  
Keyword(s):  
Drought Stress ◽  
Defense Mechanism ◽  
Southern China ◽  
Dry Weight ◽  
Pinus Massoniana ◽  
Photosynthetic Performance ◽  
Ectomycorrhizal Fungus ◽  
Severe Drought ◽  
Masson Pine ◽  
Pine Seedlings

Masson pine is an important afforestation species in southern China, where seasonal drought is common. The present study focused on the effects of Suillus placidus, an ectomycorrhizal fungus, inoculation on the growth and physiological and biochemical performance of masson pine seedlings under four different watering treatments (well-watered, mild drought, moderate drought, and severe drought) to evaluate the symbiotic relationship between S. placidus and masson pine seedlings. Ectomycorrhizal-inoculated (ECM) and non-inoculated (NM) seedlings were grown in pots and maintained for 60 days using the weighing method. Results showed that seedlings’ growth, dry weight, RWC, chlorophyll content, PSII efficiency, and photosynthesis decreased as drought stress intensified in both ECM and NM plants. This suggests that drought stress significantly limits the growth and photosynthetic performance of masson pine seedlings. Nevertheless, increased An/gs and proline contents in both NM and ECM prevented oxidative damage caused by drought stress. In addition, increased peroxidase (POD) activity is an essential defense mechanism of ECM seedling under drought stress. Compared with NM, ECM seedlings showed faster growth, higher RWC, and photosynthetic performance, and lower lipid peroxidation in cell membranes under drought stress, as indicated by higher POD activity and lower proline and malondialdehyde (MDA). Our experiment found that S. placidus inoculation can enhance the drought resistance of masson pine seedlings by increasing antioxidant enzyme activity, water use efficiency, and proline content, thereby enhancing growth under water-deficiency conditions. S. placidus can be used to cultivate high-quality seedlings and improve their survival in regions that experience seasonal droughts.

scholarly journals Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

2020 ◽  
Author(s):  
Pawel Sega ◽  
Katarzyna Kruszka ◽  
Dawid Bielewicz ◽  
Wojciech Karlowski ◽  
Przemyslaw Nuc ◽  
...  
Keyword(s):  
Small Rnas ◽  
Plant Stress ◽  
Perfect Match ◽  
Regulatory Elements ◽  
Differentially Expressed ◽  
Proximal Promoter ◽  
Nutrient Mobilization ◽  
Pi Starvation ◽  
Low Pi Stress ◽  
Pi Stress

Abstract Background: Small RNAs (sRNAs) are 18–24 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, Bonferroni correction). In roots, a more abundant and diverse set of other sRNAs (1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are upregulated in both organs. Additionally, in barley shoots, upregulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identify 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi scarcity through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

scholarly journals Combined Transcriptome and Proteome Analysis of Masson Pine (Pinus massoniana Lamb.) Seedling Root in Response to Nitrate and Ammonium Supplementations

2020 ◽  
Vol 21 (20) ◽  
pp. 7548
Author(s):  
Qifei Ren ◽  
Yunchao Zhou ◽  
Xinwei Zhou
Keyword(s):  
Transcription Factors ◽  
Lateral Roots ◽  
Pinus Massoniana ◽  
Malate Synthase ◽  
Root Tips ◽  
Masson Pine ◽  
Pine Seedlings ◽  
N Assimilation ◽  
Pinus Massoniana Lamb ◽  
Glutathione Cycle

Nitrogen (N) is an essential nutrient for plant growth and development. Plant species respond to N fluctuations and N sources, i.e., ammonium or nitrate, differently. Masson pine (Pinus massoniana Lamb.) is one of the pioneer plants in the southern forests of China. It shows better growth when grown in medium containing ammonium as compared to nitrate. In this study, we had grown masson pine seedlings in medium containing ammonium, nitrate, and a mixture of both, and performed comparative transcriptome and proteome analyses to observe the differential signatures. Our transcriptome and proteome resulted in the identification of 1593 and 71 differentially expressed genes and proteins, respectively. Overall, the masson pine roots had better performance when fed with a mixture of ammonium and nitrate. The transcriptomic and proteomics results combined with the root morphological responses suggest that when ammonium is supplied as a sole N-source to masson pine seedlings, the expression of ammonium transporters and other non-specific NH4+-channels increased, resulting in higher NH4+ concentrations. This stimulates lateral roots branching as evidenced from increased number of root tips. We discussed the root performance in association with ethylene responsive transcription factors, WRKYs, and MADS-box transcription factors. The differential analysis data suggest that the adaptability of roots to ammonium is possibly through the promotion of TCA cycle, owing to the higher expression of malate synthase and malate dehydrogenase. Masson pine seedlings managed the increased NH4+ influx by rerouting N resources to asparagine production. Additionally, flavonoid biosynthesis and flavone and flavonol biosynthesis pathways were differentially regulated in response to increased ammonium influx. Finally, changes in the glutathione s-transferase genes suggested the role of glutathione cycle in scavenging the possible stress induced by excess NH4+. These results demonstrate that masson pine shows increased growth when grown under ammonium by increased N assimilation. Furthermore, it can tolerate high NH4+ content by involving asparagine biosynthesis and glutathione cycle.

scholarly journals Differential Gene Expression Responding to Low Phosphate Stress in Leaves and Roots of Maize by cDNA-SRAP

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Lei Yan ◽  
Liang Su ◽  
Rui Li ◽  
Hao Li ◽  
Jianrong Bai ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Complex Adaptive ◽  
Differential Gene ◽  
Low Pi Stress ◽  
Leaves And Roots ◽  
Diverse Groups ◽  
Pi Stress

Phosphate (Pi) deficiency in soil can have severe impacts on the growth, development, and production of maize worldwide. In this study, a cDNA-sequence-related amplified polymorphism (cDNA-SRAP) transcript profiling technique was used to evaluate the gene expression in leaves and roots of maize under Pi stress for seven days. A total of 2494 differentially expressed fragments (DEFs) were identified in response to Pi starvation with 1202 and 1292 DEFs in leaves and roots, respectively, using a total of 60 primer pairs in the cDNA-SRAP analysis. These DEFs were categorized into 13 differential gene expression patterns. Results of sequencing and functional analysis showed that 63 DEFs (33 in leaves and 30 in roots) were annotated to a total of 54 genes involved in diverse groups of biological pathways, including metabolism, photosynthesis, signal transduction, transcription, transport, cellular processes, genetic information, and organismal system. This study demonstrated that (1) the cDNA-SRAP transcriptomic profiling technique is a powerful method to analyze differential gene expression in maize showing advantageous features among several transcriptomic methods; (2) maize undergoes a complex adaptive process in response to low Pi stress; and (3) a total of seven differentially expressed genes were identified in response to low Pi stress in leaves or roots of maize and could be used in the genetic modification of maize.

scholarly journals Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pawel Sega ◽  
Katarzyna Kruszka ◽  
Dawid Bielewicz ◽  
Wojciech Karlowski ◽  
Przemyslaw Nuc ◽  
...  
Keyword(s):  
Small Rnas ◽  
Plant Stress ◽  
Regulatory Elements ◽  
Differentially Expressed ◽  
Proximal Promoter ◽  
Rna Seq ◽  
Nutrient Mobilization ◽  
Pi Starvation ◽  
Low Pi Stress ◽  
Pi Stress

Abstract Background Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, Bonferroni adjusted p-value < 0.05) are represented by 15 molecules in shoot and 13 in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13% from the average of the unique small RNA expressed under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01%). More than 80% of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3′-5′ exonuclease). This suggests that most small RNAs may be generated upon nucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools. Conclusions Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

scholarly journals POS0359 MOLECULAR PROFILING OF RADIOGRAPHIC AXIAL SPONDYLOARTHRITIS PATIENTS REVEALS AN ASSOCIATION BETWEEN INNATE AND ADAPTIVE CELL POPULATIONS AND THERAPEUTIC RESPONSE TO ADALIMUMAB

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 410.1-410
Author(s):  
D. Sobral ◽  
A. F. Fernandes ◽  
A. Mashayekhi Sardoo ◽  
M. Bernardes ◽  
P. Pinto ◽  
...  
Keyword(s):  
Disease Activity ◽  
Immune Cell ◽  
Axial Spondyloarthritis ◽  
Therapeutic Option ◽  
Differential Expression Analysis ◽  
Differentially Expressed Gene ◽  
Molecular Profiling ◽  
Response To Therapy ◽  
Differentially Expressed ◽  
Response To Treatment

Background:The response to treatment in spondylarthropaties is heterogeneous, due to factors yet to be better described. For that reason, it is important to find tools that might help clinicians to decide what is the best available therapeutic option for each patient.Objectives:The goal of this study is to use comprehensive molecular profiling to characterize clinical response to therapy in a real-world setting. Specifically, to identify molecular biomarkers differentiating good responders and non-responders to TNF inhibitors (TNFi) treatment, using adalimumab, in radiographic axial spondyloarthritis | ankylosing spondylitis (r-axSpA|AS) patients context.Methods:Whole-blood mRNA and plasma proteins were measured in a cohort of biologic naïve r-axSpA|AS patients (n = 35) from the Bioefficacy study (Biomarkers identification of anti-TNF alpha agent efficacy in AS patients using RNA sequencing and mass spectrometry), pre and post (14 weeks) TNFi treatment using adalimumab. Response to treatment was categorized according to ASAS20. Results of differential expression analysis were used to identify the most enriched pathways and in predictive models to distinguish responses to TNFi.Results:A treatment-related signature, independent of the type of response, suggests a reduction in inflammatory disease activity. We found genes and proteins robustly differentially expressed between baseline and week 14 in responders, including the GWAS AS-associated genes TNFRSF1A, FCGR2A, TYK2, TBKBP1, IL1R1, IL6R, ICOSLG, IL7R, HHAT and LTBR. Moreover, CRP and HP proteins showed strong and early decrease in the plasma of AS patients, while a cluster of apolipoproteins (APO1, APO2, APO3) showed an increased expression at week 14. Good responders to TNFi treatment tend to have higher expression of innate immunity genes at baseline, and lower expression of markers associated with adaptive immunity, particularly B-cells. A logistic regression model incorporating ASDAS-CRP, gender and Gene x, the top differentially expressed gene at baseline between responders and non-responders, enabled an accurate prediction of response to adalimumab in our cohort (AUC=0.97).Conclusion:Differences in disease activity and/or innate/adaptive immune cell type composition at baseline may be a major contributor to response to adalimumab in r-axSpA|AS. Alternatively, a model including clinical and gene expression variables could be considered, particularly in patients with mild disease activity.Disclosure of Interests:None declared

scholarly journals Pi-starvation induced transcriptional changes in barley revealed by a comprehensive RNA-Seq and degradome analyses

2020 ◽  
Author(s):  
Pawel Sega ◽  
Katarzyna Kruszka ◽  
Dawid Bielewicz ◽  
Wojciech Karlowski ◽  
Przemyslaw Nuc ◽  
...  
Keyword(s):  
Small Rnas ◽  
Plant Stress ◽  
Regulatory Elements ◽  
Differentially Expressed ◽  
Proximal Promoter ◽  
Rna Seq ◽  
Nutrient Mobilization ◽  
Pi Starvation ◽  
Low Pi Stress ◽  
Pi Stress

Abstract Background: Small RNAs (sRNAs) are 20–30 nt regulatory elements which are responsible for plant development regulation and participate in many plant stress responses. Insufficient inorganic phosphate (Pi) concentration triggers plant responses to balance the internal Pi level. Results: In this study, we describe Pi-starvation-responsive small RNAs and transcriptome changes in barley (Hordeum vulgare L.) using Next-Generation Sequencing (NGS) RNA-Seq data derived from three different types of NGS libraries: (i) small RNAs, (ii) degraded RNAs, and (iii) functional mRNAs. We find that differentially and significantly expressed miRNAs (DEMs, p-value < 0.05) are represented by 162 (44.88 % of total differentially expressed small RNAs) molecules in shoot and 138 (7.14 %) in root; mainly various miR399 and miR827 isomiRs. The remaining small RNAs (i.e., those without perfect match to reference sequences deposited in miRBase) are considered as differentially expressed other sRNAs (DESs, p-value Bonferroni correction < 0.05). In roots, a more abundant and diverse set of other sRNAs (DESs, 1796 unique sequences, 0.13 % from total unique reads obtained under low-Pi) contributes more to the compensation of low-Pi stress than that in shoots (DESs, 199 unique sequences, 0.01 %). More than 80 % of differentially expressed other sRNAs are up-regulated in both organs. Additionally, in barley shoots, up-regulation of small RNAs is accompanied by strong induction of two nucleases (S1/P1 endonuclease and 3’-5’ exonuclease). This suggests that most small RNAs may be generated upon endonucleolytic cleavage to increase the internal Pi pool. Transcriptomic profiling of Pi-starved barley shoots identifies 98 differentially expressed genes (DEGs). A majority of the DEGs possess characteristic Pi-responsive cis-regulatory elements (P1BS and/or PHO element), located mostly in the proximal promoter regions. GO analysis shows that the discovered DEGs primarily alter plant defense, plant stress response, nutrient mobilization, or pathways involved in the gathering and recycling of phosphorus from organic pools.Conclusions: Our results provide comprehensive data to demonstrate complex responses at the RNA level in barley to maintain Pi homeostasis and indicate that barley adapts to Pi-starvation through elicitation of RNA degradation. Novel P-responsive genes were selected as putative candidates to overcome low-Pi stress in barley plants.

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