scholarly journals Shared differentially expressed genes of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) seedlings under low nitrogen and phosphorus stress

2017 ◽  
Author(s):  
JianHui Li ◽  
GuiFang Ma ◽  
DingWei Luo ◽  
ZaiKang Tong ◽  
Jinliang Xu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Chinese Fir ◽  
Cunninghamia Lanceolata ◽  
Utilization Efficiency ◽  
Differentially Expressed ◽  
Nitrogen And Phosphorus ◽  
Stress Group ◽  
Phosphorus Stress ◽  
Low Nitrogen

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an excellent fast-growing timber species and has significant value in the forestry industry. In order to increase the nitrogen and phosphorus absorption and utilization in Chinese fir, shared differentially expressed genes under low nitrogen and phosphorus stress were screened in this study. Seedling of Chinese fir clone X6 was cultivated in aeroponic system with 3 treatments, namely, low nitrogen (LN), low phosphorus (LP) and a control check (with nitrogen and phosphorus sufficient, CK). After 4 months of treatment, the roots from the LN, LP and CK groups were collected and transcriptome sequencing was done by LC Sciences (USA) using an Illumina platform. When comparing the LN stress group with the CK group, 977 SDGEs were detected, 264 of which had KEGG annotations; 931 SDGEs were detected when comparing the LP stress group with the CK group, of which 189 had KEGG annotations; 297 SDGEs were detected in both the LN stress and LP stress groups, 78 of which had KEGG annotations representing 98 metabolic pathways. Among the 78 selected SDEGs that were differentially expressed under both LN and LP stress conditions, Twenty-one SDEGs were selected based on the metabolic pathways that nitrogen and phosphorus are involved in, these genes are PNR, PSBA, EGLC, GLC, END, BGLU, AMY, A1E, PAL, GOGAT, NIR1, NIR2, C4M, PAL, PRDX6, POX, CCR, CCoAOMT, FDH, CHS and ANR. These genes can potentially be used in breeding to improve both nitrogen and phosphorus utilization efficiency in Chinese fir.

scholarly journals Shared differentially expressed genes of Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) seedlings under low nitrogen and phosphorus stress

2017 ◽  
Author(s):  
JianHui Li ◽  
GuiFang Ma ◽  
DingWei Luo ◽  
ZaiKang Tong ◽  
Jinliang Xu ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Chinese Fir ◽  
Cunninghamia Lanceolata ◽  
Utilization Efficiency ◽  
Differentially Expressed ◽  
Nitrogen And Phosphorus ◽  
Stress Group ◽  
Phosphorus Stress ◽  
Low Nitrogen

Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) is an excellent fast-growing timber species and has significant value in the forestry industry. In order to increase the nitrogen and phosphorus absorption and utilization in Chinese fir, shared differentially expressed genes under low nitrogen and phosphorus stress were screened in this study. Seedling of Chinese fir clone X6 was cultivated in aeroponic system with 3 treatments, namely, low nitrogen (LN), low phosphorus (LP) and a control check (with nitrogen and phosphorus sufficient, CK). After 4 months of treatment, the roots from the LN, LP and CK groups were collected and transcriptome sequencing was done by LC Sciences (USA) using an Illumina platform. When comparing the LN stress group with the CK group, 977 SDGEs were detected, 264 of which had KEGG annotations; 931 SDGEs were detected when comparing the LP stress group with the CK group, of which 189 had KEGG annotations; 297 SDGEs were detected in both the LN stress and LP stress groups, 78 of which had KEGG annotations representing 98 metabolic pathways. Among the 78 selected SDEGs that were differentially expressed under both LN and LP stress conditions, Twenty-one SDEGs were selected based on the metabolic pathways that nitrogen and phosphorus are involved in, these genes are PNR, PSBA, EGLC, GLC, END, BGLU, AMY, A1E, PAL, GOGAT, NIR1, NIR2, C4M, PAL, PRDX6, POX, CCR, CCoAOMT, FDH, CHS and ANR. These genes can potentially be used in breeding to improve both nitrogen and phosphorus utilization efficiency in Chinese fir.

Transcriptional identification of differentially expressed genes during the prepupal–pupal transition in the oriental armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae)

2021 ◽  
pp. 1-14
Author(s):  
Peirong Li ◽  
Xinru Li ◽  
Wei Wang ◽  
Xiaoling Tan ◽  
Xiaoqi Wang ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Developmental Stages ◽  
Kegg Pathway ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Mythimna Separata ◽  
Kegg Pathway Analysis ◽  
Oriental Armyworm ◽  
Lepidoptera Noctuidae

Abstract The oriental armyworm, Mythimna separata (Walker) is a serious pest of agriculture that does particular damage to Gramineae crops in Asia, Europe, and Oceania. Metamorphosis is a key developmental stage in insects, although the genes underlying the metamorphic transition in M. separata remain largely unknown. Here, we sequenced the transcriptomes of five stages; mature larvae (ML), wandering (W), and pupation (1, 5, and 10 days after pupation, designated P1, P5, and P10) to identify transition-associated genes. Four libraries were generated, with 22,884, 23,534, 26,643, and 33,238 differentially expressed genes (DEGs) for the ML-vs-W, W-vs-P1, P1-vs-P5, and P5-vs-P10, respectively. Gene ontology enrichment analysis of DEGs showed that genes regulating the biosynthesis of the membrane and integral components of the membrane, which includes the cuticular protein (CP), 20-hydroxyecdysone (20E), and juvenile hormone (JH) biosynthesis, were enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that DEGs were enriched in the metabolic pathways. Of these DEGs, thirty CP, seventeen 20E, and seven JH genes were differentially expressed across the developmental stages. For transcriptome validation, ten CP, 20E, and JH-related genes were selected and verified by real-time PCR quantitative. Collectively, our results provided a basis for further studies of the molecular mechanism of metamorphosis in M. separata.

scholarly journals Lr34-Mediated Leaf Rust Resistance in Wheat: Transcript Profiling Reveals a High Energetic Demand Supported by Transient Recruitment of Multiple Metabolic Pathways

2008 ◽  
Vol 21 (12) ◽  
pp. 1515-1527 ◽  
Author(s):  
Melvin D. Bolton ◽  
James A. Kolmer ◽  
Wayne W. Xu ◽  
David F. Garvin
Keyword(s):  
Leaf Rust ◽  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Puccinia Triticina ◽  
Leaf Rust Resistance ◽  
Differentially Expressed ◽  
Metabolic Responses ◽  
Metabolism Enzymes ◽  
Wheat Gene ◽  
Energetic Demand

The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent of wheat leaf rust. However, the biological basis for the exceptional durability of Lr34 is unclear. We used the Affymetrix GeneChip Wheat Genome Array to compare transcriptional changes of near-isogenic lines of Thatcher wheat in a compatible interaction, an incompatible interaction conferred by the resistance gene Lr1, and the race-nonspecific response conditioned by Lr34 3 and 7 days postinoculation (dpi) with P. triticina. No differentially expressed genes were detected in Lr1 plants at either timepoint whereas, in the compatible Thatcher interaction, differentially expressed genes were detected only at 7 dpi. In contrast, differentially expressed genes were identified at both timepoints in P. triticina-inoculated Lr34 plants. At 3 dpi, upregulated genes associated with Lr34-mediated resistance encoded various defense and stress-related proteins, secondary metabolism enzymes, and transcriptional regulation and cellular-signaling proteins. Further, coordinated upregulation of key genes in several metabolic pathways that can contribute to increased carbon flux through the tricarboxylic cycle was detected. This indicates that Lr34-mediated resistance imposes a high energetic demand that leads to the induction of multiple metabolic responses to support cellular energy requirements. These metabolic responses were not sustained through 7 dpi, and may explain why Lr34 fails to inhibit the pathogen fully but does increase the latent period.

scholarly journals RNAseq Analysis Reveals Altered Expression of Key Ion Transporters Causing Differential Uptake of Selective Ions in Canola (Brassica napus L.) Grown under NaCl Stress

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 891 ◽  
Author(s):  
Mobina Ulfat ◽  
Habib-ur-Rehman Athar ◽  
Zaheerud-din Khan ◽  
Hazem M. Kalaji
Keyword(s):  
Salt Stress ◽  
Brassica Napus ◽  
Differentially Expressed Genes ◽  
Nacl Stress ◽  
Utilization Efficiency ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Salt Tolerant ◽  
Brassica Napus L ◽  
Salt Tolerant Cultivars

Salinity is one of the major abiotic stresses prevailing throughout the world that severely limits crop establishment and production. Every crop has an intra-specific genetic variation that enables it to cope with variable environmental conditions. Hence, this genetic variability is a good tool to exploit germplasms in salt-affected areas. Further, the selected cultivars can be effectively used by plant breeders and molecular biologists for the improvement of salinity tolerance. In the present study, it was planned to identify differential expression of genes associated with selective uptake of different ions under salt stress in selected salt-tolerant canola (Brassica napus L.) cultivar. For the purpose, an experiment was carried out to evaluate the growth response of different salt-sensitive and salt-tolerant canola cultivars. Plants were subjected to 200 mM NaCl stress. Canola cultivars—Faisal Canola, DGL, Dunkled, and CON-II—had higher growth than in cvs Cyclone, Ac-EXcel, Legend, and Oscar. Salt-tolerant cultivars were better able to maintain plant water status probably through osmotic adjustment as compared to salt-sensitive cultivars. Although salt stress increased shoot Na+ and shoot Cl− contents in all canola cultivars, salt-tolerant cultivars had a lower accumulation of these toxic nutrients. Similarly, salt stress reduced shoot K+ and Ca2+ contents in all canola cultivars, while salt-tolerant cultivars had a higher accumulation of K+ and Ca2+ in leaves, thereby having greater shoot K+/Na+ and Ca2+/Na+ ratios. Nutrient utilization efficiency decreased significantly in all canola cultivars due to the imposition of salt stress; however, it was greater in salt-tolerant cultivars—Faisal Canola, DGL, and Dunkled. Among four salt-tolerant canola cultivars, cv Dunkled was maximal in physiological attributes, and thus differentially expressed genes (DEGs) were assessed in it by RNA-seq analysis using next-generation sequencing (NGS) techniques. The differentially expressed genes (DEG) in cv Dunkled under salt stress were found to be involved in the regulation of ionic concentration, photosynthesis, antioxidants, and hormonal metabolism. However, the most prominent upregulated DEGs included Na/K transporter, HKT1, potassium transporter, potassium channel, chloride channel, cation exchanger, Ca channel. The RNA-seq data were validated through qRT-PCR. It was thus concluded that genes related to the regulation of ionic concentrate are significantly upregulated and expressed under salt stress, in the cultivar Dunkled.

scholarly journals Transcriptomic and Proteomic Profiling of Anabaena sp. Strain 90 under Inorganic Phosphorus Stress

2015 ◽  
Vol 81 (15) ◽  
pp. 5212-5222 ◽  
Author(s):  
Jonna Teikari ◽  
Julia Österholm ◽  
Matthias Kopf ◽  
Natalia Battchikova ◽  
Matti Wahlsten ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Cyanobacterial Bloom ◽  
Inorganic Phosphorus ◽  
Cellular Growth ◽  
Differentially Expressed ◽  
Cyanobacterial Blooms ◽  
Limiting Factors ◽  
Transport Systems ◽  
Phosphorus Starvation ◽  
Phosphorus Stress

ABSTRACTInorganic phosphorus (Pi) is one of the main growth-limiting factors of diazotrophic cyanobacteria. Due to human activity, the availability of Pihas increased in water bodies, resulting in eutrophication and the formation of massive cyanobacterial blooms. In this study, we examined the molecular responses of the cyanobacteriumAnabaenasp. strain 90 to phosphorus deprivation, aiming at the identification of candidate genes to monitor the Pistatus in cyanobacteria. Furthermore, this study increased the basic understanding of how phosphorus affects diazotrophic and bloom-forming cyanobacteria as a major growth-limiting factor. Based on RNA sequencing data, we identified 246 differentially expressed genes after phosphorus starvation and 823 differentially expressed genes after prolonged Pilimitation, most of them related to central metabolism and cellular growth. The transcripts of the genes related to phosphorus transport and assimilation (phoregulon) were most upregulated during phosphorus depletion. One of the most increased transcripts encodes a giant protein of 1,869 amino acid residues, which contains, among others, a phytase-like domain. Our findings predict its crucial role in phosphorus starvation, but future studies are still needed. Using two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we found 43 proteins that were differentially expressed after prolonged phosphorus stress. However, correlation analysis unraveled an association only to some extent between the transcriptomic and proteomic abundances. Based on the present results, we suggest that the method used for monitoring the Pistatus in cyanobacterial bloom should contain wider combinations ofphoregulon genes (e.g., PstABCS transport systems) in addition to the commonly used alkaline phosphatase gene alone.

scholarly journals A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]

2020 ◽  
Author(s):  
Shunkai Hu ◽  
Mi Zhang ◽  
Yiqing Yang ◽  
Wei Xuan ◽  
Zhongwei Zou ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factors ◽  
Differentially Expressed Genes ◽  
Lateral Roots ◽  
Nitrogen Concentration ◽  
Tea Plant ◽  
Differentially Expressed ◽  
Auxin Signaling ◽  
Tea Plants ◽  
Low Nitrogen

Abstract Abstract Background Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverage worldwide. Lateral roots (LRs) of tea plant are the main organ used for tea plant to absorb soil moisture and nutrients. Lateral roots formation and development are tightly regulated by the nitrogen and auxin signaling pathway. In order to understand the function of auxin and nitrogen signaling in LRs formation and development, transcriptome analysis was applied to investigate the differentially expressed genes involved in lateral roots of tea plants treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high nitrogen concentration. Results A total of 296 common differentially expressed genes were mainly identified and annotated to four signaling pathways, such as nitrogen metabolism, plant hormone signal transduction, Glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of transcripts, thereby regulating lateral roots formation. Furthermore, metabolism of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to the lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration in lateral roots was increased, while the nitrogen level decreased. Thus, tea plant lateral roots formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation. Conclusion This study provides new insights into the mechanisms associated with nitrogen and auxin signaling pathways to regulate LRs formation and arises new clues for the efficient utilization of nitrogen in tea plant at the genetic level.

scholarly journals Transcriptome Analysis of Salt-Sensitive and Tolerant Genotypes Reveals Salt-Tolerance Metabolic Pathways in Sugar Beet

2019 ◽  
Vol 20 (23) ◽  
pp. 5910 ◽  
Author(s):  
Gui Geng ◽  
Chunhua Lv ◽  
Piergiorgio Stevanato ◽  
Renren Li ◽  
Hui Liu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Sugar Beet ◽  
Differentially Expressed Genes ◽  
Metabolic Pathways ◽  
Defense Responses ◽  
Transport Processes ◽  
Differentially Expressed ◽  
Salt Tolerant ◽  
Gene Markers

Soil salinization is a common environmental problem that seriously affects the yield and quality of crops. Sugar beet (Beta vulgaris L.), one of the main sugar crops in the world, shows a strong tolerance to salt stress. To decipher the molecular mechanism of sugar beet under salt stress, we conducted transcriptomic analyses of two contrasting sugar beet genotypes. To the best of our knowledge, this is the first comparison of salt-response transcriptomes in sugar beet with contrasting genotypes. Compared to the salt-sensitive cultivar (S710), the salt-tolerant one (T710MU) showed better growth and exhibited a higher chlorophyll content, higher antioxidant enzyme activity, and increased levels of osmotic adjustment molecules. Based on a high-throughput experimental system, 1714 differentially expressed genes were identified in the leaves of the salt-sensitive genotype, and 2912 in the salt-tolerant one. Many of the differentially expressed genes were involved in stress and defense responses, metabolic processes, signal transduction, transport processes, and cell wall synthesis. Moreover, expression patterns of several genes differed between the two cultivars in response to salt stress, and several key pathways involved in determining the salt tolerance of sugar beet, were identified. Our results revealed the mechanism of salt tolerance in sugar beet and provided potential metabolic pathways and gene markers for growing salt-tolerant cultivars.

Identification and analysis of differentially expressed genes in differentiating xylem of Chinese fir (Cunninghamia lanceolata) by suppression subtractive hybridization

Genome ◽  
2007 ◽  
Vol 50 (12) ◽  
pp. 1141-1155 ◽  
Author(s):  
Guifeng Wang ◽  
Yan Gao ◽  
Liwei Yang ◽  
Jisen Shi
Keyword(s):  
Real Time ◽  
Suppression Subtractive Hybridization ◽  
Real Time Pcr ◽  
Molecular Mechanisms ◽  
Subtractive Hybridization ◽  
Wood Formation ◽  
Chinese Fir ◽  
Cunninghamia Lanceolata ◽  
Differentially Expressed ◽  
Xylem Differentiation

Wood is an important raw material for global industries with rapidly increasing demand. To isolate the genes differentially expressed during xylogenesis of Chinese fir ( Cunninghamia lanceolata (Lamb.) Hook.), we used a novel system. Forward and reverse subtracted cDNA libraries were constructed using the suppression subtractive hybridization method; for the forward library we used cDNA from the mutant Dugansha as the tester and cDNA from the wild-type clone Jurong 0 as the driver, and for the reverse library we used Jurong 0 cDNA as the tester and Dugansha cDNA as the driver. Transcriptional profiling was performed using a macroarray with 4 digoxigenin-labeled probes. We obtained 618 and 409 clones from the forward and the reverse subtracted library, respectively. A total of 405 unique expressed sequence tags (ESTs) were obtained. Forty percent of the ESTs exhibited homologies with proteins of known function and fell into 4 major classes: metabolism, cell wall biogenesis and remodeling, signal transduction, and stress. Real-time PCR was performed to confirm the results. The expression levels of 11 selected ESTs were consistent with both macroarray and real-time PCR results. The systematic analysis of genes involved in wood formation in Chinese fir provides valuable insights into the molecular mechanisms involved in xylem differentiation and is an important resource for forest research that can be directed toward understanding the genetic control of wood formation and future endeavors to modify wood and fiber properties for industrial use.

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