scholarly journals Integrated Transcriptome and Proteome Analysis Reveals Complex Regulatory Mechanism of Cotton in Response to Salt Stress

2020 ◽  
Author(s):  
Lin Chen ◽  
Heng Sun ◽  
Jie Kong ◽  
Haijiang Xu ◽  
Xiyan Yang
Keyword(s):  
Salt Stress ◽  
Proteome Analysis ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Complex Signal ◽  
Calcium Signal ◽  
Signal Pathways ◽  
Yield And Quality ◽  
Signal Cascade

Abstract BackgroundSoil salt stress seriously restricts the yield and quality of cotton worldwide. To investigate the molecular mechanism of cotton response to salt stress, a main cultivated variety Gossypium hirsutum L. acc. Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis. ResultsThrough transcriptome analysis of cotton treated with salt stress for 0 h (T0), 3 h (T3) and 12 h (T12), we identified 8,436, 11,628 and 6,311 differentially expressed genes (DEGs) inT3 / T0, T12 / T0 and T12 / T3, respectively. A total of 459 differentially expressed proteins (DEPs) were identified by proteomic analysis, of which 273, 99 and 260 DEPs were identified in T3 / T0, T12 / T0 and T12 / T3, respectively. Metabolic pathways, biosynthesis of secondary metabolites, photosynthesis and plant hormone signal transduction were the main enrichment pathways by annotation of DEGs or DEPs. Detail analysis of the DEGs or DEPs revealed that complex signal pathways, such as ABA and JA signal, calcium signal, MAPK signal cascade, transcription factors, followed by activation of antioxidant and ion transporters, were identified to participate in regulating salt response in cotton.ConclusionsOur results not only contribute to understand the mechanism of cotton response to salt stress, but also provide nine candidate genes, which might be used for molecular breeding to improve salt-tolerance in cotton.

scholarly journals Integrated transcriptome and proteome analysis reveals complex regulatory mechanism of cotton in response to salt stress

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Lin CHEN ◽  
Heng SUN ◽  
Jie KONG ◽  
Haijiang XU ◽  
Xiyan YANG
Keyword(s):  
Salt Stress ◽  
Proteome Analysis ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Integrated Analysis ◽  
Yield And Quality ◽  
Mitogen Activated Protein ◽  
Complex Signaling ◽  
Ja Signaling

Abstract Background Soil salt stress seriously restricts the yield and quality of cotton worldwide. To investigate the molecular mechanism of cotton response to salt stress, a main cultivated variety Gossypium hirsutum L. acc. Xinluzhong 54 was used to perform transcriptome and proteome integrated analysis. Results Through transcriptome analysis in cotton leaves under salt stress for 0 h (T0), 3 h (T3) and 12 h (T12), we identified 8 436, 11 628 and 6 311 differentially expressed genes (DEGs) in T3 vs. T0, T12 vs. T0 and T12 vs. T3, respectively. A total of 459 differentially expressed proteins (DEPs) were identified by proteomic analysis, of which 273, 99 and 260 DEPs were identified in T3 vs. T0, T12 vs. T0 and T12 vs. T3, respectively. Metabolic pathways, biosynthesis of secondary metabolites, photosynthesis and plant hormone signal transduction were enriched among the identified DEGs or DEPs. Detail analysis of the DEGs or DEPs revealed that complex signaling pathways, such as abscisic acid (ABA) and jasmonic acid (JA) signaling, calcium signaling, mitogen-activated protein kinase (MAPK) signaling cascade, transcription factors, activation of antioxidant and ion transporters, were participated in regulating salt response in cotton. Conclusions Our research not only contributed to understand the mechanism of cotton response to salt stress, but also identified nine candidate genes, which might be useful for molecular breeding to improve salt-tolerance in cotton.

scholarly journals Comprehensive Analysis of Transcriptome and Metabolome Reveals the Flavonoid Metabolic Pathway Is Associated with Fruit Peel Coloration of Melon

Molecules ◽  
2021 ◽  
Vol 26 (9) ◽  
pp. 2830
Author(s):  
Aiai Zhang ◽  
Jing Zheng ◽  
Xuemiao Chen ◽  
Xueyin Shi ◽  
Huaisong Wang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Comprehensive Analysis ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Fruit Peel ◽  
External Quality ◽  
Color Formation ◽  
Peel Color ◽  
Dark Green

The peel color is an important external quality of melon fruit. To explore the mechanisms of melon peel color formation, we performed an integrated analysis of transcriptome and metabolome with three different fruit peel samples (grey-green ‘W’, dark-green ‘B’, and yellow ‘H’). A total of 40 differentially expressed flavonoids were identified. Integrated transcriptomic and metabolomic analyses revealed that flavonoid biosynthesis was associated with the fruit peel coloration of melon. Twelve differentially expressed genes regulated flavonoids synthesis. Among them, nine (two 4CL, F3H, three F3′H, IFS, FNS, and FLS) up-regulated genes were involved in the accumulation of flavones, flavanones, flavonols, and isoflavones, and three (2 ANS and UFGT) down-regulated genes were involved in the accumulation of anthocyanins. This study laid a foundation to understand the molecular mechanisms of melon peel coloration by exploring valuable genes and metabolites.

scholarly journals RsSOS1 Responding to Salt Stress Might Be Involved in Regulating Salt Tolerance by Maintaining Na+ Homeostasis in Radish (Raphanus sativus L.)

Horticulturae ◽  
2021 ◽  
Vol 7 (11) ◽  
pp. 458
Author(s):  
Wanting Zhang ◽  
Jingxue Li ◽  
Junhui Dong ◽  
Yan Wang ◽  
Liang Xu ◽  
...  
Keyword(s):  
Plasma Membrane ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Functional Characterization ◽  
Vital Role ◽  
Salt Stress Response ◽  
Reading Frame ◽  
Yield And Quality

Radish is a kind of moderately salt-sensitive vegetable. Salt stress seriously decreases the yield and quality of radish. The plasma membrane Na+/H+ antiporter protein Salt Overly Sensitive 1 (SOS1) plays a crucial role in protecting plant cells against salt stress, but the biological function of the RsSOS1 gene in radish remains to be elucidated. In this study, the RsSOS1 gene was isolated from radish genotype ‘NAU-TR17’, and contains an open reading frame of 3414 bp encoding 1137 amino acids. Phylogenetic analysis showed that RsSOS1 had a high homology with BnSOS1, and clustered together with Arabidopsis plasma membrane Na+/H+ antiporter (AtNHX7). The result of subcellular localization indicated that the RsSOS1 was localized in the plasma membrane. Furthermore, RsSOS1 was strongly induced in roots of radish under 150 mmol/L NaCl treatment, and its expression level in salt-tolerant genotypes was significantly higher than that in salt-sensitive ones. In addition, overexpression of RsSOS1 in Arabidopsis could significantly improve the salt tolerance of transgenic plants. Meanwhile, the transformation of RsSOS1△999 could rescue Na+ efflux function of AXT3 yeast. In summary, the plasma membrane Na+/H+ antiporter RsSOS1 plays a vital role in regulating salt-tolerance of radish by controlling Na+ homeostasis. These results provided useful information for further functional characterization of RsSOS1 and facilitate clarifying the molecular mechanism underlying salt stress response in radish.

scholarly journals Transcriptome Analysis to Identify Putative Genes Involved in Flowering Time Under Different Photoperiods in ‘Hong jin gou’ Common Bean

2019 ◽  
Vol 144 (4) ◽  
pp. 274-279
Author(s):  
Xiaoxu Yang ◽  
Chang Liu ◽  
Zhishan Yan ◽  
Youjun Fan ◽  
Guojun Feng ◽  
...  
Keyword(s):  
Common Bean ◽  
Flowering Time ◽  
Response Regulator ◽  
Differentially Expressed ◽  
Day Length ◽  
Rna Seq ◽  
Yield And Quality ◽  
Highly Sensitive ◽  
Pseudo Response Regulator

Flowering time influences pod yield and quality of common bean (Phaseolus vulgaris); however, our knowledge of flowering time genes and flowering mechanisms in common bean remain limited. We performed RNA-sequencing (RNA-seq) analyses [long-day (LD) condition and short-day (SD) condition] to identify the flowering time genes and analyzed differentially expressed genes to examine their expression levels in relation to flowering time in ‘Hong Jin Gou’ common bean, a cultivar highly sensitive to photoperiod. The circadian patterns of related genes were identified using quantitative real-time polymerase chain reaction (qRT-PCR). Flowering time in ‘Hong Jin Gou’ was influenced by day length: SD conditions promoted flowering. A total of eight flowering time–related genes were identified, which were classified into photoperiod pathways. Homologs of pseudo-response regulator 5, pseudo-response regulator 7, and gigantea were more highly expressed under SD conditions than under LD conditions. Homologs of late elongated hypocotyl and timing of cab expression 1 were differentially expressed under light and dark conditions. Early flowering 3 is a key regulator of the pathway, which coordinates light and circadian clock inputs in leaves to trigger the expression of downstream genes. The present study provides critical information that could facilitate further investigations on the genetic mechanism of flowering time in common bean.

scholarly journals Integrated transcriptome and proteome analysis provides insights into leaf color differences between red-leaved poplar cultivars (‘Quanhong’ and ‘Xuanhong’) and ‘Zhonglin 2025’ (Populus deltoides cv. ‘Zhonglin 2025’)

2020 ◽  
Author(s):  
Xinghao Chen ◽  
Hanqi Liu ◽  
Shijie Wang ◽  
Chao Zhang ◽  
Minsheng Yang ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Populus Deltoides ◽  
Proteome Analysis ◽  
Differentially Expressed ◽  
Anthocyanin Synthesis ◽  
Integrated Analysis ◽  
Physiological Indicators ◽  
Protein Levels ◽  
Color Differences ◽  
Leaf Coloration

Abstract BackgroundThe red-leaved poplar cultivars ‘Quanhong’ and ‘Xuanhong’ are bud mutations of Populus deltoides cv. ‘Zhonglin 2025’. These cultivars are valued for their beautiful shape, lack of flying catkins, and ornamental leaf colors. The molecular mechanism that leads to different leaf colors between these red-leaved poplars and ‘Zhonglin 2025’ remains unclear.ResultsIn this study, we analyzed growth and physiological indicators in the ‘Quanhong’, ‘Xuanhong’, and ‘Zhonglin 2025’ poplar cultivars, and performed transcriptome and proteome analysis of their leaves. The results showed that plant height and ground diameter were significantly lower in both red-leaved poplars than in ‘Zhonglin 2025’, indicating that their growth and development were markedly inhibited. The ratio of anthocyanin to total chlorophyll and photosynthetic capacity of the leaves were higher and lower, respectively, in the red-leaved cultivars than in ‘Zhonglin 2025’. At the transcript and protein levels, 6,792 differentially expressed genes (DEGs) and 2,786 differentially expressed proteins (DEPs) were screened in the ‘Quanhong’ cultivar, respectively, and 4,398 DEGs and 2,333 DEPs were screened in the ‘Xuanhong’ cultivar, respectively. We screened 769 DEGs/DEPs in ‘Quanhong’ and 399 DEGs/DEPs in ‘Xuanhong’ in an integrated transcriptomics/proteomics analysis. Based on the results of this integrated analysis, 15 and 11 genes/proteins involved in anthocyanin synthesis were further identified in ‘Quanhong’ and ‘Xuanhong’, respectively, including the CHS , F3H , and DFR genes. Among the 120 transcription factors, 3 (HY5, HYH, and TTG2), may be directly involved in the regulation of anthocyanin synthesis in both red-leaved poplars.ConclusionsBy comparing the proteomes and transcriptomes of red-leaved poplar cultivars and ‘Zhonglin 2025’, we identified the key genes and proteins related to red leaf coloration. The findings of this study provided insights that may aid further studies of the molecular mechanism of leaf red coloration in red-leaved poplars.

scholarly journals Identification of Differentially Expressed miRNAs and mRNAs in Vestibular Schwannoma by Integrated Analysis

2019 ◽  
Vol 2019 ◽  
pp. 1-10
Author(s):  
Yanhua Lei ◽  
Ping Guo ◽  
Xiuguo Li ◽  
Yuanyuan Zhang ◽  
Ting Du
Keyword(s):  
Vestibular Schwannoma ◽  
Functional Annotation ◽  
Expression Profiles ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Protein Protein Interaction ◽  
Mirna Expression Profiles ◽  
Differentially Expressed Mirnas

Background.Vestibular schwannoma (VS) is benign, slow-growing brain tumor that negatively impacts patient quality of life, which may cause even death. This study aimed to explore key genes and microRNAs (miRNAs) associated with VS.Methods.The mRNA and miRNA expression profiles of VS downloaded from Gene Expression Omnibus (GEO) database were included in this study to perform an integrated analysis. The differentially expressed mRNAs (DEmRNAs) and miRNAs (DEmiRNAs) were identified. Then, functional annotation and protein-protein interaction networks (PPI) of DEmRNAs were constructed. DEmiRNA-target DEmRNAs analysis and functional annotation of DEmiRNA-target DEmRNAs were performed.Results.A total of 2627 DEmRNAs (1194 upregulated and 1433 downregulated DEmRNAs) and 21 DEmiRNAs (12 upregulated and 9 downregulated DEmiRNAs) were identified. ISG15, TLE1, and XPC were three hub proteins of VS-specific PPI network. A total of 2970 DEmiRNAs-DEmRNAs pairs were obtained. Among which, hsa-miR-181a-5p, hsa-miR-106-5p, and hsa-miR-34a-5p were the top three DEmiRNAs that covered most DEmRNAs. The functional annotation of DEmiRNA-target DEmRNAs revealed that the DEmiRNA-target DEmRNAs were significantly enriched in cGMP-PKG signaling pathway, adrenergic signaling in cardiomyocytes, and pathways in cancer.Conclusion.The results of this present study may provide a comprehensive understanding for the roles of DEmRNAs and DEmiRNAs in the pathogenesis of VS and developing potential biomarkers of VS.

scholarly journals Integrative Analysis of Transcriptome and Metabolome Reveals Salt Stress Orchestrating the Accumulation of Specialized Metabolites in Lycium barbarum L. Fruit

2021 ◽  
Vol 22 (9) ◽  
pp. 4414
Author(s):  
Shuang Lin ◽  
Shaohua Zeng ◽  
Biao A ◽  
Xiaoman Yang ◽  
Tianshun Yang ◽  
...  
Keyword(s):  
Salt Stress ◽  
Pearson Correlation ◽  
Structural Genes ◽  
Lycium Barbarum ◽  
Specialized Metabolites ◽  
Yield And Quality ◽  
Solid Foundation ◽  
Pearson Correlation Analysis ◽  
Stress Influences

Salt stress seriously affects yield and quality of crops. The fruit of Lycium barbarum (LBF) is extensively used as functional food due to its rich nutrient components. It remains unclear how salt stress influences the quality of LBF. In this study, we identified 71 differentially accumulated metabolites (DAMs) and 1396 differentially expressed genes (DEGs) among ripe LBF with and without 300 mM of NaCl treatment. Pearson correlation analysis indicated that the metabolomic changes caused by salt stress were strongly related to oxidoreductases; hydrolases; and modifying enzymes, in particular, acyltransferases, methyltransferases and glycosyltransferases. Further analysis revealed that salt stress facilitated flavonoid glycosylation and carotenoid esterification by boosting the expression of structural genes in the biosynthetic pathways. These results suggested that salt stress prompts the modification of flavonoids and carotenoids to alleviate ROS damage, which in turn improves the quality of LBF. Our results lay a solid foundation for uncovering the underlying molecular mechanism of salt stress orchestrating LBF quality, and the candidate genes identified will be a valuable gene resource for genetic improvement of L. barbarum.

An integrated analysis of mRNA and miRNA in skeletal muscle from myostatin-edited Meishan pigs

Genome ◽  
2019 ◽  
Vol 62 (5) ◽  
pp. 305-315 ◽  
Author(s):  
Shanshan Xie ◽  
Xiang Li ◽  
Lili Qian ◽  
Chunbo Cai ◽  
Gaojun Xiao ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Growth And Development ◽  
Target Genes ◽  
Muscle Growth ◽  
Genetically Engineered ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Signal Pathways ◽  
Skeletal Muscle Growth ◽  
Differentially Expressed Mirnas

Myostatin (MSTN) is a key muscle factor that negatively regulates skeletal muscle growth and development. Our laboratory recently produced genetically engineered Meishan pigs containing a ZFN-edited MSTN loss-of-function mutation (MSTN−/−, MKO) that led to the hypertrophy of skeletal muscles. In this study, we performed transcriptome sequencing and miRNA sequencing in skeletal muscle samples from MKO and wildtype Meishan (MWT) pigs to investigate the effect of MSTN−/− on expression of mRNA and miRNA. Our results indicated that, compared to MWT pigs, there were 200 genes and 4 miRNAs being significantly up-regulated, and 238 genes and 5 miRNAs being significantly down-regulated in MKO pigs. Analysis by GO and KEGG pathways revealed that differentially expressed miRNAs and their target genes of those differentially expressed miRNAs were involved in the signal pathways of skeletal muscle growth and development such as AMPK, mTOR, and TGF-beta. An integrated analysis of the correlation between miRNA-mRNA and transcriptome predicated that XK and METTL8 were target genes for miR-499-5p, while LRP4 was a target gene for miR-490-3p. Our results provide important clues to help us further investigate MSTN′s regulatory mechanisms during skeletal muscle growth and development.

scholarly journals An integrated transcriptomics and proteomics study of Head and Neck Squamous Cell Carcinoma – methodological and analytical considerations.

2015 ◽  
Author(s):  
Anupama Rajan Bhat ◽  
Manoj Kumar Gupta ◽  
Priya Krithivasan ◽  
Kunal Dhas ◽  
Jayalakshmi Nair ◽  
...  
Keyword(s):  
Data Analysis ◽  
Proteome Analysis ◽  
Peptide Identification ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Primary Tumors ◽  
Normal Tissues ◽  
Tumor Tissues ◽  
The Individual ◽  
Integrated Data Analysis

High throughput molecular profiling and integrated data analysis with tumor tissues require overcoming challenges like tumor heterogeneity and tissue paucity. This study is an attempt to understand and optimize various steps during tissue processing and in establishing pipelines essential for integrated analysis. Towards this effort, we subjected laryngo-pharyngeal primary tumors and the corresponding adjacent normal tissues (n=2) to two RNA and protein isolation methods, one wherein RNA and protein were isolated from the same tissue sequentially (Method 1) and second, wherein the extraction was carried out using two independent methods (Method 2). RNA and protein from both methods were subjected to RNA-seq and iTRAQ based LC-MS/MS analysis. Transcript and peptide identification and quantification was followed by both individual -ome and integrated data analysis. As a result of this analysis, we identified a higher number of total, as well as differentially expressed (DE) transcripts (1329 vs 1134) and proteins (799 vs 408) with fold change ≥ 2.0, in Method 1. Among these, 173 and 86 entities were identified by both transcriptome and proteome analysis in Method 1 and 2, respectively, with higher concordance in the regulation trends observed in the former. The significant cancer related pathways enriched with the individual DE transcript or protein data were similar in both the methods. However, the entities mapping to them were different, allowing enhanced view of the pathways identified after integration of the data and subsequent mapping. The concordant DE transcripts and proteins also revealed key molecules of the pathways with important roles in cancer development. This study thus demonstrates that sequential extraction of the RNA and proteins from the same tissue allows for better profiling of differentially expressed entities and a more accurate integrated data analysis.

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