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.

Integrated Transcriptome and Proteome Analysis Provides Insights into Anthocyanin Accumulation in the Leaves of Red-Leaved Poplars

2021 ◽  
Author(s):  
Xinghao Chen ◽  
Hanqi Liu ◽  
Shijie Wang ◽  
Chao Zhang ◽  
Minsheng Yang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Candidate Genes ◽  
Molecular Mechanism ◽  
Populus Deltoides ◽  
Proteome Analysis ◽  
Anthocyanin Synthesis ◽  
Total Chlorophyll ◽  
Anthocyanin Accumulation ◽  
Proteome Expression ◽  
Red Coloration

Abstract The 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. However, the understanding of the molecular mechanism of anthocyanin accumulation in the leaves of red-leaved poplars is still unclear. Here, we profiled the changes of pigment content, transcriptome and proteome expression in the leaves of three poplar cultivars and the results showed that the ratios of anthocyanin to total chlorophyll in both red-leaved poplars were higher than that in ‘Zhonglin 2025’, indicating that the anthocyanin was highly accumulated in the leaves of red-leaved poplars. Based on the results of integrated transcriptome and proteome analysis, 15 and 11 differentially expressed genes/proteins involved in anthocyanin synthesis were screened 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. This study screens the candidate genes involved in anthocyanin accumulation in the leaves of red-leaved poplars and lays a foundation for further exploring the molecular mechanism of leaf red coloration in red-leaved poplars.

scholarly journals Combined Transcriptome and Proteome Analysis of Maize (Zea mays L.) Reveals A Complementary Profile in Response to Phosphate Deficiency

2021 ◽  
Vol 43 (2) ◽  
pp. 1142-1155
Author(s):  
Zhi Nie ◽  
Bowen Luo ◽  
Xiao Zhang ◽  
Ling Wu ◽  
Dan Liu ◽  
...  
Keyword(s):  
Zea Mays ◽  
Zea Mays L ◽  
Proteome Analysis ◽  
Transcript Level ◽  
Utilization Efficiency ◽  
Differentially Expressed ◽  
Phosphate Deficiency ◽  
Absolute Quantitation ◽  
Protein Levels ◽  
Isobaric Tags

A deficiency in the macronutrient phosphate (Pi) brings about various changes in plants at the morphological, physiological and molecular levels. However, the molecular mechanism for regulating Pi homeostasis in response to low-Pi remains poorly understood, particularly in maize (Zea mays L.), which is a staple crop and requires massive amounts of Pi. Therefore, in this study, we performed expression profiling of the shoots and roots of maize seedlings with Pi-tolerant genotype at both the transcriptomic and proteomic levels using RNA sequencing and isobaric tags for relative and absolute quantitation (iTRAQ). We identified 1944 differentially expressed transcripts and 340 differentially expressed proteins under low-Pi conditions. Most of the differentially expressed genes were clustered as regulators, such as transcription factors involved in the Pi signaling pathway at the transcript level. However, the more functional and metabolism-related genes showed expression changes at the protein level. Moreover, under low-Pi conditions, Pi transporters and phosphatases were specifically induced in the roots at both the transcript and protein levels, and increased amounts of mRNA and protein of two purple acid phosphatases (PAPs) and one UDP-sulfoquinovose synthase (SQD) were specifically detected in the roots. The new insights provided by this study will help to improve the P-utilization efficiency of maize.

scholarly journals Integrative Transcriptome and Proteome Analysis Identifies Major Molecular Regulation Pathways Involved in Ramie (Boehmeria nivea (L.) Gaudich) under Nitrogen and Water Co-Limitation

Plants ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 1267
Author(s):  
Jikang Chen ◽  
Gang Gao ◽  
Ping Chen ◽  
Kunmei Chen ◽  
Xiaofei Wang ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Proteome Analysis ◽  
Differentially Expressed ◽  
Poor Correlation ◽  
Factors Affecting ◽  
Protein Levels ◽  
Boehmeria Nivea ◽  
N Efficiency ◽  
New Information

Water and N are the most important factors affecting ramie (Boehmeria nivea (L.) Gaudich) growth. In this study, de novo transcriptome assembly and Tandem Mass Tags (TMT) based quantitative proteome analysis of ramie under nitrogen and water co-limitation conditions were performed, and exposed to treatments, including drought and N-deficit (WdNd), proper water but N-deficit (WNd), proper N but drought (WdN), and proper N and water (CK), respectively. A total of 64,848 unigenes (41.92% of total unigenes) were annotated in at least one database, including NCBI non-redundant protein sequences (Nr), Swiss-Prot, Protein family (Pfam), Gene Ontology (GO) and KEGG Orthology (KO), and 4268 protein groups were identified. Most significant changes in transcript levels happened under water-limited conditions, but most significant changes in protein level happened under water-limited conditions only with proper N. Poor correlation between differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) was observed in ramie responding to the treatments. DEG/DEP regulation patterns related to major metabolic processes responding to water and N deficiency were analyzed, including photosynthesis, ethylene responding, glycolysis, and nitrogen metabolism. Moreover, 41 DEGs and 61 DEPs involved in regulating adaptation of ramie under water and N stresses were provided in the study, including DEGs/DEPs related to UDP—glucuronosyhransferase (UGT), ATP synthase, and carbonate dehydratase. The strong dependency of N-response of ramie on water conditions at the gene and protein levels was highlighted. Advices for simultaneously improving water and N efficiency in ramie were also provided, especially in breeding N efficient varieties with drought resistance. This study provided extensive new information on the transcriptome, proteome, their correlation, and diversification in ramie responding to water and N co-limitation.

Bioinformatics Combined with Quantitative Proteomics Analyses and Identification of Potential Biomarkers in Cholangiocarcinoma

2020 ◽  
Author(s):  
Zijian Da ◽  
Long Gao ◽  
Gang Su ◽  
Jia Yao ◽  
Wenkang Fu ◽  
...  
Keyword(s):  
Risk Factor ◽  
Poor Prognosis ◽  
Independent Risk Factor ◽  
Primary Tumour ◽  
Absolute Quantification ◽  
Gene Expression Omnibus ◽  
The Cancer Genome Atlas ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Protein Levels

Abstract Background Cholangiocarcinoma(CCA)is an invasive malignancy arising from biliary epithelial cells; it is the most common primary tumour of the bile tract and has a poor prognosis. The aim of this study was to screen prognostic biomarkers for CCA by integrated multiomics analysis. Methods The GSE32225 dataset was derived from the Gene Expression Omnibus (GEO) database and comprehensively analysed by using R software and The Cancer Genome Atlas (TCGA) database to obtain the differentially expressed RNAs (DERNAs) associated with CCA prognosis. Quantitative isobaric tags for relative and absolute quantification (iTRAQ) proteomics was used to screen differentially expressed proteins (DEPs) between CCA and nontumour tissues. Through integrated analysis of DERNA and DEP data, we obtained candidate proteins APOF, ITGAV and CASK, and immunohistochemistry was used to detect the expression of these proteins in CCA. The relationship between CASK expression and CCA prognosis was further analysed. Results Through bioinformatics analysis, 875 DERNAs were identified, of which 10 were associated with the prognosis of the CCA patients. A total of 487 DEPs were obtained by using the iTRAQ technique. Comprehensive analysis of multiomics data showed that CASK, ITGAV and APOF expression at both the mRNA and protein levels were different in CCA compared with nontumour tissues. CASK was found to be expressed in the cytoplasm and nucleus of CCA cells in 38 (45%) of 84 patients with CCA. Our results suggested that patients with positive CASK expression had significantly better overall survival (OS) and recurrence-free survival (RFS) than those with negative CASK expression. Univariate and multivariate analyses demonstrated that negative expression of CASK was a significantly independent risk factor for OS and RFS in CCA patients. Conclusions CASK may be a tumour suppressor; its low expression is an independent risk factor for a poor prognosis in CCA patients, and so it could be used as a clinically valuable prognostic marker.

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 analysis of the proteome and transcriptome in human ischemic cardiomyopathy

2020 ◽  
Author(s):  
Kai Zhang ◽  
Xianyu Qin ◽  
Min Wu ◽  
Pengju Wen ◽  
Yueheng Wu ◽  
...  
Keyword(s):  
Ischemic Cardiomyopathy ◽  
Molecular Mechanisms ◽  
Left Ventricular ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Central Position ◽  
Mortality And Morbidity ◽  
Protein Levels ◽  
Data Independent Acquisition ◽  
Key Genes

Abstract Background: Ischemic cardiomyopathy (ICM) is the primary cause of heart failure, which leads to an unacceptable rate of mortality and morbidity. The molecular mechanisms involved in ICM remains incompletely understood. This study aimed to investigate the molecular mechanisms of ICM by integrated proteome and transcriptome analyses.Methods and Results: Data independent acquisition (DIA) mass spectrometry and RNA-seq technologies were performed in left ventricular species from 5 ICM patients and 5 unused non-failing donors. A total of 546 differentially expressed proteins (DEPs) and 1080 mRNAs (DEGs) were identified in ICM compared with control, which were mainly involved in inflammatory/immune response, response to stress (such as hypoxia and reactive oxidative species), oxidative stress, and ECM (extracellular matrix) organization. Moreover, though the low correlation between transcriptome and proteome, 41 key genes were identified, which showed the same expression directions at mRNA and protein levels. Among them, HSP90AA1 occupied a central position in the PPI network. Furthermore, a differentially expressed lncRNA-mRNA-protein network was constructed, which consisted of 13, 11, and 11 differentially expressed lncRNAs, mRNAs, and proteins, respectively, and the expression of this network were validated by qRT-PCR.Conclusion: This identified some key genes and a lncRNA-mRNA-protein regulatory network involved in ICM, which should provide a framework for an in-depth interrogation into the complex molecular mechanisms of ICM.

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.

scholarly journals Integrated Analysis of microRNA and mRNA Transcriptome Reveals the Molecular Mechanism of Solanum lycopersicum Response to Bemisia tabaci and Tomato chlorosis virus

2021 ◽  
Vol 12 ◽  
Author(s):  
Hao Yue ◽  
Li-Ping Huang ◽  
Ding-Yi-Hui Lu ◽  
Zhan-Hong Zhang ◽  
Zhuo Zhang ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Bemisia Tabaci ◽  
Tomato Plant ◽  
Carbon Fixation ◽  
Mapk Signaling ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Control Group ◽  
Tomato Plants ◽  
Tomato Chlorosis Virus

Tomato chlorosis virus (ToCV), is one of the most devastating cultivated tomato viruses, seriously threatened the growth of crops worldwide. As the vector of ToCV, the whitefly Bemisia tabaci Mediterranean (MED) is mainly responsible for the rapid spread of ToCV. The current understanding of tomato plant responses to this virus and B. tabaci is very limited. To understand the molecular mechanism of the interaction between tomato, ToCV and B. tabaci, we adopted a next-generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed under the infection of B. tabaci and ToCV in tomato plants. Our data revealed that 6199 mRNAs were significantly regulated, and the differentially expressed genes were most significantly associated with the plant-pathogen interaction, the MAPK signaling pathway, the glyoxylate, and the carbon fixation in photosynthetic organisms and photosynthesis related proteins. Concomitantly, 242 differentially expressed miRNAs were detected, including novel putative miRNAs. Sly-miR159, sly-miR9471b-3p, and sly-miR162 were the most expressed miRNAs in each sample compare to control group. Moreover, we compared the similarities and differences of gene expression in tomato plant caused by infection or co-infection of B. tabaci and ToCV. Taken together, the analysis reported in this article lays a solid foundation for further research on the interaction between tomato, ToCV and B. tabaci, and provide evidence for the identification of potential key genes that influences virus transmission in tomato plants.

scholarly journals Hypothalamic Transcriptome Analysis Reveals the Crucial MicroRNAs and mRNAs Affecting Litter Size in Goats

2021 ◽  
Vol 8 ◽  
Author(s):  
Chen Liang ◽  
Miaoceng Han ◽  
Zuyang Zhou ◽  
Yufang Liu ◽  
Xiaoyun He ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Molecular Mechanism ◽  
Litter Size ◽  
Transcriptome Analysis ◽  
Target Genes ◽  
Hormone Secretion ◽  
Follicular Phase ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Integrated Analysis

The hypothalamus was the coordination center of the endocrine system, which played an important role in goat reproduction. However, the molecular mechanism of hypothalamus regulating litter size in goats was still poorly understood. This study aims to investigate the key functional genes associated with prolificacy by hypothalamus transcriptome analysis of goats. In this research, an integrated analysis of microRNAs (miRNAs)-mRNA was conducted using the hypothalamic tissue of Yunshang black goats in the follicular stage. A total of 72,220 transcripts were detected in RNA-seq. Besides, 1,836 differentially expressed genes (DEGs) were identified between high fecundity goats at the follicular phase (FP-HY) and low fecundity goats at the follicular phase (FP-LY). DEGs were significantly enriched in 71 Gene Ontology (GO) terms and 8 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The transcriptome data suggested that DEGs such as BMPR1B, FGFR1, IGF1 and CREB1 are directly or indirectly involved in many processes like hypothalamic gonadal hormone secretion. The miRNA-seq identified 1,837 miRNAs, of which 28 differentially expressed miRNAs (DEMs). These DEMs may affect the nerve cells survival of goat hypothalamic regulating the function of target genes and further affect the hormone secretion activities related to reproduction. They were enriched in prolactin signaling pathway, Jak-STAT signaling pathway and GnRH signaling pathway, as well as various metabolic pathways. Integrated analysis of DEMs and DEGs showed that 87 DEGs were potential target genes of 28 DEMs. After constructing a miRNA-mRNA pathway network, we identified several mRNA-miRNAs pairs by functional enrichment analysis, which was involved in hypothalamic nerve apoptosis. For example, NTRK3 was co-regulated by Novel-1187 and Novel-566, as well as another target PPP1R13L regulated by Novel-566. These results indicated that these key genes and miRNAs may play an important role in the development of goat hypothalamus and represent candidate targets for further research. This study provides a basis for further explanation of the basic molecular mechanism of hypothalamus, but also provides a new idea for a comprehensive understanding of prolificacy characteristics in Yunshang black goats.

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.

Sign in / Sign up

Export Citation Format

Share Document