scholarly journals RNA-seq Profiling Showed Divergent Carbohydrate-Active Enzymes (CAZymes) Expression Patterns in Lentinula edodes at Brown Film Formation Stage Under Blue Light Induction

2020 ◽  
Vol 11 ◽  
Author(s):  
Xiying Huang ◽  
Runji Zhang ◽  
Yijie Qiu ◽  
Haibing Wu ◽  
Quanju Xiang ◽  
...  
Keyword(s):  
Blue Light ◽  
Lentinula Edodes ◽  
Film Formation ◽  
Expression Patterns ◽  
Light Induction ◽  
Rna Seq ◽  
Carbohydrate Active Enzymes ◽  
Formation Stage

scholarly journals Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9859
Author(s):  
Tingting Song ◽  
Yingyue Shen ◽  
Qunli Jin ◽  
Weilin Feng ◽  
Lijun Fan ◽  
...  
Keyword(s):  
Blue Light ◽  
Molecular Mechanisms ◽  
Lentinula Edodes ◽  
Film Formation ◽  
Quantitative Information ◽  
Light Signal ◽  
Post Translational Modification ◽  
Bioinformatics Analyses ◽  
Phosphorylated Proteins ◽  
Liquid Chromatography Tandem Mass

Light plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. A total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. Our study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.

Comparative phosphoproteome analysis to identify candidate phosphoproteins involved in blue light-induced brown film formation in Lentinula edodes

2020 ◽  
Author(s):  
Tingting Song ◽  
Yingyue Shen ◽  
Qunli Jin ◽  
Weilin Feng ◽  
Lijun Fan ◽  
...  
Keyword(s):  
Blue Light ◽  
Molecular Mechanisms ◽  
Lentinula Edodes ◽  
Film Formation ◽  
Quantitative Information ◽  
Light Signal ◽  
Post Translational Modification ◽  
Bioinformatics Analyses ◽  
Phosphorylated Proteins ◽  
Liquid Chromatography Tandem Mass

Abstract BackgroundLight plays an important role in the growth and differentiation of Lentinula edodes mycelia, and mycelial morphology is influenced by light wavelengths. The blue light-induced formation of brown film on the vegetative mycelial tissues of L. edodes is an important process. However, the mechanisms of L. edodes’ brown film formation, as induced by blue light, are still unclear. Using a high-resolution liquid chromatography-tandem mass spectrometry integrated with a highly sensitive immune-affinity antibody method, phosphoproteomes of L. edodes mycelia under red- and blue-light conditions were analyzed. ResultsA total of 11,224 phosphorylation sites were identified on 2,786 proteins, of which 9,243 sites on 2,579 proteins contained quantitative information. In total, 475 sites were up-regulated and 349 sites were down-regulated in the blue vs red group. To characterize the differentially phosphorylated proteins, systematic bioinformatics analyses, including gene ontology annotations, domain annotations, subcellular localizations, and Kyoto Encyclopedia of Genes and Genomes pathway annotations, were performed. These differentially phosphorylated proteins were correlated with light signal transduction, cell wall degradation, and melanogenesis, suggesting that these processes are involved in the formation of the brown film. ConclusionsOur study provides new insights into the molecular mechanisms of the blue light-induced brown film formation at the post-translational modification level.

scholarly journals Transcriptome Profile Analysis of Strawberry Leaves Reveals Flowering Regulation under Blue Light Treatment

2021 ◽  
Vol 2021 ◽  
pp. 1-18
Author(s):  
Yuntian Ye ◽  
Yongqiang Liu ◽  
Xiaolong Li ◽  
Qing Chen ◽  
Yong Zhang ◽  
...  
Keyword(s):  
Blue Light ◽  
Profile Analysis ◽  
Expression Patterns ◽  
Light Treatment ◽  
Rna Seq ◽  
Function Annotation ◽  
Data Resource ◽  
Kegg Pathways ◽  
Flowering Regulation ◽  
Go Terms

Blue light is an important signal that regulates the flowering of strawberry plants. To reveal the mechanism of early flowering under blue light treatment at the transcriptional regulation level, seedlings of cultivated strawberry (Fragaria × ananassa Duch.) “Benihoppe” were subjected to a white light treatment (WL) and blue light treatment (BL) until their flowering. To detect the expression patterns of genes in response to BL, a transcriptome analysis was performed based on RNA-Seq. The results identified a total of 6875 differentially expressed genes (DEGs) that responded to BL, consisting of 3138 (45.64%) downregulated ones and 3737 (54.36%) upregulated ones. These DEGs were significantly enriched into 98 GO terms and 71 KEGG pathways based on gene function annotation. Among the DEGs, the expression levels of genes that might participate in light signaling (PhyB, PIFs, and HY5) and circadian rhythm (FKF1, CCA1, LHY, and CO) in plants were altered under BL. The BBX transcription factors which responded to BL were also identified. The result showed that the FaBBX29, one of strawberry’s BBX family genes, may play an important role in flowering regulation. Our results provide a timely, comprehensive view and a reliable reference data resource for further study of flowering regulation under different light qualities.

scholarly journals Integration of transcriptomic data identifies key hallmark genes in hypertrophic cardiomyopathy

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jing Xu ◽  
Xiangdong Liu ◽  
Qiming Dai
Keyword(s):  
Machine Learning ◽  
Hypertrophic Cardiomyopathy ◽  
Heart Diseases ◽  
Expression Patterns ◽  
Support Vector ◽  
Rna Seq ◽  
Ppi Network ◽  
Learning Methods ◽  
Transcriptomic Data ◽  
Machine Learning Methods

Abstract Background Hypertrophic cardiomyopathy (HCM) represents one of the most common inherited heart diseases. To identify key molecules involved in the development of HCM, gene expression patterns of the heart tissue samples in HCM patients from multiple microarray and RNA-seq platforms were investigated. Methods The significant genes were obtained through the intersection of two gene sets, corresponding to the identified differentially expressed genes (DEGs) within the microarray data and within the RNA-Seq data. Those genes were further ranked using minimum-Redundancy Maximum-Relevance feature selection algorithm. Moreover, the genes were assessed by three different machine learning methods for classification, including support vector machines, random forest and k-Nearest Neighbor. Results Outstanding results were achieved by taking exclusively the top eight genes of the ranking into consideration. Since the eight genes were identified as candidate HCM hallmark genes, the interactions between them and known HCM disease genes were explored through the protein–protein interaction (PPI) network. Most candidate HCM hallmark genes were found to have direct or indirect interactions with known HCM diseases genes in the PPI network, particularly the hub genes JAK2 and GADD45A. Conclusions This study highlights the transcriptomic data integration, in combination with machine learning methods, in providing insight into the key hallmark genes in the genetic etiology of HCM.

scholarly journals Genome-Wide Identification of the B-BOX Genes that Respond to Multiple Ripening Related Signals in Sweet Cherry Fruit

2021 ◽  
Vol 22 (4) ◽  
pp. 1622
Author(s):  
Yanyan Wang ◽  
Zefeng Zhai ◽  
Yueting Sun ◽  
Chen Feng ◽  
Xiang Peng ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Stress Responses ◽  
Fruit Development ◽  
Sweet Cherry ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Light Induction ◽  
Promoter Regions ◽  
Genome Database ◽  
Gene Structures

B-BOX proteins are zinc finger transcription factors that play important roles in plant growth, development, and abiotic stress responses. In this study, we identified 15 PavBBX genes in the genome database of sweet cherry. We systematically analyzed the gene structures, clustering characteristics, and expression patterns of these genes during fruit development and in response to light and various hormones. The PavBBX genes were divided into five subgroups. The promoter regions of the PavBBX genes contain cis-acting elements related to plant development, hormones, and stress. qRT-PCR revealed five upregulated and eight downregulated PavBBX genes during fruit development. In addition, PavBBX6, PavBBX9, and PavBBX11 were upregulated in response to light induction. We also found that ABA, BR, and GA3 contents significantly increased in response to light induction. Furthermore, the expression of several PavBBX genes was highly correlated with the expression of anthocyanin biosynthesis genes, light-responsive genes, and genes that function in multiple hormone signaling pathways. Some PavBBX genes were strongly induced by ABA, GA, and BR treatment. Notably, PavBBX6 and PavBBX9 responded to all three hormones. Taken together, BBX proteins likely play major roles in regulating anthocyanin biosynthesis in sweet cherry fruit by integrating light, ABA, GA, and BR signaling pathways.

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