scholarly journals Transcriptome profiles revealed molecular mechanisms of alternating temperatures in breaking the epicotyl morphophysiological dormancy of Polygonatum sibiricum seeds

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Dengqun Liao ◽  
Ruipeng An ◽  
Jianhe Wei ◽  
Dongmei Wang ◽  
Xianen Li ◽  
...  
Keyword(s):  
Seed Dormancy ◽  
Seedling Establishment ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Seedling Emergence ◽  
Differentially Expressed ◽  
Natural Environments ◽  
Sequencing Analysis ◽  
Dormancy Release ◽  
Morphophysiological Dormancy

Abstract Background To adapt seasonal climate changes under natural environments, Polygonatum sibiricum seeds have a long period of epicotyl morphophysiological dormancy, which limits their wide-utilization in the large-scale plant progeny propagation. It has been proven that the controlled consecutive warm and cold temperature treatments can effectively break and shorten this seed dormancy status to promote its successful underdeveloped embryo growth, radicle emergence and shoot emergence. To uncover the molecular basis of seed dormancy release and seedling establishment, a SMRT full-length sequencing analysis and an Illumina sequencing-based comparison of P. sibiricum seed transcriptomes were combined to investigate transcriptional changes during warm and cold stratifications. Results A total of 87,251 unigenes, including 46,255 complete sequences, were obtained and 77,148 unigenes (88.42%) were annotated. Gene expression analyses at four stratification stages identified a total of 27,059 DEGs in six pairwise comparisons and revealed that more differentially expressed genes were altered at the Corm stage than at the other stages, especially Str_S and Eme. The expression of 475 hormone metabolism genes and 510 hormone signaling genes was modulated during P. sibiricum seed dormancy release and seedling emergence. One thousand eighteen transcription factors and five hundred nineteen transcription regulators were detected differentially expressed during stratification and germination especially at Corm and Str_S stages. Of 1246 seed dormancy/germination known DEGs, 378, 790, and 199 DEGs were associated with P. sibiricum MD release (Corm vs Seed), epicotyl dormancy release (Str_S vs Corm), and the seedling establishment after the MPD release (Eme vs Str_S). Conclusions A comparison with dormancy- and germination-related genes in Arabidopsis thaliana seeds revealed that genes related to multiple plant hormones, chromatin modifiers and remodelers, DNA methylation, mRNA degradation, endosperm weakening, and cell wall structures coordinately mediate P. sibiricum seed germination, epicotyl dormancy release, and seedling establishment. These results provided the first insights into molecular regulation of P. sibiricum seed epicotyl morphophysiological dormancy release and seedling emergence. They may form the foundation of future studies regarding gene interaction and the specific roles of individual tissues (endosperm, newly-formed corm) in P. sibiricum bulk seed dormancy.

Morphophysiological dormancy and germination ecology in diaspores of the subtropical palm Phoenix canariensis Chabaud

Botany ◽  
2021 ◽  
Author(s):  
Lanlan He ◽  
Ganesh K. Jaganathan ◽  
Baolin Liu
Keyword(s):  
Seed Dormancy ◽  
Seedling Emergence ◽  
Primary Root ◽  
Germination Percentage ◽  
Early Summer ◽  
Germination Ecology ◽  
Phoenix Canariensis ◽  
Morphophysiological Dormancy ◽  
Cotyledonary Petiole ◽  
Seed Dormancy And Germination

The timing of germination is a crucial event in a plant’s life cycle. Seed dormancy and germination mechanisms are important factors regulating seedling emergence. Since detailed experimental evidence for germination pattern of Phoenix canariensis colonizing sub-tropical climate is scarce, we investigated seed dormancy and germination ecology of P. canariensis. We found that the embryo is underdeveloped at the time of dispersal and doubles in size before the cotyledonary petiole (CP) protrudes through the operculum. The primary root and plumule emerge from the elongated CP outside the seed. In light/dark at 30/25°C, the CP emerged from 8% of the diaspores within 30 days and from 76% within 14 weeks. Thus, 8% of the diaspores have MD and the others MPD. Removal of the pericarp and operculum resulted in 100% germination within 5 days in light/dark at 30/25°C. Cold and warm stratification as well as treatment with GA3 significantly increased the germination speed, but the final germination percentage was not significantly increased. Seed germination was synchronized in early summer when seed dormancy was released by cold stratification in the soil over winter. A remote-tubular germination type and intricate root system provide an ecological advantage to the seedling establishment.

scholarly journals Different levels of morphophysiological seed dormancy in Ribes alpinum and R. uva-crispa (Grossulariaceae) facilitate adaptation to differentiated habitats

2020 ◽  
Vol 29 (2) ◽  
pp. e017
Author(s):  
Raquel Herranz-Ferrer ◽  
Miguel Ángel Copete-Carreño ◽  
José María Herranz-Sanz ◽  
Elena Copete-Carreño ◽  
Pablo Ferrandis-Gotor
Keyword(s):  
Seed Dormancy ◽  
Seedling Emergence ◽  
Late Summer ◽  
Late Winter ◽  
Minimal Size ◽  
Morphophysiological Dormancy ◽  
Radicle Emergence ◽  
Embryo Length ◽  
Different Levels ◽  
Morphological Dormancy

Aim of the study: To study the germination ecology of two species of the genus Ribes to reveal their levels of morphophysiological dormancy (MPD) and to facilitate the production of plants from seeds, a key tool for population reinforcement.Area of study: Experiments were carried out both outdoors and in the laboratory in Albacete (Spain) with seeds from the Meridional Iberian System mountain range.Material and methods: Seeds from one population of Ribes alpinum and from other of Ribes uva-crispa were collected during several years. Embryo length, radicle and seedling emergence, and effects on germination of stratification and GA3 were analysed to determine the level of MPD.Main results: In R. alpinum, embryo length in fresh seeds was 0.49 mm, needing to grow to 1.30 mm to germinate. Warm stratification (25/10ºC) promoted embryo length enlargement to 0.97 mm. Afterwards, seeds germinated within a wide temperature range. Embryo growth and seedling emergence occur late summer-early autumn. In R. uva-crispa, embryo length in fresh seeds was 0.52 mm, being 2.10 mm the minimal size to germinate. Embryos exposed to a moderately warm stratification (20/7ºC + 15/4ºC) followed by cold (5ºC) grew to 2.30 mm. Then, seeds germinated ≥ 80% when incubated at temperatures ≥ 15/4ºC. Embryos grew in autumn/early winter, and seedlings emerged late winter-early spring.Research highlights: These results showed that R. alpinum seeds have a nondeep simple MPD while R. uva-crispa seeds have a nondeep complex MPD. Moreover, the different germinative models found for each species help explain their installation in distinct habitats.Keywords: Ribes; seed dormancy break; radicle emergence; seedling emergence; nondeep simple and nondeep complex MPD.Abbreviations used: Morphophysiological dormancy (MPD), morphological dormancy (MD), Gibberellic acid (GA3), months (m).

scholarly journals Construction and analysis of mRNA, miRNA, lncRNA, and TF regulatory networks reveal the key genes in prostate cancer

2018 ◽  
Author(s):  
Su-Liang Li ◽  
Yun Ye ◽  
Sheng-Yu Wang
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Scale Effects ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Regulation Of Transcription ◽  
Normal Prostate ◽  
Ppi Networks

AbstractPurpose: Prostate cancer (PCa) causes a common male urinary system malignant tumour, and the molecular mechanisms of PCa remain poorly understood. This study aims to investigate the underlying molecular mechanisms of PCa with bioinformatics.Methods: Original gene expression profiles were obtained from the GSE64318 and GSE46602 datasets in the Gene Expression Omnibus (GEO). We conducted differential screens of the expression of genes (DEGs) between two groups using the R software limma package. The interactions between the differentially expressed miRNAs, mRNAs and lncRNAs were predicted and merged with the target genes. Co-expression of the miRNAs, lncRNAs and mRNAs were selected to construct the mRNA-miRNA and-lncRNA interaction networks. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed for the DEGs. The protein-protein interaction (PPI) networks were constructed, and the transcription factors were annotated. The expression of hub genes in the TCGA datasets was verified to improve the reliability of our analysis.Results: The results demonstrated that 60 miRNAs, 1578 mRNAs and 61 lncRNAs were differentially expressed in PCa. The mRNA-miRNA-lncRNA networks were composed of 5 miRNA nodes, 13 lncRNA nodes, and 45 mRNA nodes. The DEGs were mainly enriched in the nuclei and cytoplasm and were involved in the regulation of transcription, related to sequence-specific DNA binding, and participated in the regulation of the PI3K-Akt signalling pathway. These pathways are related to cancer and focal adhesion signalling pathways. Furthermore, we found that 5 miRNAs, 6 lncRNAs, 6 mRNAs and 2 TFs play important regulatory roles in the interaction network. The expression levels of EGFR, VEGFA, PIK3R1, DLG4, TGFBR1 and KIT were significantly different between PCa and normal prostate tissue.Conclusion: Based on the current study, large-scale effects of interrelated mRNAs, miRNAs, lncRNAs, and TFs were revealed and a model for predicting the mechanism of PCa was provided. This study provides new insight for the exploration of the molecular mechanisms of PCa and valuable clues for further research.

scholarly journals Transcriptomic Analysis Provides Novel Insights into Heat Stress Responses in Sheep

Animals ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 387 ◽  
Author(s):  
Zengkui Lu ◽  
Mingxing Chu ◽  
Qing Li ◽  
Meilin Jin ◽  
Xiaojuan Fei ◽  
...  
Keyword(s):  
Heat Stress ◽  
Differentially Expressed Genes ◽  
Stress Responses ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
P Value ◽  
Comprehensive Overview

With the intensified and large-scale development of sheep husbandry and global warming, sheep heat stress has become an increasingly important issue. However, little is known about the molecular mechanisms related to sheep responses to heat stress. In this study, transcriptomic analysis of liver tissues of sheep in the presence and absence of heat stress was conducted, with the goal of identifying genes and pathways related to regulation when under such stress. After a comparison with the sheep reference genome, 440,226,436 clean reads were obtained from eight libraries. A p-value ≤ 0.05 and fold change ≥ 2 were taken as thresholds for categorizing differentially expressed genes, of which 1137 were identified. The accuracy and reliability of the RNA-Seq results were confirmed by qRT-PCR. The identified differentially expressed genes were significantly associated with 419 GO terms and 51 KEGG pathways, which suggested their participation in biological processes such as response to stress, immunoreaction, and fat metabolism. This study’s results provide a comprehensive overview of sheep heat stress-induced transcriptional expression patterns, laying a foundation for further analysis of the molecular mechanisms of sheep heat stress.

scholarly journals Examining the molecular mechanisms contributing to the success of an invasive species across different ecosystems

2020 ◽  
Author(s):  
Sarah K. Lamar ◽  
Ian Beddows ◽  
Charlyn G. Partridge
Keyword(s):  
Invasive Species ◽  
Molecular Mechanisms ◽  
Germination Rate ◽  
Seedling Emergence ◽  
Common Garden ◽  
The United States ◽  
Differentially Expressed ◽  
Molecular Processes ◽  
Emergence Success ◽  
Two Populations

ABSTRACTInvasive species provide an opportune system to investigate how populations respond to new environments. Baby’s breath (Gypsophila paniculata) was introduced to North America in the 1800’s and has since spread throughout the United States and western Canada. We used an RNA-seq approach to explore how molecular processes contribute to the success of invasive populations with similar genetic backgrounds across distinct habitats. Transcription profiles were constructed from seedlings collected from a sand dune ecosystem in Petoskey, MI (PSMI) and a sagebrush ecosystem in Chelan, WA (CHWA). We assessed differential gene expression and identified SNPs within differentially expressed genes. We identified 1,146 differentially expressed transcripts across all sampled tissues between the two populations. GO processes enriched in PSMI were associated with nutrient starvation, while enriched processes in CHWA were associated with abiotic stress. Only 7.4% of the differentially expressed transcripts contained SNPs differing in allele frequencies of at least 0.5 between populations. Common garden studies found the two populations differed in germination rate and seedling emergence success. Our results suggest the success of G. paniculata in these two environments is likely due to plasticity in specific molecular processes responding to different environmental conditions, although some genetic divergence may be contributing to these differences.

scholarly journals Identification and validation of hub genes of synovial tissue for patients with osteoarthritis and rheumatoid arthritis

2021 ◽  
Author(s):  
Yanzhi Ge ◽  
Zuxiang Chen ◽  
Yanbin Fu ◽  
Li Zhou ◽  
Haipeng Xu ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Immune Cell ◽  
Interaction Network ◽  
Differentially Expressed ◽  
Specific Gene ◽  
Hub Genes

Abstract Osteoarthritis (OA) and rheumatoid arthritis (RA) were two major joint diseases with partially common phenotypes and genotypes. This study aimed to determine the mechanistic similarities and differences between osteoarthritis and rheumatoid arthritis by analyzing the differentially expressed genes and signaling pathways. Microarray data of osteoarthritis and rheumatoid arthritis were obtained from the Gene Expression Omnibus. By integrating multiple gene data sets, specific differentially expressed genes (DEGs) were identified in synovial membrane samples from patients and healthy donations. Then, the Gene ontology significant functions annotation, Kyoto Encyclopedia of Genes and Genomes pathways and protein-protein interaction network analysis were conducted. Moreover, CIBERSORT was used to further distinguish OA and RA in immune infiltration. Finally, animal experimentation was conducted and the establishment of model, which was verified using PCR in the mouse. As an overlapping process, we identified 1116 DEGs between OA and RA. It was indicated that specific gene signatures differed significantly between OA and RA connected with the distinct pathways. Of identified DEGs, 9 immune cell types among 22 were identified to distinguish from each other. The qRT-PCR result showed that the eight-tenths expression levels of the hub genes were significantly increased in OA samples (P < 0.05). This large-scale gene expression study provided new insights for disease-associated genes and molecular mechanisms as well as their associated function in osteoarthritis and rheumatoid arthritis, which simultaneously offer a new direction for biomarker development and the distinguishment of gene-level mechanisms between osteoarthritis and rheumatoid arthritis.

scholarly journals RNA-sequencing Analysis Identifies Genes Associated with Chilling-mediated Endodormancy Release in Apple

2018 ◽  
Vol 143 (3) ◽  
pp. 194-206 ◽  
Author(s):  
Takanori Takeuchi ◽  
Miwako Cecile Matsushita ◽  
Soichiro Nishiyama ◽  
Hisayo Yamane ◽  
Kiyoshi Banno ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Selection Strategy ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Screening Criteria ◽  
Physiological Processes ◽  
Transcription Factor Genes

Endodormancy release and the fulfillment of the chilling requirement (CR) are critical physiological processes that enable uniform blooming in fruit tree species, including apple (Malus ×domestica). However, the molecular mechanisms underlying these traits have not been fully characterized. The objective of this study was to identify potential master regulators of endodormancy release and the CR in apple. We conducted RNA-Sequencing (RNA-seq) analyses and narrowed down the number of candidates among the differentially expressed genes (DEGs) based on the following two strict screening criteria: 1) the gene must be differentially expressed between endodormant and ecodormant buds under different environmental conditions and 2) the gene must exhibit chill unit (CU)–correlated expression. The results of our cluster analysis suggested that global expression patterns varied between field-grown buds and continuously chilled buds, even though they were exposed to similar amounts of chilling and were expected to have a similar dormancy status. Consequently, our strict selection strategy resulted in narrowing down the number of possible candidates and identified the DEGs strongly associated with the transition between dormancy stages. The genes included four transcription factor genes, PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), FLOWERING LOCUS C (FLC)-LIKE, APETALLA2 (AP2)/ETHYLENE-RESPONSIVE 113 (ERF113), and MYC2. Their expressions were upregulated during endodormancy release, and were correlated with the CU, suggesting that these transcription factors are closely associated with chilling-mediated endodormancy release in apple.

scholarly journals Global Gene Responses of Resistant and Susceptible Sugarcane Cultivars to Acidovorax avenae subsp. avenae Identified Using Comparative Transcriptome Analysis

2019 ◽  
Vol 8 (1) ◽  
pp. 10 ◽  
Author(s):  
Na Chu ◽  
Jing-Ru Zhou ◽  
Hua-Ying Fu ◽  
Mei-Ting Huang ◽  
Hui-Li Zhang ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Defense Responses ◽  
Differentially Expressed ◽  
Mitogen Activated Protein Kinase ◽  
Post Inoculation ◽  
Rna Seq ◽  
Mitogen Activated Protein

Red stripe disease in sugarcane caused by Acidovorax avenae subsp. avenae (Aaa) is related to serious global losses in yield. However, the underlying molecular mechanisms associated with responses of sugarcane plants to infection by this pathogen remain largely unknown. Here, we used Illumina RNA-sequencing (RNA-seq) to perform large-scale transcriptome sequencing of two sugarcane cultivars to contrast gene expression patterns of plants between Aaa and mock inoculations, and identify key genes and pathways involved in sugarcane defense responses to Aaa infection. At 0–72 hours post-inoculation (hpi) of the red stripe disease-resistant cultivar ROC22, a total of 18,689 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples. Of these, 8498 and 10,196 genes were up- and downregulated, respectively. In MT11-610, which is susceptible to red stripe disease, 15,782 genes were differentially expressed between Aaa-inoculated and mock-inoculated samples and 8807 and 6984 genes were up- and downregulated, respectively. The genes that were differentially expressed following Aaa inoculation were mainly involved in photosynthesis and carbon metabolism, phenylpropanoid biosynthesis, plant hormone signal transduction, and plant–pathogen interaction pathways. Further, qRT-PCR and RNA-seq used for additional validation of 12 differentially expressed genes (DEGs) showed that eight genes in particular were highly expressed in ROC22. These eight genes participated in the biosynthesis of lignin and coumarin, as well as signal transduction by salicylic acid, jasmonic acid, ethylene, and mitogen-activated protein kinase (MAPK), suggesting that they play essential roles in sugarcane resistance to Aaa. Collectively, our results characterized the sugarcane transcriptome during early infection with Aaa, thereby providing insights into the molecular mechanisms responsible for bacterial tolerance.

Serum Proteomic Profiling in Patients with Advanced Schistosoma Japonicum-Induced Hepatic Fibrosis

2021 ◽  
Author(s):  
Jing Huang ◽  
Xinguang Yin ◽  
Lifang Zhang ◽  
Ming Yao ◽  
Dahai Wei ◽  
...  
Keyword(s):  
Schistosoma Japonicum ◽  
Hepatic Fibrosis ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Rapid Progression ◽  
Proteomic Profiling ◽  
Serum Samples ◽  
Data Independent Acquisition ◽  
Fundamental Information

Abstract Background: Schistosoma japonicum (S. japonicum) is a parasitic flatworm that is the aetiological agent of human schistosomiasis, an important cause of hepatic fibrosis. Schistosomiasis-induced hepatic fibrosis is a consequence of the highly fibrogenic nature of egg-induced granulomatuous lesions, the main pathogenic factor of schistosomiasis. Although global awareness of the association between schistosomiasis-indued hepatic fibrosis and s. japonicum infection is increasing, little is known about the mechanism mediating the rapid progression to schistosomiasis in cirrhotic patients.Methods: We systematically used data-independent acquisition (DIA)-based liquid chromatography-mass spectrometry to identify differentially expressed proteins in serum samples from patients with advanced S. japonicum-induced hepatic fibrosis.Results: On the basis of our analysis, we identified 1,144 proteins, among which 67 were differentially expressed between the healthy control and SHF-F2 groups and 214 were differentially expressed between the SHF-F2 and SHF-F4 groups (up- or downregulation of at least 1.5-fold in serum samples). Furthermore, our results indicated that two selected proteins (C1QA and CFD) are potential biomarkers for distinguishing patients with cirrhosis resulting from S. japonicum infection.Conclusions: This report is the first to provide a global proteomic profile of serum samples from patients with advanced S. japonicum-induced hepatic fibrosis. Our results shed new light on the molecular mechanisms that are dysregulated in and contribute to the pathogenesis of schistosomiasis-induced hepatic fibrosis. C1QA and CFD are promising diagnostic markers for patients with cirrhosis resulting from S. japonicum infection, although further large-scale studies are needed. Our DIA-based quantitative proteomic analysis revealed molecular differences among individuals with different stages of advanced S. japonicum-induced hepatic fibrosis and might provide fundamental information for further detailed investigations.

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