scholarly journals Small RNA Sequencing Analysis of miRNA Expression Reveals Novel Insihts into Root Formation under Root Restriction Cultivation in Grapevine (Vitis vinifera L.)

2020 ◽  
Vol 21 (10) ◽  
pp. 3513
Author(s):  
Hui Li ◽  
Zhen Gao ◽  
Muhammad Salman Zahid ◽  
Dongmei Li ◽  
Hafiz Umer Javed ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Root Development ◽  
Small Rna ◽  
Mirna Expression ◽  
Lateral Root ◽  
Differentially Expressed ◽  
Root Tip ◽  
Small Rna Sequencing ◽  
Sequencing Analysis ◽  
Root Restriction

Root restriction cultivation (RRC) can influence plant root architecture, but its root phenotypic changes and molecular mechanisms are still unknown. In this study, phenotype observations of grapevine root under RRC and control cultivation (nRC) at 12 time points were conducted, and the root phenotype showed an increase of adventitious and lateral root numbers and root tip degeneration after RRC cultivation from 70 days after planting (DAP). The 70 and 125 DAP sampling of two different cultivations, named nR70, RR70, nR125, and RR125, were selected for small RNA sequencing. A total of 153 known miRNAs and 119 predicted novel miRNAs were obtained. Furthermore, BLAST was used to predict the novel miRNAs with miRBase databases using the default parameters; 96 of the 119 predicted novel miRNAs were similar to other species, and the remaining 23 grapevine-specific novel miRNAs were obtained. There were 26, 33, 26, and 32 miRNAs that were differentially expressed in different comparison groups (RR70 vs. nR70, RR125 vs. nR125, nR125 vs. nR70 and RR125 vs. RR70). Target genes prediction of differentially expressed miRNAs was annotated on a variety of biological processes, and 24 participated in root development. Moreover, multiple miRNAs were found to jointly regulate lateral root development under root restriction conditions. The miRNA expression pattern comparison between RRC and nRC may provide a framework for the future analysis of miRNAs associated with root development in grapevine.

scholarly journals Small RNA Sequencing Reveals Differentially Expressed miRNAs in Necrotizing Enterocolitis in Rats

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Ren-qiang Yu ◽  
Min Wang ◽  
Shan-yu Jiang ◽  
Ying-hui Zhang ◽  
Xiao-yu Zhou ◽  
...  
Keyword(s):  
Wnt Signaling ◽  
Signaling Pathway ◽  
Rna Sequencing ◽  
Necrotizing Enterocolitis ◽  
Small Rna ◽  
Mirna Expression ◽  
Expression Patterns ◽  
Wnt Signaling Pathway ◽  
Differentially Expressed ◽  
Small Rna Sequencing

Necrotizing enterocolitis (NEC) is the leading cause of death due to gastrointestinal disease in preterm infants. The role of miRNAs in NEC is still unknown. The objective of this study was to identify differentially expressed (DE) miRNAs in rats with NEC and analyze their possible roles. In this study, a NEC rat model was established using Sprague-Dawley rat pups. Small RNA sequencing was used to analyze the miRNA expression profiles in the NEC and control rats. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were carried out to identify target mRNAs for the DE miRNAs and to explore their potential roles. The DE miRNAs were verified by real-time quantitative PCR (RT-qPCR). The status of intestinal injury and the elevated levels of inflammatory cytokines in the NEC group confirmed that the NEC model was successfully established. The 16 miRNAs were found to be differentially expressed between the NEC group and the control group of rats. Bioinformatics analysis indicated that the parental genes of the DE miRNAs were predominantly implicated in the phosphorylation, cell migration, and protein phosphorylation processes. Moreover, the DE miRNAs were mainly found to be involved in the pathways of axon guidance, endocytosis, and focal adhesion, as well as in the Wnt signaling pathway, which is related to colitis. The expression patterns of the candidate miRNAs (rno-miR-27a-5p and rno-miR-187-3p), as assessed by RT-qPCR, were in accordance with the expression patterns obtained by miRNA-sequencing. The miRNA/mRNA/pathway network revealed that rno-miR-27a-5p and rno-miR-187-3p might be involved in NEC via the Wnt signaling pathway. We found an altered miRNA expression pattern in rats with NEC. We hypothesize that rno-miR-27a-5p and rno-miR-187-3p might mediate the NEC pathophysiological processes via the Wnt signaling pathway.

scholarly journals Integrated analyses of the transcriptome and small RNA of the hemiparasitic plant Monochasma savatieri before and after establishment of parasite-host association

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Lanlan Chen ◽  
Qiaosheng Guo ◽  
Zaibiao Zhu ◽  
Hefang Wan ◽  
Yuhao Qin ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Sequencing Analysis ◽  
Relationship Analysis ◽  
Differentially Expressed Mirnas ◽  
Before And After ◽  
Aba Content ◽  
Host Associations

Abstract Background Monochasma savatieri is a medicinal root hemiparasitic herb that extracts water and nutrients from the host plant via a haustorium. M. savatieri exhibits an enhanced growth after the establishment of parasite-host associations, but little is known about the molecular mechanism responsible. In this study, endogenous hormones, RNA sequencing and small RNA sequencing analysis were performed on M. savatieri before and after establishment of parasite-host associations. Results When grown with the host, decreased contents of jasmonic acid (JA) and indole-3-acetic acid (IAA) and increased abscisic acid (ABA) content were observed in M. savatieri with the established parasitic relationship. When grown with the host, 46,424 differentially expressed genes (DEGs) and 162 differentially expressed miRNAs (DEmiRs) were identified in the comparison between M. savatieri with the established parasitic relationship and without the established parasitic relationship. Analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that these DEGs and targets of DEmiRs mostly participated in plant hormone signal transduction, starch and sucrose metabolism, carbohydrate metabolism, cell growth and death, and transport and catabolism. Furthermore, correlation analysis of mRNA and miRNA revealed that 10 miRNA-target pairs from novel_mir65, novel_mir40, novel_mir80, miR397-5p_1, novel_mir36, novel_mir25 and novel_mir17 may have important roles in regulating the parasitic development of M. savatieri. Conclusions Our study not only expands the understanding of enhanced growth in M. savatieri after the establishment of parasite-host associations, but also first provides abundant resources for future molecular and genetic studies in M. savatieri.

scholarly journals Transcriptome analysis of miRNAs expression reveals novel insights into root formation under Root restriction cultivation in grapevine (Vitis vinifera L.)

2020 ◽  
Author(s):  
Hui Li ◽  
Zhen Gao ◽  
Muhammad Salman Zahid ◽  
Dong Mei Li ◽  
Hafiz Umer Javed ◽  
...  
Keyword(s):  
Root Development ◽  
Target Genes ◽  
Lateral Roots ◽  
Family Members ◽  
Differentially Expressed ◽  
Root Tip ◽  
Small Rna Sequencing ◽  
Vitis Vinifera L ◽  
Specific Expression ◽  
Root Restriction

Abstract Background: Root restriction cultivation not only promotes maturation and quality of fruit, but optimizes the architecture of root, especially in enhancing the occurrence of adventitious and lateral roots. While the molecular mechanism of this phenotype is still unknown. Results: In this study, the development of roots was observed at 12 different time points under Root restriction and normal cultivations (control). Root phenotype showed a significantly different feature start from the seventh sampling, mainly in the increasing of adventitious roots numbers, degeneration of root tip and subsequent mass of lateral roots development. The 7th and 12th sampling of two different cultivations, named nR7, nR12, RR7, and RR12, were selected for small RNA sequencing. 214,439,588 raw reads were obtained and 168,741,687 clean reads were remained after the quality control steps, and finally got a total of 153 known miRNAs, and 119 predicted novel miRNAs. The predicted novel miRNAs blasted with the miRVIT and miRBase databases simultaneously. 96 new family members of grapevine miRNA and 23 grapevine-specific novel miRNAs were obtained. Differentially expressed miRNAs (DEMs) analysis showed that 26 and 33 miRNAs were differentially expressed in two different cultivation models (RR7 vs nR7; RR12 vs nR12), while 26 and 32 DEMs were obtained in different root development stages (nR12 vs nR7; RR12 vs RR7). MiRNA expression levels analysis found that conserved miRNA s were in higher expression level than novel miRNAs. The predicted target genes of DEMs were annotated on a variety of biological processes, and 24 participated in root development. An analysis of vvi-miR160 family members revealed that vvi-miR160c was highly expressed in grapevine root, indicating the potential role of miR160c in root development, which in accordance with the previous report in Arabidopsis . Conclusions: Multiple miRNAs were jointly to regulate root development on Root restriction condition, mainly in lateral root development. And the specific expression of vvi-miR160c in the apex may be the main cause of apical degradation. Moreover, there were multiple miRNAs related to biotic or abiotic stresses, which indicated that multiple minor stresses exist in root development after Root restriction cultivation.

scholarly journals Small RNA Sequencing Uncovers New miRNAs and moRNAs Differentially Expressed in Normal and Primary Myelofibrosis CD34+ Cells

PLoS ONE ◽  
2015 ◽  
Vol 10 (10) ◽  
pp. e0140445 ◽  
Author(s):  
Paola Guglielmelli ◽  
Andrea Bisognin ◽  
Claudia Saccoman ◽  
Carmela Mannarelli ◽  
Alessandro Coppe ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Primary Myelofibrosis ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Cd34 Cells

Transcriptome and small RNA sequencing analysis of a new dwarf mutant in Gossypium hirsutum L

2014 ◽  
Vol 31 ◽  
pp. S55 ◽  
Author(s):  
Xiongming Du ◽  
Wen-yan An ◽  
Jun-ling Sun ◽  
Wen-fang Gong ◽  
Shou-pu He ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Rna Sequencing ◽  
Small Rna ◽  
Dwarf Mutant ◽  
Small Rna Sequencing ◽  
Sequencing Analysis ◽  
Gossypium Hirsutum L

scholarly journals Survey and Diversity of Grapevine Pinot gris virus in Algeria and Comprehensive High-Throughput Small RNA Sequencing Analysis of Two Isolates from Vitis vinifera cv. Sabel Revealing High Viral Diversity

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1110
Author(s):  
Aleš Eichmeier ◽  
Eliška Peňázová ◽  
Jana Čechová ◽  
Akila Berraf-Tebbal
Keyword(s):  
Vitis Vinifera ◽  
Rna Sequencing ◽  
Small Rna ◽  
Phylogenetic Analyses ◽  
Small Rna Sequencing ◽  
Sequencing Analysis ◽  
Hop Stunt Viroid ◽  
Grapevine Virus B ◽  
Grapevine Pinot Gris Virus ◽  
Rupestris Stem Pitting

Grapevine Pinot gris virus (GPGV) is a putative causal agent of grapevine leaf mottling and deformation disease that has been reported worldwide throughout the grapevine-growing regions. Fifty-four grapevines collected from five Algerian grapevine-growing regions were tested for the presence of GPGV in phloem tissues. Eight of the tested grapevines were infected by GPGV. Viromes of two selected Vitis vinifera cv. Sabel grapevines infected by GPGV and showing virus-like symptoms were analyzed by small RNA sequencing. Phylogenetic analyses of the partial coding sequence (cds) of the RNA-dependent RNA polymerase (RdRp) domain showed that all Algerian GPGV isolates were grouped with some already-described asymptomatic isolates. This study provides the first survey of the occurrence of GPGV in Algeria. Moreover, Grapevine fleck virus, Grapevine rupestris stem pitting-associated virus, Grapevine virus B, Grapevine rupestris vein feathering virus, Hop stunt viroid and Grapevine yellow speckle viroid 1 were detected in Algeria for the first time.

scholarly journals Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Liang ◽  
Kunhua Wei ◽  
Fan Wei ◽  
Shuangshuang Qin ◽  
Chuanhua Deng ◽  
...  
Keyword(s):  
Drought Stress ◽  
Rna Sequencing ◽  
Small Rna ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Severe Drought ◽  
A Genome ◽  
Sophora Tonkinensis

Abstract Background Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood. Results To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs. Conclusion This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.

scholarly journals Identification of conserved miRNA molecules in einkorn wheat ( Triticum monococcum subsp. monococcum ) by using small RNA sequencing analysis

2018 ◽  
Vol 42 (6) ◽  
pp. 527-536
Author(s):  
Ercan Selçuk ÜNLÜ ◽  
Sara BATAW ◽  
Didem ASLAN ŞEN ◽  
Yunus ŞAHİN ◽  
Nusret ZENCİRCİ
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Triticum Monococcum ◽  
Small Rna Sequencing ◽  
Sequencing Analysis ◽  
Einkorn Wheat

scholarly journals Transcriptional Analysis Reveals Alteration of Lung Macrophages Following Mesenchymal Stem Cell Therapy in Neonatal Mice With Hyperoxia-Induced Injury

2020 ◽  
Author(s):  
Ali Al-Rubaie ◽  
Robert DeMatteo ◽  
Foula Sozo ◽  
Timothy Cole ◽  
Richard Harding ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Pathway Analysis ◽  
Small Rna ◽  
Differentially Expressed ◽  
Transcriptional Analysis ◽  
Small Rna Sequencing ◽  
Specific Gene ◽  
Lung Macrophages ◽  
Neonatal Mice ◽  
Neonatal Hyperoxia

Abstract Background Lung immaturity is one of the most serious consequences of growth restriction and premature birth. Preterm babies often require mechanical ventilation to survive, but exposure to high levels of oxygen can permanently damage the lungs and interrupts normal development. As lung macrophages play an important role in hyperoxic lung injury and repair, our objective was to use next generation sequencing (NGS) to identify changes in the macrophage transcriptome following neonatal hyperoxia, with and without treatment with human mesenchymal stem cells (hMSCs). We provide the first report of RNA-sequencing of lung macrophages following neonatal hyperoxia and hMSCs therapy. Methods Neonatal mice exposed to normoxia (21%O2) or hyperoxia (90% O2) from birth to postnatal day 4 were randomized to receive either hMSCs or vehicle via intratracheal delivery on postnatal day 4. Mouse lungs from normoxia and hyperoxia groups with and without hMSCs therapy were examined at day 14. RNA-sequencing was performed on flow-cytometric CD45+CD11b+CD11c+ sorted lung macrophages. Purified total RNA was used to construct barcoded multiplex-compatible sequencing libraries using: 1) Illumina Stranded mRNA Sample Preparation chemistry (for transcriptomics) and 2) Bio Scientific NEXTFlex Small RNA chemistry (for small RNA). Results Sorted CD45+CD11b+CD11c+ lung macrophages from hyperoxia-exposed neonatal mice showed differentially expressed macrophage genes and miRNA compared to mice exposed to normoxia or hyperoxia+hMSCs. The administration of hMSCs was found to differentially upregulate 421 genes and downregulate 651 genes in CD45+CD11b+CD11c+ lung macrophages from neonatal mice exposed to hyperoxia, compared to normoxia. Integrity pathway analysis (IPA) analysis of macrophage-specific gene pathways revealed the effectiveness of hMSCs in altering macrophage function towards an anti-inflammatory ‘M2’ phenotype. Small-RNA sequencing provided further evidence on the effects of hMSCs, where 1,098 small RNAs transcriptomes were expressed as either significantly up- or down-regulated in response to hMSCs therapy following hyperoxia-induced lung damage. Conclusions Pathway analysis of the predicted mRNA targets of differentially expressed genes provides insight into miRNAs that preferentially target several important pathways. These miRNAs will be functionally relevant for lung macrophages, and will provide a greater understanding of the interaction between macrophage genotype and the associated phenotypes in the setting of inflammation or tissue repair.

Sign in / Sign up

Export Citation Format

Share Document