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 Identification of microRNAs in Silver Carp (Hypophthalmichthys molitrix) Response to Hypoxia Stress

Animals ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 2917
Author(s):  
Qiaoxin Wang ◽  
Xiaohui Li ◽  
Hang Sha ◽  
Xiangzhong Luo ◽  
Guiwei Zou ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Target Genes ◽  
Silver Carp ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Hypophthalmichthys Molitrix ◽  
Hypoxia Stress ◽  
Differentially Expressed Mirnas

Hypoxia is one of the serious stresses in fish culture, which can lead to physical and morphological changes, and cause injury and even death to fish. Silver carp (Hypophthalmichthys molitrix) is an important economic fish and widely distributed in China. MicroRNA is a kind of endogenous non-coding single-stranded small RNA, which is involved in cell development, and immune response and gene expression regulation. In this study, silver carp were kept in the closed containers for hypoxia treatment by spontaneous oxygen consumption. The samples of heart, brain, liver and gill were collected, and the total RNAs extracted separately from the four tissues were mixed in equal amounts according to the concentration. Afterwards, the RNA pool was constructed for high-throughput sequencing, and based on the small RNA sequencing, the differentially expressed microRNAs were identified. Furthermore, their target gene prediction and enrichment analyses were carried out. The results showed that a total of 229 known miRNAs and 391 putative novel miRNAs were identified, which provided valuable resources for further study on the regulatory mechanism of miRNAs in silver carp under hypoxia stress. The authors verified 16 differentially expressed miRNAs by qRT-PCR, and the results were consistent with small RNA sequencing (sRNA-seq). The predicted target genes number of differentially expressed miRNAs was 25,146. GO and KEGG functional enrichment analysis showed that these target genes were mainly involved in the adaption of hypoxia stress in silver carp through biological regulation, catalytic activity and apoptosis. This study provides references for further study of interaction between miRNAs and target genes, and the basic data for the response mechanism under hypoxia stress in silver carp.

scholarly journals Identification of manganese-responsive microRNAs in Arabidopsis by small RNA sequencing

2019 ◽  
Vol 55 (No. 2) ◽  
pp. 76-82
Author(s):  
Jian Gong ◽  
Dong Li ◽  
Hao Li ◽  
Huakun Zhou ◽  
Jin Xu
Keyword(s):  
Arabidopsis Thaliana ◽  
Rna Sequencing ◽  
Small Rna ◽  
Growth And Development ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Mn Toxicity ◽  
Differentially Expressed Mirnas ◽  
Toxicity Response ◽  
Transport Stress

Manganese (Mn) is an important micronutrient for growth and development in plants, however, excess Mn is harmful by disrupting photosynthesis system and inducing oxidative damage in leaves. MicroRNAs (miRNAs) play key roles in regulating Mn toxicity tolerance in plants. Here, we identified Mn toxicity-responsive miRNAs in Arabidopsis by using small RNA sequencing. Eighteen differentially expressed miRNAs were identified in Arabidopsis thaliana seedlings in response to Mn toxicity. These differentially expressed miRNAs are involved in regulating nutrition homeostasis, transport, stress response, and developmental processes. Our results indicated that these miRNAs play a key role in Mn toxicity response in plants.  

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 evaluation of renal microRNA biomarkers in dogs with X-linked hereditary nephropathy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Candice P. Chu ◽  
Shiguang Liu ◽  
Wenping Song ◽  
Ethan Y. Xu ◽  
Mary B. Nabity
Keyword(s):  
Small Rna ◽  
Target Genes ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Ckd Progression ◽  
Critical Pathways ◽  
Qrt Pcr ◽  
Hereditary Nephropathy ◽  
Differentially Expressed Mirnas

AbstractDogs with X-linked hereditary nephropathy (XLHN) are an animal model for Alport syndrome in humans and progressive chronic kidney disease (CKD). Using mRNA sequencing (mRNA-seq), we have characterized the gene expression profile affecting the progression of XLHN; however, the microRNA (miRNA, miR) expression remains unknown. With small RNA-seq and quantitative RT-PCR (qRT-PCR), we used 3 small RNA-seq analysis tools (QIAGEN OmicSoft Studio, miRDeep2, and CPSS 2.0) to profile differentially expressed renal miRNAs, top-ranked miRNA target genes, and enriched biological processes and pathways in CKD progression. Twenty-three kidney biopsies were collected from 5 dogs with XLHN and 4 age-matched, unaffected littermates at 3 clinical time points (T1: onset of proteinuria, T2: onset of azotemia, and T3: advanced azotemia). We identified up to 23 differentially expressed miRNAs at each clinical time point. Five miRNAs (miR-21, miR-146b, miR-802, miR-142, miR-147) were consistently upregulated in affected dogs. We identified miR-186 and miR-26b as effective reference miRNAs for qRT-PCR. This study applied small RNA-seq to identify differentially expressed miRNAs that might regulate critical pathways contributing to CKD progression in dogs with XLHN.

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 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 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.

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