scholarly journals Comparative Transcriptomic Analysis to Identify the Genes Related to Delayed Gland Morphogenesis in Gossypium bickii

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 472 ◽  
Author(s):  
Mushtaque Ali ◽  
Hailiang Cheng ◽  
Mahtab Soomro ◽  
Li Shuyan ◽  
Muhammad Bilal Tufail ◽  
...  
Keyword(s):  
Network Analysis ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Natural Fibers ◽  
Differentially Expressed ◽  
Sequencing Technology ◽  
Polymerase Chain ◽  
Gland Morphogenesis ◽  
Insight Into ◽  
Comparative Transcriptomic Analysis

Cotton is one of the major industrial crops that supply natural fibers and oil for industries. This study was conducted to understand the mechanism of delayed gland morphogenesis in seeds of Gossypium bickii. In this study, we compared glandless seeds of G. bickii with glanded seeds of Gossypium arboreum. High-throughput sequencing technology was used to explore and classify the expression patterns of gland-related genes in seeds and seedlings of cotton plants. Approximately 131.33 Gigabases of raw data from 12 RNA sequencing samples with three biological replicates were generated. A total of 7196 differentially-expressed genes (DEGs) were identified in all transcriptome data. Among them, 3396 genes were found up-regulated and 3480 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations were performed to identify different functions between genes unique to glandless imbibed seeds and glanded seedlings. Co-expression network analysis revealed four modules that were identified as highly associated with the development of glandless seeds. Here the hub genes in each module were identified by weighted gene co-expression network analysis (WGCNA). In total, we have selected 13 genes involved in transcription factors, protein and MYB-related functions, that were differentially expressed in transcriptomic data and validated by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). These selected genes may play an important role for delayed gland morphogenesis. Our study provides comprehensive insight into the key genes related to glandless traits of seeds and plants, and can be further exploited by functional and molecular studies.

scholarly journals Identification of MicroRNAs That Respond to Soybean Cyst Nematode Infection in Early Stages in Resistant and Susceptible Soybean Cultivars

2019 ◽  
Vol 20 (22) ◽  
pp. 5634 ◽  
Author(s):  
Piao Lei ◽  
Bing Han ◽  
Yuanyuan Wang ◽  
Xiaofeng Zhu ◽  
Yuanhu Xuan ◽  
...  
Keyword(s):  
Small Rna ◽  
Soybean Cyst Nematode ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Cyst Nematode ◽  
Differentially Expressed ◽  
Early Stages ◽  
Differentially Expressed Mirnas ◽  
Plant Pathogen Interactions ◽  
Insight Into

Soybean cyst nematode (SCN) causes heavy losses to soybean yield. In order to investigate the roles of soybean miRNAs during the early stages of infection (1 and 5 dpi), 24 small RNA libraries were constructed from SCN resistant cultivar Huipizhi (HPZ) and the susceptible Williams 82 (W82) cultivar for high-throughput sequencing. By sequencing the small RNA libraries, a total of 634 known miRNAs were identified, and 252 novel miRNAs were predicted. Altogether, 14 known miRNAs belonging to 13 families, and 26 novel miRNAs were differentially expressed and may respond to SCN infection in HPZ and W82. Similar expression results were also confirmed by qRT-PCR. Further analysis of the biological processes that these potential target genes of differentially expressed miRNAs regulate found that they may be strongly related to plant–pathogen interactions. Overall, soybean miRNAs experience profound changes in early stages of SCN infection in both HPZ and W82. The findings of this study can provide insight into miRNAome changes in both HPZ and W82 at the early stages of infection, and may provide a stepping stone for future SCN management.

scholarly journals Immune-related miRNA-mRNA regulation network in the livers of DHAV-3-infected ducklings

2019 ◽  
Author(s):  
Fengyao Wu ◽  
Fengying Lu ◽  
Xin Fan ◽  
Jin Chao ◽  
Chuanmin Liu ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Integrated Analysis ◽  
Mrna Regulation ◽  
Duck Hepatitis ◽  
Differentially Expressed Mirnas ◽  
Regulation Network

Abstract Background: Duck hepatitis A virus type 3 (DHAV-3) is one of the most harmful pathogens in the duck industry. However, the molecular mechanism underlying DHAV-3 infection in ducklings is remain poorly understood. To elucidate the genetic regulatory network for miRNA-mRNA and the signaling pathways involved in DHAV-3 infection in ducklings, we conducted global miRNA and mRNA expression profiling of duckling liver tissues infected with lethal DHAV-3 using high-throughput sequencing. Results: We found 156 differentially expressed miRNAs (DEMs) and 7717 differentially expressed miRNAs (DEGs) between mock-infected and DHAV-3-infected duckling livers. A total of 19,606 miRNA-mRNA pairs with negatively correlated expression patterns were identified in miRNA-mRNA networks constructed on the basis of these DEMs and DEGs. Moreover, immune-related pathways including the cytokine-cytokine receptor interaction, apoptosis, Toll-like receptor, Jak-STAT, and RIG-I-like receptor signaling pathway were significantly enriched through analyzing functions of mRNAs in the network in response to DHAV-3 infection. Besides, apl-miR-32-5p, apl-miR-125-5p, apl-miR-128-3p, apl-miR-460-5p, and novel-m0012-3p were identified as potential regulators in the immune-related signaling pathways during the DHAV-3 infection. Conclusions: To our knowledge, this is the first report on integrated analysis of miRNA-seq and mRNA-seq in DHAV-3-infected ducklings. The results indicated the important roles of miRNAs in regulating immune response genes and revealed the immune related miRNA-mRNA regulation network in the DHAV-3-infected duckling liver. Our findings may provide valuable information to further investigate the roles of miRNAs and their target genes in DHAV-3 replication and pathogenesis; additionally, they may offer clues for further understanding host-virus interactions.

scholarly journals Genome-wide analysis of lncRNAs and mRNAs expression during the differentiation of abdominal preadipocytes in chicken

2016 ◽  
Author(s):  
Tao Zhang ◽  
Xiangqian Zhang ◽  
Kunpeng Han ◽  
Genxi Zhang ◽  
Jinyu Wang ◽  
...  
Keyword(s):  
Network Analysis ◽  
Rna Sequencing ◽  
Early Stage ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Valuable Resource ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
And Function ◽  
Jinghai Yellow Chicken

AbstractlncRNAs regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in preadipocytes differentiation of chicken. Here, we identified lncRNAs in preadipocytes of different differentiation stages by RNA-sequencing using Jinghai Yellow chicken. A total of 1,300,074,528 clean reads and 27,023 lncRNAs were obtained from twenty samples. 3095 genes (1,336 lncRNAs and 1,759 mRNAs) were differentially expressed among different stages, of which the number of DEGs decreased with the differentiation, demonstrating that the early stage might be most important for chicken preadipocytes differentiation. Furthermore, 3,095 DEGs were clustered into 8 clusters with their expression patterns by K-means clustering. We identified six stage-specific modules related to A0, A2 and A6 stages using weighted co-expression network analysis. Many well-known/novel pathways associated with preadipocytes differentiation were found. We also identified highly connected genes in each module and visualized them by cytoscape. Many well-known genes related to preadipocytes differentiation were found such as IGFBP2 and JUN. Yet, the majority of high connected genes were unknown in chicken preadipocytes. This study provides a valuable resource for chicken lncRNA study and contributes to batter understanding the biology of preadipocytes differentiation in chicken.

scholarly journals Identification and Characterization of miRNAs in Self-Rooted and Grafted Malus Reveals Critical Networks Associated with Flowering

2018 ◽  
Vol 19 (8) ◽  
pp. 2384 ◽  
Author(s):  
Na An ◽  
Sheng Fan ◽  
Yang Yang ◽  
Xilong Chen ◽  
Feng Dong ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Fruit Trees ◽  
Differentially Expressed ◽  
Flowering Genes ◽  
Differentially Expressed Mirnas ◽  
Flowering Rate ◽  
Carbohydrate Contents

Grafting can improve the agricultural traits of crop plants, especially fruit trees. However, the regulatory networks and differentially expressed microRNAs (miRNAs) related to grafting in apple remain unclear. Herein, we conducted high-throughput sequencing and identified differentially expressed miRNAs among self-rooted Fuji, self-rooted M9, and grafted Fuji/M9. We analyzed the flowering rate, leaf morphology, and nutrient and carbohydrate contents in the three materials. The flowering rate, element and carbohydrate contents, and expression levels of flowering genes were higher in Fuji/M9 than in Fuji. We detected 206 known miRNAs and 976 novel miRNAs in the three materials, and identified those that were up- or downregulated in response to grafting. miR156 was most abundant in Fuji, followed by Fuji/M9, and then self-rooted M9, while miR172 was most abundant in M9, followed by Fuji/M9, and then Fuji. These expression patterns suggest that that these miRNAs were related to grafting. A Gene Ontology (GO) analysis showed that the differentially expressed miRNAs controlled genes involved in various biological processes, including cellular biosynthesis and metabolism. The expression of differentially expressed miRNAs and flowering-related genes was verified by qRT-PCR. Altogether, this comprehensive analysis of miRNAs related to grafting provides valuable information for breeding and grafting of apple and other fruit trees.

scholarly journals Exploring miRNA-mRNA regulatory network in cardiac pathology in Na+/H+ exchanger isoform 1 transgenic mice

2018 ◽  
Vol 50 (10) ◽  
pp. 846-861 ◽  
Author(s):  
Jin Xue ◽  
Dan Zhou ◽  
Orit Poulsen ◽  
Iain Hartley ◽  
Toshihiro Imamura ◽  
...  
Keyword(s):  
Hypertrophic Cardiomyopathy ◽  
Transgenic Mice ◽  
Cardiac Hypertrophy ◽  
Rna Sequencing ◽  
High Throughput Sequencing ◽  
Interstitial Fibrosis ◽  
Expression Patterns ◽  
Cardiac Injury ◽  
Differentially Expressed ◽  
Mrna Targets

Numerous studies have demonstrated that Na+/H+ exchanger isoform 1 (NHE1) is elevated in myocardial diseases and its effect is detrimental. To better understand the involvement of NHE1, we have previously studied cardiac-specific NHE1 transgenic mice and shown that these mice develop cardiac hypertrophy, interstitial fibrosis, and cardiac dysfunction. The purpose of current study was to identify microRNAs and their mRNA targets involved in NHE1-mediated cardiac injury. An unbiased high-throughput sequencing study was performed on both microRNAs and mRNAs. RNA sequencing showed that differentially expressed genes were enriched in hypertrophic cardiomyopathy pathway by Kyoto Encyclopedia of Genes and Genomes annotation in NHE1 transgenic hearts. These genes were classified as contraction defects (e.g., Myl2, Myh6, Mybpc3, and Actb), impaired intracellular Ca2+ homeostasis (e.g., SERCA2a, Ryr2, Rcan1, and CaMKII delta), and signaling molecules for hypertrophic cardiomyopathy (e.g., Itga/b, IGF-1, Tgfb2/3, and Prkaa1/2). microRNA sequencing revealed that 15 microRNAs were differentially expressed (2-fold, P < 0.05). Six of them (miR-1, miR-208a-3p, miR-199a-5p, miR-21-5p, miR-146a-5p, and miR-30c-5p) were reported to be related to cardiac pathological functions. The integrative analysis of microRNA and RNA sequencing data identified several crucial microRNAs including miR-30c-5p, miR-199a-5p, miR-21-5p, and miR-34a-5p as well as 10 of their mRNA targets that may affect the heart via NFAT hypertrophy and cardiac hypertrophy signaling. Furthermore, important microRNAs and mRNA targets were validated by quantitative PCR. Our study comprehensively characterizes the expression patterns of microRNAs and mRNAs, establishes functional microRNA-mRNA pairs, elucidates the potential signaling pathways, and provides novel insights on the mechanisms underlying NHE1-medicated cardiac injury.

scholarly journals Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Min Li ◽  
Wenye Zhu ◽  
Chu Wang ◽  
Yuanyuan Zheng ◽  
Shibo Sun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Differentially Expressed Genes ◽  
Immune Status ◽  
Expression Patterns ◽  
Gene Expression Pattern ◽  
Gene Set Enrichment Analysis ◽  
Functional Enrichment ◽  
Differentially Expressed ◽  
Hub Genes

Abstract Background Asthma is a heterogeneous disease that can be divided into four inflammatory phenotypes: eosinophilic asthma (EA), neutrophilic asthma (NA), mixed granulocytic asthma (MGA), and paucigranulocytic asthma (PGA). While research has mainly focused on EA and NA, the understanding of PGA is limited. In this study, we aimed to identify underlying mechanisms and hub genes of PGA. Methods Based on the dataset from Gene Expression Omnibus(GEO), weighted gene coexpression network analysis (WGCNA), differentially expressed genes (DEGs) analysis and protein–protein interaction (PPI) network analysis were conducted to construct a gene network and to identify key gene modules and hub genes. Functional enrichment analyses were performed to investigate the biological process, pathways and immune status of PGA. The hub genes were validated in a separate dataset. Results Compared to non-PGA, PGA had a different gene expression pattern, in which 449 genes were differentially expressed. One gene module significantly associated with PGA was identified. Intersection between the differentially expressed genes (DEGs) and the genes from the module that were most relevant to PGA were mainly enriched in inflammation and immune response regulation. The single sample Gene Set Enrichment Analysis (ssGSEA) suggested a decreased immune infiltration and function in PGA. Finally six hub genes of PGA were identified, including ADCY2, CXCL1, FPRL1, GPR109B, GPR109A and ADCY3, which were validated in a separate dataset of GSE137268. Conclusions Our study characterized distinct gene expression patterns, biological processes and immune status of PGA and identified hub genes, which may improve the understanding of underlying mechanism and provide potential therapeutic targets for PGA.

scholarly journals Identification of miRNAs and Their Target Genes Involved in Cucumber Fruit Expansion Using Small RNA and Degradome Sequencing

Biomolecules ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 483 ◽  
Author(s):  
Sun ◽  
Luo ◽  
Chang ◽  
Li ◽  
Zhou ◽  
...  
Keyword(s):  
Small Rna ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Sequencing Data ◽  
Degradome Sequencing ◽  
Complex Biological Process ◽  
Cucumber Fruit ◽  
Differentially Expressed Mirnas

Fruit expansion is an essential and very complex biological process. Regulatory roles of microRNAs (miRNAs) and miRNA–mRNA modules in the cucumber fruit expansion are not yet to be investigated. In this work, 1253 known and 1269 novel miRNAs were identified from nine cucumber fruit small RNA (sRNA) libraries through high-throughput sequencing. A total of 105 highly differentially expressed miRNAs were recognized in the fruit on five days post anthesis with pollination (EXP_5d) sRNA library. Further, expression patterns of 11 differentially expressed miRNAs were validated by quantitative real-time PCR (qRT-PCR). The expression patterns were similar to sRNAs sequencing data. Transcripts of 1155 sequences were predicted as target genes of differentially expressed miRNAs by degradome sequencing. Gene Ontology (GO) enrichment showed that these target genes were involved in 24 biological processes, 15 cell components and nine molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that these target genes were significantly enriched in 19 pathways and the enriched KEGG pathways were associated with environmental adaptation, signal transduction and translation. Based on the functional prediction of miRNAs and target genes, our findings suggest that miRNAs have a potential regulatory role in cucumber fruit expansion by targeting their target genes, which provide important data for understanding the miRNA-mediated regulatory networks controlling fruit expansion in cucumber. Specific miRNAs could be selected for further functional research and molecular breeding in cucumber.

scholarly journals Genome-wide Identification and Expression Pattern Analysis of BRI1-EMS–suppressor Transcription Factors in Tomato under Abiotic Stresses

2018 ◽  
Vol 143 (1) ◽  
pp. 84-90 ◽  
Author(s):  
Yingmei Gao ◽  
Jingkang Hu ◽  
Tingting Zhao ◽  
Xiangyang Xu ◽  
Jingbin Jiang ◽  
...  
Keyword(s):  
Environmental Changes ◽  
Expression Patterns ◽  
Bioinformatic Analysis ◽  
Functional Identification ◽  
Tomato Plants ◽  
Protein Motifs ◽  
Genome Wide ◽  
Polymerase Chain ◽  
Regulated Gene Expression ◽  
Insight Into

BRI1-EMS-suppressor 1 (BES1) is a transcription factor (TF) that functions as a master regulator of brassinosteroid (BR)-regulated gene expression. Here, we provide a complete overview of Solanum lycopersicum BES1 (SLB) genes, including phylogeny, gene structure, protein motifs, chromosome locations and expression characteristics. Through bioinformatic analysis, we compared the sequences of SLB genes, arabidopsis (Arabidopsis thaliana) genes, and chinese cabbage (Brassica pekinensis) genes. All of the gene sequences were divided into three groups by cluster analysis. SLB genes were mapped to the eight tomato (S. lycopersicum) chromosomes. Bioinformatic analysis showed that SLB genes shares similarities with the proteins from other plants, though different species exhibit specific features. The expression patterns of SLB genes in various tissues and under different abiotic conditions were analyzed by quantitative reverse transcription polymerase chain reaction. SLB genes were found to be induced by multiple stresses, particularly salt stress, indicating that SLB genes may have important roles in the response to unfavorable environmental changes. This study provides insight into the evolution of SLB genes and may aid in the further functional identification of BES1 proteins and the response of tomato plants to different stresses.

scholarly journals Gene network approach reveals co-expression patterns in nasal and bronchial epithelium

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kai Imkamp ◽  
Victor Bernal ◽  
Marco Grzegorzcyk ◽  
Peter Horvatovich ◽  
Cornelis J. Vermeulen ◽  
...  
Keyword(s):  
Gene Expression ◽  
Network Analysis ◽  
Gene Expression Profiling ◽  
Graphical Models ◽  
Expression Profiling ◽  
Expression Patterns ◽  
Bronchial Epithelium ◽  
Differentially Expressed ◽  
Tobacco Exposure ◽  
Genome Wide

Abstract Nasal gene expression profiling is a new approach to investigate the airway epithelium as a biomarker to study the activity and treatment responses of obstructive pulmonary diseases. We investigated to what extent gene expression profiling of nasal brushings is similar to that of bronchial brushings. We performed genome wide gene expression profiling on matched nasal and bronchial epithelial brushes from 77 respiratory healthy individuals. To investigate differences and similarities among regulatory modules, network analysis was performed on correlated, differentially expressed and smoking-related genes using Gaussian Graphical Models. Between nasal and bronchial brushes, 619 genes were correlated and 1692 genes were differentially expressed (false discovery rate <0.05, |Fold-change|>2). Network analysis of correlated genes showed pro-inflammatory pathways to be similar between the two locations. Focusing on smoking-related genes, cytochrome-P450 pathway related genes were found to be similar, supporting the concept of a detoxifying response to tobacco exposure throughout the airways. In contrast, cilia-related pathways were decreased in nasal compared to bronchial brushes when focusing on differentially expressed genes. Collectively, while there are substantial differences in gene expression between nasal and bronchial brushes, we also found similarities, especially in the response to the external factors such as smoking.

scholarly journals Genome-Wide Analysis of the miRNA–mRNAs Network Involved in Cold Tolerance in Populus simonii × P. nigra

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 430 ◽  
Author(s):  
Bo Zhou ◽  
Yutong Kang ◽  
Jingtong Leng ◽  
Qijiang Xu
Keyword(s):  
Cold Tolerance ◽  
High Throughput Sequencing ◽  
Expression Patterns ◽  
Differential Expression Analysis ◽  
Chilling Injury ◽  
Cold Treatment ◽  
Differentially Expressed ◽  
Integrated Analysis ◽  
Populus Simonii ◽  
Cold Induction

Background: Cold tolerance is important for plants’ geographical distribution and survival in extreme seasonal variations of climate. However, Populus simonii × P. nigra shows wide adaptability and strong cold resistance. Transcriptional and post-transcriptional regulation of cold-responsive genes is crucial for cold tolerance in plants. To understand the roles of regulatory RNAs under cold induction in Populus simonii × P. nigra, we constructed cDNA and small RNA libraries from leaf buds treated or not with −4 °C for 8 h for analysis. Results: Through high-throughput sequencing and differential expression analysis, 61 miRNAs and 1229 DEGs were identified under cold induction condition in Populus simonii × P. nigra. The result showed that miR167a, miR1450, miR319a, miR395b, miR393a-5p, miR408-5p, and miR168a-5p were downregulated, whereas transcription level of miR172a increased under the cold treatment. Thirty-one phased-siRNA were also obtained (reads ≥ 4) and some of them proceeded from TAS3 loci. Analysis of the differentially expressed genes (DEGs) showed that transcription factor genes such as Cluster-15451.2 (putative MYB), Cluster-16493.29872 (putative bZIP), Cluster-16493.29175 (putative SBP), and Cluster-1378.1 (putative ARF) were differentially expressed in cold treated and untreated plantlets of Populus simonii × P. nigra. Integrated analysis of miRNAs and transcriptome showed miR319, miR159, miR167, miR395, miR390, and miR172 and their target genes, including MYB, SBP, bZIP, ARF, LHW, and ATL, were predicted to be involved in ARF pathway, SPL pathway, DnaJ related photosystem II, and LRR receptor kinase, and many of them are known to resist chilling injury. Particularly, a sophisticated regulatory model including miRNAs, phasiRNAs, and targets of them was set up. Conclusions: Integrated analysis of miRNAs and transcriptome uncovered the complicated regulation of the tolerance of cold in Populus simonii × P. nigra. MiRNAs, phasiRNAs, and gene-encoded transcription factors were characterized at a whole genome level and their expression patterns were proved to be complementary. This work lays a foundation for further research of the pathway of sRNAs and regulatory factors involved in cold tolerance.

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