scholarly journals Transcriptional evidence for cross talk between JA and ET or SA during root-knot nematode invasion in tomato

2018 ◽  
Vol 50 (3) ◽  
pp. 197-207 ◽  
Author(s):  
Wenchao Zhao ◽  
Xiaoxuan Zhou ◽  
Hui Lei ◽  
Jingwei Fan ◽  
Rui Yang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Expression Patterns ◽  
Defense Responses ◽  
Differentially Expressed ◽  
Root Knot Nematode ◽  
Real Time Quantitative Pcr ◽  
Copy Numbers ◽  
Transcription Factor Genes ◽  
Acid Pathway ◽  
Ja Signaling

studies have demonstrated that jasmonic acid (JA) reduces root-knot nematode (RKN) infections in tomato plants. RKN invasion is sensed by roots, and root-derived JA signaling activates systemic defense responses, though this is poorly understood. Here, we investigate variations in the RKN-induced transcriptome in scion phloem between two tomato plant grafts: CM/CM ( Lycopersicum esculentum Mill. cv. Castlemart) and CM/ spr2 (a JA-deficient mutant). A total of 8,716 genes were differentially expressed in the scion phloem of the plants with JA-deficient rootstock via RNA sequencing. Among these genes, 535 upregulated and 153 downregulated genes with high copy numbers were identified as significantly differentially expressed. Among them, 34 predicted transcription factor genes were identified. Additionally, we used real-time quantitative PCR to analyze the expression patterns of 42 genes involved in the JA, ethylene, or salicylic acid pathway in phloem under RKN infection. The results suggested that in the absence of JA signaling, the ET signaling pathway is enhanced after RKN infection; however, alterations in the SA signaling pathway were not observed.

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.

Transcriptome sequencing revealed the genes and pathways involved in salinity stress of Chinese mitten crab, Eriocheir sinensis

2014 ◽  
Vol 46 (5) ◽  
pp. 177-190 ◽  
Author(s):  
Erchao Li ◽  
Shaolin Wang ◽  
Chao Li ◽  
Xiaodan Wang ◽  
Ke Chen ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Salinity Stress ◽  
Transcriptome Sequencing ◽  
Muscle Protein ◽  
Expression Patterns ◽  
Eriocheir Sinensis ◽  
Differentially Expressed ◽  
Control Group ◽  
Protein Ubiquitination ◽  
Mitten Crab

A total of 276.9 million reads were obtained and assembled into 206, 371 contigs with an average length of 614 bp and N50 of 1,470 bp. Comparison of digital gene expression between treatment and control group reveals 1,151 and 941 genes were significantly differentially expressed in crab gill and muscle, respectively. In gill and muscle, protein ubiquitination, ubiquinone biosynthesis, oxidative phosphorylation, and mitochondria dysfunction pathways were the top pathways differentially expressed following the challenge. EIF 2 signaling pathway and IGF-1 signaling pathway were the top ones among the signal-related pathways. Most of the amino acid metabolism pathways were found to be involved in this process. The expression patterns of 15 differentially expressed genes were validated by quantitative real-time RT-PCR (average correlation coefficient 0.80). This is the first report of expression analysis of genes and pathways involved in osmoregulation of Eriocheir sinensis through transcriptome sequencing. The findings of this study will further promote the understanding of the underlying molecular mechanism of salinity stress adaptation for crustacean species.

scholarly journals Transcriptomic analysis reveals distinct resistant response by physcion and chrysophanol against cucumber powdery mildew

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1991 ◽  
Author(s):  
Yanping Li ◽  
Shilin Tian ◽  
Xiaojun Yang ◽  
Xin Wang ◽  
Yuhai Guo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Disease Resistance ◽  
Powdery Mildew ◽  
Differentially Expressed Genes ◽  
Expression Patterns ◽  
Defense Responses ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Sequencing Data ◽  
Transcriptional Change

Physcion and chrysophanol induce defense responses against powdery mildew in cucumbers. The combination of these two compounds has synergistic interaction against the disease. We performed RNA-seq on cucumber leaf samples treated with physcion and chrysophanol alone and with their combination. We generated 17.6 Gb of high-quality sequencing data (∼2 Gb per sample) and catalogued the expressions profiles of 12,293 annotated cucumber genes in each sample. We identified numerous differentially expressed genes that exhibited distinct expression patterns among the three treatments. The gene expression patterns of the Chr and Phy treatments were more similar to each other than to the Phy × Chr treatment. The Phy × Chr treatment induced the highest number of differentially expressed genes. This dramatic transcriptional change after Phy × Chr treatment leaves reflects that physcion combined with chrysophanol treatment was most closely associated with induction of disease resistance. The analysis showed that the combination treatment caused expression changes of numerous defense-related genes. These genes have known or potential roles in structural, chemical and signaling defense responses and were enriched in functional gene categories potentially responsible for cucumber resistance. These results clearly demonstrated that disease resistance in cucumber leaves was significantly influenced by the combined physcion and chrysophanol treatment. Thus, physcion and chrysophanol are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms related to the defense response.

scholarly journals Identification and Characterization of MAPK Signaling Pathway Genes and Associated lncRNAs in the Ileum of Piglets Infected by Clostridium perfringens Type C

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Ruirui Luo ◽  
Xiaoyu Huang ◽  
Zunqiang Yan ◽  
Xiaoli Gao ◽  
Pengfei Wang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Clostridium Perfringens ◽  
Expression Patterns ◽  
Strong Support ◽  
Mapk Signaling ◽  
Mapk Signaling Pathway ◽  
Differentially Expressed ◽  
Economic Losses ◽  
Sequencing Data ◽  
Type C

Clostridium perfringens type C (C. perfringens type C) is one of the main microbial pathogens responsible for piglet diarrhea worldwide, causing substantial economic losses for pig-rearing industries. The mitogen-activated protein kinase (MAPK) signaling pathway is a key regulator of inflammatory bowel disease, especially necrotic enteritis. However, whether and how the MAPK signaling pathway is involved in regulating the process of piglet diarrhea when challenged by C. perfringens type C are still unknown. Here, we screened 38 differentially expressed genes (DEGs) in piglets’ ileum tissues experimentally infected with C. perfringens type C that were enriched in the Sus scrofa MAPK signaling pathway, based on our previous transcriptome data. Of these DEGs, 12 genes (TRAF2, MAPK8, and GADD45G, among others) were upregulated whereas 26 genes (MAPK1, TP53, and CHUK, among others) were downregulated in the infected group. Our results showed that MAPK1, TP53, MAPK8, MYC, and CHUK were in the core nodes of the PPI network. Additionally, we obtained 35 lncRNAs from the sequencing data, which could be trans-targeted to MAPK signaling pathway genes and were differentially expressed in the ileum tissues infected with C. perfringens. We used qRT-PCR to verify the expression levels of genes and lncRNAs related to the MAPK signaling pathway; their expression patterns were consistent with RNA sequencing data. Our results provide strong support for deeply exploring the role of the MAPK signaling pathway in diarrhea caused by C. perfringens type C.

scholarly journals Pochonia chlamydosporia Isolate PC-170-Induced Expression of Marker Genes for Defense Pathways in Tomatoes Challenged by Different Pathogens

2021 ◽  
Vol 9 (9) ◽  
pp. 1882
Author(s):  
Xia Zhuang ◽  
Jian-Long Zhao ◽  
Miao Bai ◽  
Xing-Xing Ping ◽  
Yan-Lin Li ◽  
...  
Keyword(s):  
Jasmonic Acid ◽  
Defense Responses ◽  
Systemic Resistance ◽  
Marker Genes ◽  
Root Knot Nematode ◽  
Pochonia Chlamydosporia ◽  
Susceptibility To Infection ◽  
Nematode Eggs ◽  
Mutant Lines ◽  
Ja Signaling

Pochonia chlamydosporia is a fungal parasite of nematode eggs. Studies have shown that some strains of Pochonia chlamydosporia can promote plant growth and induce plants’ systemic resistance to root-knot nematodes by colonizing in their roots. This study aimed to verify the effect of the PC-170 strain on tomato growth and systemic resistance. Split-root experiments were conducted to observe the systemic resistance induced by PC-170. To explore the defense pathway that was excited due to the colonization by PC-170, we tested the expression of marker genes for defense pathways, and used mutant lines to verify the role of plant defense pathways. Our results showed that PC-170 can colonize roots, and promotes growth. We found a role for jasmonic acid (JA) in modulating tomato colonization by PC-170. PC-170 can activate tomato defense responses to reduce susceptibility to infection by the root-knot nematode Meloidogyne incognita, and induced resistance to some pathogens in tomatoes. The marker genes of the defense pathway were significantly induced after PC-170 colonization. However, salicylic acid (SA)- and jasmonic acid (JA)-dependent defenses in roots were variable with the invasion of different pathogens. Defense pathways play different roles at different points in time. SA- and JA-dependent defense pathways were shown to cross-communicate. Different phytohormones have been involved in tomato plants’ responses against different pathogens. Our study confirmed that adaptive JA signaling is necessary to regulate PC-170 colonization and induce systemic resistance in tomatoes.

scholarly journals CircRNA expression profile and functional analysis in testicular tissue of patients with non-obstructive azoospermia

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Pan Ge ◽  
Jian Zhang ◽  
Liang Zhou ◽  
Mo-qi Lv ◽  
Yi-xin Li ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Expression Profile ◽  
Function Analysis ◽  
Expression Patterns ◽  
Testicular Tissue ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Transferase Activity ◽  
Obstructive Azoospermia ◽  
Qrt Pcr

Abstract Background Non-obstructive azoospermia (NOA) is a multifactorial disorder whose molecular basis remains largely unknown. Circular RNAs (CircRNAs), a novel class of endogenous RNAs, have been recognized to play important roles in many biological processes. However, little is known about the expression patterns and functions of circRNAs in human testes involved in NOA. Methods In this study, the testicular circRNA expression profile were explored in NOA patients and the controls by high-throughput circRNA microarray. Real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) was performed to confirm the microarray data. Bioinformatics analyses including the circRNA/miRNA/mRNA interaction network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used to predict the functions of differentially expressed circRNAs. Results A total of 368 differentially down-regulated and 526 up-regulated circRNAs were detected in NOA patients. These findings have been verified by qRT-PCR on 6 selected circRNAs. Among these differentially expressed circRNAs, the hsa_circRNA_0023313 was obviously up-regulated in testicular tissue of NOA patients. The most likely potential target miRNA for hsa_circRNA_0023313 include hsa-miR-520d-3p, hsa-miR-373-3p, hsa-miR-372-3p, hsa-miR-302c-3p and hsa-miR-130b-5p. Function analysis indicated that hsa_circRNA_0023313 was ubiquitin-protein transferase activity and chromatin binding. KEGG analysis revealed that the top five pathways related to hsa_circRNA_0023313 were endocytosis, meiosis, FoxO signaling pathway, ubiquitin mediated proteolysis and AMPK signaling pathway. Conclusions This is the first report that the testicular circRNA expression profile is altered in NOA patients indicating circRNAs might play important roles in regulating spermatogenesis and be potential biomarkers for the diagnosis and treatment of NOA.

scholarly journals Transcriptome Analysis of Early Defenses in Rice against Fusarium fujikuroi

Rice ◽  
2020 ◽  
Vol 13 (1) ◽  
Author(s):  
An-Po Cheng ◽  
Szu-Yu Chen ◽  
Ming-Hsin Lai ◽  
Dong-Hong Wu ◽  
Shih-Shun Lin ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Defense Mechanisms ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Leaf Angle ◽  
Fusarium Fujikuroi ◽  
Marker Genes ◽  
Post Inoculation ◽  
Disease Development ◽  
Ja Signaling

Abstract Background Bakanae is a seedborne disease caused by Fusarium fujikuroi. Rice seedlings emerging from infected seeds can show diverse symptoms such as elongated and slender stem and leaves, pale coloring, a large leaf angle, stunted growth and even death. Little is known about rice defense mechanisms at early stages of disease development. Results This study focused on investigating early defenses against F. fujikuroi in a susceptible cultivar, Zerawchanica karatals (ZK), and a resistant cultivar, Tainung 67 (TNG67). Quantitative PCR revealed that F. fujikuroi colonizes the root and stem but not leaf tissues. Illumina sequencing was conducted to analyze the stem transcriptomes of F. fujikuroi-inoculated and mock-inoculated ZK and TNG67 plants collected at 7 days post inoculation (dpi). More differentially expressed genes (DEGs) were identified in ZK (n = 169) than TNG67 (n = 118), and gene ontology terms related to transcription factor activity and phosphorylation were specifically enriched in ZK DEGs. Among the complex phytohormone biosynthesis and signaling pathways, only DEGs involved in the jasmonic acid (JA) signaling pathway were identified. Fourteen DEGs encoding pattern-recognition receptors, transcription factors, and JA signaling pathway components were validated by performing quantitative reverse transcription PCR analysis of individual plants. Significant repression of jasmonate ZIM-domain (JAZ) genes (OsJAZ9, OsJAZ10, and OsJAZ13) at 3 dpi and 7 dpi in both cultivars, indicated the activation of JA signaling during early interactions between rice and F. fujikuroi. Differential expression was not detected for salicylic acid marker genes encoding phenylalanine ammonia-lyase 1 and non-expressor of pathogenesis-related genes 1. Moreover, while MeJA did not affect the viability of F. fujikuroi, MeJA treatment of rice seeds (prior to or after inoculation) alleviated and delayed bakanae disease development in susceptible ZK. Conclusions Different from previous transcriptome studies, which analyzed the leaves of infected plants, this study provides insights into defense-related gene expression patterns in F. fujikuroi–colonized rice stem tissues. Twelve out of the 14 selected DEGs were for the first time shown to be associated with disease resistance, and JA-mediated resistance was identified as a crucial component of rice defense against F. fujikuroi. Detailed mechanisms underlying the JA-mediated bakanae resistance and the novel defense-related DEGs are worthy of further investigation.

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.

scholarly journals Toxocara canis Infection Alters lncRNA and mRNA Expression Profiles of Dog Bone Marrow

2021 ◽  
Vol 9 ◽  
Author(s):  
Wen-Bin Zheng ◽  
Yang Zou ◽  
Qing Liu ◽  
Min-Hua Hu ◽  
Hany M. Elsheikha ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Mrna Expression ◽  
Signaling Pathway ◽  
Post Infection ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Toxocara Canis ◽  
Differentially Expressed ◽  
Global Changes ◽  
Hematopoietic Organ

Bone marrow is the main hematopoietic organ that produces red blood cells, granulocytes, monocyte/macrophages, megakaryocytes, lymphocytes, and myeloid dendritic cells. Many of these cells play roles in the pathogenesis of Toxocara canis infection, and understanding how infection alters the dynamics of transcription regulation in bone marrow is therefore critical for deciphering the global changes in the dog transcriptional signatures during T. canis infection. In this study, long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in the bone marrow of Beagle dogs infected with T. canis were determined at 12 h post-infection (hpi), 24 hpi, 96 hpi, and 36 days post-infection (dpi). RNA-sequencing and bioinformatics analysis identified 1,098, 984, 1,120, and 1,305 differentially expressed lncRNAs (DElncRNAs), and 196, 253, 223, and 328 differentially expressed mRNAs (DEmRNAs) at 12 h, 24 h, 96 h, and 36 days after infection, respectively. We also identified 29, 36, 38, and 68 DEmRNAs potentially cis-regulated by 44, 44, 51, and 80 DElncRNAs at 12 hpi, 24 hpi, 96 hpi, and 36 dpi, respectively. To validate the sequencing findings, qRT-PCR was performed on 10 randomly selected transcripts. Many altered genes were involved in the differentiation of bone marrow cells. GO of DElncRNAs and GO and KEGG pathway analyses of DEmRNAs revealed alterations in several signaling pathways, including pathways involved in energy metabolism, amino acid biosynthesis and metabolism, Wnt signaling pathway, Huntington's disease, HIF-1 signaling pathway, cGMP–PKG signaling pathway, dilated cardiomyopathy, and adrenergic signaling in cardiomyocytes. These findings revealed that bone marrow of T. canis-infected dogs exhibits distinct lncRNA and mRNA expression patterns compared to healthy control dogs. Our data provide novel insights into T. canis interaction with the definitive host and shed light on the significance of the non-coding portion of the dog genome in the pathogenesis of toxocariasis.

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