scholarly journals Magnesium Deficiency Induced Global Transcriptome Change in Citrus sinensis Leaves Revealed by RNA-Seq

2019 ◽  
Vol 20 (13) ◽  
pp. 3129 ◽  
Author(s):  
Yang ◽  
Zhou ◽  
Wang ◽  
Wu ◽  
Ye ◽  
...  
Keyword(s):  
Citrus Sinensis ◽  
Molecular Mechanisms ◽  
Magnesium Deficiency ◽  
Enrichment Analysis ◽  
Co2 Assimilation ◽  
Soluble Carbohydrates ◽  
H2o2 Production ◽  
Rna Seq ◽  
Mg Deficiency ◽  
Real Time Quantitative Pcr

Magnesium (Mg) deficiency is one of the major constraining factors that limit the yield and quality of agricultural products. Uniform seedlings of the Citrus sinensis were irrigated with Mg deficient (0 mM MgSO4) and Mg sufficient (1 mM MgSO4) nutrient solutions for 16 weeks. CO2 assimilation, starch, soluble carbohydrates, TBARS content and H2O2 production were measured. Transcriptomic analysis of C. sinensis leaves was performed by Illumina sequencing. Our results showed that Mg deficiency decreased CO2 assimilation, but increased starch, sucrose, TBARS content and H2O2 production in C. sinensis leaves. A total of 4864 genes showed differential expression in response to Mg deficiency revealed by RNA-Seq and the transcriptomic data were further validated by real-time quantitative PCR (RT-qPCR). Gene ontology (GO) enrichment analysis indicated that the mechanisms underlying Mg deficiency tolerance in C. sinensis may be attributed to the following aspects: a) enhanced microtubule-based movement and cell cycle regulation; b) elevated signal transduction in response to biotic and abiotic stimuli; c) alteration of biological processes by tightly controlling phosphorylation especially protein phosphorylation; d) down-regulation of light harvesting and photosynthesis due to the accumulation of carbohydrates; e) up-regulation of cell wall remodeling and antioxidant system. Our results provide a comprehensive insight into the transcriptomic profile of key components involved in the Mg deficiency tolerance in C. sinensis and enrich our understanding of the molecular mechanisms by which plants adapted to a Mg deficient condition.

Molecular mechanisms for magnesium-deficiency-induced leaf vein lignification, enlargement and cracking in Citrus sinensis revealed by RNA-Seq

2020 ◽  
Author(s):  
Xin Ye ◽  
Hui-Yu Huang ◽  
Feng-Lin Wu ◽  
Li-Ya Cai ◽  
Ning-Wei Lai ◽  
...  
Keyword(s):  
Cell Wall ◽  
Citrus Sinensis ◽  
Molecular Mechanisms ◽  
Magnesium Deficiency ◽  
Lignin Biosynthesis ◽  
Common Elements ◽  
Rna Seq ◽  
Transcript Levels ◽  
Mg Deficiency ◽  
Leaf Vein

Abstract Citrus sinensis (L.) Osbeck seedlings were fertigated with nutrient solution containing 2 [magnesium (Mg)-sufficiency] or 0 mM (Mg-deficiency) Mg(NO3)2 for 16 weeks. Thereafter, RNA-Seq was used to investigate Mg-deficiency-responsive genes in the veins of upper and lower leaves in order to understand the molecular mechanisms for Mg-deficiency-induced vein lignification, enlargement and cracking, which appeared only in the lower leaves. In this study, 3065 upregulated and 1220 downregulated, and 1390 upregulated and 375 downregulated genes were identified in Mg-deficiency veins of lower leaves (MDVLL) vs Mg-sufficiency veins of lower leaves (MSVLL) and Mg-deficiency veins of upper leaves (MDVUL) vs Mg-sufficiency veins of upper leaves (MSVUL), respectively. There were 1473 common differentially expressed genes (DEGs) between MDVLL vs MSVLL and MDVUL vs MSVUL, 1463 of which displayed the same expression trend. Magnesium-deficiency-induced lignification, enlargement and cracking in veins of lower leaves might be related to the following factors: (i) numerous transciption factors and genes involved in lignin biosynthesis pathways, regulation of cell cycle and cell wall metabolism were upregulated; and (ii) reactive oxygen species, phytohormone and cell wall integrity signalings were activated. Conjoint analysis of proteome and transcriptome indicated that there were 287 and 56 common elements between DEGs and differentially abundant proteins (DAPs) identified in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, and that among these common elements, the abundances of 198 and 55 DAPs matched well with the transcript levels of the corresponding DEGs in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively, indicating the existence of concordances between protein and transcript levels.

Molecular and physiological mechanisms underlying magnesium-deficiency-induced enlargement, cracking and lignification of Citrus sinensis leaf veins

2020 ◽  
Vol 40 (9) ◽  
pp. 1277-1291 ◽  
Author(s):  
Xin Ye ◽  
Xu-Feng Chen ◽  
Li-Ya Cai ◽  
Ning-Wei Lai ◽  
Chong-Ling Deng ◽  
...  
Keyword(s):  
Cell Wall ◽  
Citrus Sinensis ◽  
Molecular Mechanisms ◽  
Rho Gtpase ◽  
Magnesium Deficiency ◽  
Lignin Biosynthesis ◽  
Starch Accumulation ◽  
Ascorbate Oxidase ◽  
Mg Deficiency ◽  
Leaf Veins

Abstract Little is known about the physiological and molecular mechanisms underlying magnesium (Mg)-deficiency-induced enlargement, cracking and lignification of midribs and main lateral veins of Citrus leaves. Citrus sinensis (L.) Osbeck seedlings were irrigated with nutrient solution at a concentration of 0 (Mg-deficiency) or 2 (Mg-sufficiency) mM Mg(NO3)2 for 16 weeks. Enlargement, cracking and lignification of veins occurred only in lower leaves, but not in upper leaves. Total soluble sugars (glucose + fructose + sucrose), starch and cellulose concentrations were less in Mg-deficiency veins of lower leaves (MDVLL) than those in Mg-sufficiency veins of lower leaves (MSVLL), but lignin concentration was higher in MDVLL than that in MSVLL. However, all four parameters were similar between Mg-deficiency veins of upper leaves (MDVUL) and Mg-sufficiency veins of upper leaves (MSVUL). Using label-free, liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis, we identified 1229 and 492 differentially abundant proteins (DAPs) in MDVLL vs MSVLL and MDVUL vs MSVUL, respectively. Magnesium-deficiency-induced alterations of Mg, nonstructural carbohydrates, cell wall components, and protein profiles were greater in veins of lower leaves than those in veins of upper leaves. The increased concentration of lignin in MDVLL vs MSVLL might be caused by the following factors: (i) repression of cellulose and starch accumulation promoted lignin biosynthesis; (ii) abundances of proteins involved in phenylpropanoid biosynthesis pathway, hormone biosynthesis and glutathione metabolism were increased; and (iii) the abundances of the other DAPs [viz., copper/zinc-superoxide dismutase, ascorbate oxidase (AO) and ABC transporters] involved in lignin biosynthesis were elevated. Also, the abundances of several proteins involved in cell wall metabolism (viz., expansins, Rho GTPase-activating protein gacA, AO, monocopper oxidase-like protein and xyloglucan endotransglucosylase/hydrolase) were increased in MDVLL vs MSVLL, which might be responsible for the enlargement and cracking of leaf veins.

Analysis of Expression Profiles of mRNA and lncRNA in Oviduct During Estrus Phase of Sheep (Ovis Aries) with Two Fecundity (FecB Gene) Genotypes

2021 ◽  
Author(s):  
Weihao Chen ◽  
Zhifeng Li ◽  
Wei Sun ◽  
Mingxing Chu
Keyword(s):  
Embryo Development ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Ovis Aries ◽  
Functional Enrichment ◽  
Saga Complex ◽  
Rna Seq ◽  
Estrus Phase

Abstract Background:In sheep, FecB is the essential biomarker of the fertility, previous researches have provided a detailed insight on the regulation involved estrus phase and FecB in the reproductive-related tissues including hypothalamus, pituitary, and ovary. However, as the host of embryo development and connection between the ovary and the uterus, little is known about the interaction between mRNAs and lncRNAs in sheep oviduct. In the present study, RNA-Seq was performed to identify the transcriptomic profiles of mRNAs and lncRNAs in oviduct during estrus phase of sheep with FecBBB/++ genotypes.Results:In total, 21,863 lncRNAs and 43,674 mRNAs were identified, 57 DE lncRNAs and 637 DE mRNAs were revealed in the comparisons between follicular phase and luteal phase, 26 DE lncRNAs and 421 DE lncRNAs were revealed in the comparisons between FecB BB genotype and FecB ++ genotype. Functional enrichment analysis suggested that GO and KEGG terms related to reproduction such as SAGA complex, ATP-binding cassette (ABC), Nestin, and Hippo signalling pathway. DE-interaction network suggested that LNC_018420 maybe the key regulators related to embryo development in sheep oviduct.Conclusion:This was the first study to reveal the transcriptomic profiles of mRNAs and lncRNAs in the oviduct of FecB BB/++ sheep at estrus phase using RNA-Seq. Our findings can provide new understanding on the molecular mechanisms of mRNAs and lncRNAs underlying sheep embryo development and also opening new lines of investigation in sheep reproduction.

P5398CircRNAs deregulation in heart failure patients

2019 ◽  
Vol 40 (Supplement_1) ◽  
Author(s):  
S Greco ◽  
A Made' ◽  
M Longo ◽  
R Tikhomirov ◽  
S Castelvecchio ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Functional Characterization ◽  
Enrichment Analysis ◽  
Host Gene ◽  
Circular Rnas ◽  
Amplification Efficiency ◽  
Rna Seq ◽  
Bioinformatics Pipeline

Abstract Background Circular RNAs (circRNAs) are an emerging class of noncoding RNAs stemming from the splicing and circularization of pre-mRNAs exons. CircRNAs can regulate transcription and splicing, sequester microRNAs acting as “sponge” and inducing the respective targets, and bind to RNA binding proteins. Recently, they have been found deregulated in dilated cardiomyopathies (DCM), one of the cardiovascular diseases with the worst rate of morbidity and mortality, and whose molecular mechanisms are only partially known. Purpose Therein, we will evaluate in ischemic DCM patients the modulation of 17 circRNAs, 14 out of them obtained from literature data on DCM ischemic or not, while the other 3 were circRNAs not characterized in the heart previously. The study aims to identify circRNAs candidates for further functional characterization in DCM. In addition, as differential expression (DE) analysis is not easily performed for circRNAs in RNA-seq datasets, the validated circRNAs will be used to set up the most specific and sensitive bioinformatics pipeline for circRNA-DE analysis. Methods We designed divergent and convergent specific primers for 17 circRNAs and their host gene, respectively, and their amplification efficiency was measured by RT-qPCR. Transcripts expression was measured in left ventricle biopsies of 12 patients affected by non end-stage ischemic HF and of 12 matched controls. Results We identified cPVT1, cANKRD17, cBPTF as DE, and validated the modulation of 5 out of the 14 DCM-related circRNAs (cHIPK3, cALPK2, cPCMTD1, cNEBL, cSLC8A1), while cPDRM5, cTTN1 showed opposite modulation, which may be due to the specific disease condition. All of them were modulated differently from the respective host gene. CircRNA/miRNA interactions were predicted using Starbase 3.0. Next, mRNAs-targets of the identified miRNAs were predicted by mirDIP 4.1 and intersected with gene expression datasets of the same patients, previously obtained by microarray analysis. We found that cBPTF and cANKRD17 might sponge 12 and 2 miRNAs, respectively. Enrichment analysis of the relevant targets identified several important pathways implicated in DCM, such as MAPK, FoxO, EGFR, VEGF and Insulin/IGF pathways. In addition, deep RNA-Seq analysis that is currently ongoing and the validated circRNAs will be used to optimize the bioinformatics pipeline for circRNA DE analysis. Conclusions We identified a subset of circRNAs deregulated in ischemic HF potentially implicated in HF pathogenesis.

scholarly journals Dietary Enteromorpha Polysaccharides Supplementation Improves Breast Muscle Yield and Is Associated With Modification of mRNA Transcriptome in Broiler Chickens

2021 ◽  
Vol 8 ◽  
Author(s):  
Yue Zhao ◽  
Balamuralikrishnan Balasubramanian ◽  
Yan Guo ◽  
Sheng-Jian Qiu ◽  
Rajesh Jha ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Broiler Chickens ◽  
Molecular Mechanisms ◽  
Carcass Traits ◽  
Enrichment Analysis ◽  
Dietary Supplementation ◽  
Breast Muscle ◽  
Rna Seq ◽  
Feeding Trial ◽  
Mrna Transcriptome

The present study evaluated the effects of dietary supplementation of Enteromorpha polysaccharides (EP) on carcass traits of broilers and potential molecular mechanisms associated with it. This study used RNA-Sequencing (RNA-Seq) to detect modification in mRNA transcriptome and the cognate biological pathways affecting the carcass traits. A total of 396 one-day-old male broilers (Arbor Acres) were randomly assigned to one of six dietary treatments containing EP at 0 (CON), 1000 (EP_1000), 2500 (EP_2500), 4000 (EP_4000), 5500 (EP_5500), and 7000 (EP_7000) mg/kg levels for a 35-d feeding trial with 6 replicates/treatment. At the end of the feeding trial, six birds (one bird from each replicate cage) were randomly selected from each treatment and slaughtered for carcass traits analysis. The results showed that the dietary supplementation of EP_7000 improved the breast muscle yield (p < 0.05). Subsequently, six breast muscle samples from CON and EP_7000 groups (three samples from each group) were randomly selected for RNA-Seq analysis. Based on the RNA-Seq results, a total of 154 differentially expressed genes (DEGs) were identified (p < 0.05). Among the DEGs, 112 genes were significantly upregulated, whereas 42 genes were significantly down-regulated by EP_7000 supplementation. Gene Ontology enrichment analysis showed that the DEGs were mainly enriched in immune-related signaling pathways, macromolecule biosynthetic, DNA-templated, RNA biosynthetic, and metabolic process (p < 0.05). Kyoto Encyclopedia of Genes and Genomes pathway analysis showed that the DEGs were enriched in signaling pathways related to viral infectious diseases and cell adhesion molecules (p < 0.05). In conclusion, dietary inclusion of EP_7000 improves the breast muscle yield, which may be involved in improving the immunity and the cell differentiation of broilers, thus promoting the muscle growth of broilers. These findings could help understand the molecular mechanisms that enhance breast muscle yield by dietary supplementation of EP in broilers.

scholarly journals Analysis of Transcriptome and miRNAome in the Muscle of Bamei Pigs at Different Developmental Stages

Animals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1198 ◽  
Author(s):  
Guofang Wu ◽  
Lin Ma ◽  
Lei Wang ◽  
Jiping Zhou ◽  
Yuhong Ma ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Meat Quality ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Developmental Stages ◽  
Enrichment Analysis ◽  
Rna Seq ◽  
Developmental Processes ◽  
Citrate Cycle ◽  
Molecular Approaches

The growth of skeletal muscle involves complex developmental processes that play an important part in the determinization of pork quality. The investigation of skeletal muscle mRNA or miRNA profiles is especially important for finding molecular approaches to improve meat quality in pig breeding. Therefore, we studied the transcriptome (mRNA and miRNA) profiles of skeletal muscle with RNA-Seq in three developmental stages of pigs: 65-day embryonic (E65), postnatal 0 days (natal) and 10 months (adult). We found 10,035, 9050 and 4841 differentially expressed (DE) genes for natal vs. E65, adult vs. E65 and adult vs. natal, 55, 101 and 85 DE miRNA for natal vs. E65, adult vs. E65 and adult vs. natal, respectively. In addition, the target genes of DE miRNA that was in a negative correlation with the corresponding miRNA in the same comparison group were selected for enrichment analysis. Gene Ontology terms were mainly classified into developmental processes. Pathway analysis revealed enrichment in the Rap1 signaling pathway, citrate cycle and oxidative phosphorylation and carbon. Finally, RT-PCR was employed for validating the level of expression of 11 DE miRNA and 14 DEGs. The transcriptome profiles of skeletal muscle from the different developmental stages of the Bamei pigs were obtained. From these data, hundreds of DE miRNA and mRNA, and the miRNA–mRNA regulatory network can provide valuable insights into further understanding of key molecular mechanisms and improving the meat quality in pig breeding.

scholarly journals Insights into the Synthesis, Secretion and Curing of Barnacle Cyprid Adhesive via Transcriptomic and Proteomic Analyses of the Cement Gland

Marine Drugs ◽  
2020 ◽  
Vol 18 (4) ◽  
pp. 186
Author(s):  
Guoyong Yan ◽  
Jin Sun ◽  
Zishuai Wang ◽  
Pei-Yuan Qian ◽  
Lisheng He
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Lysyl Oxidase ◽  
Enrichment Analysis ◽  
Salivary Secretion ◽  
Cement Gland ◽  
Differentially Expressed ◽  
Model Organisms ◽  
Rna Seq ◽  
Secretion Pathway

Barnacles represent one of the model organisms used for antifouling research, however, knowledge regarding the molecular mechanisms underlying barnacle cyprid cementation is relatively scarce. Here, RNA-seq was used to obtain the transcriptomes of the cement glands where adhesive is generated and the remaining carcasses of Megabalanus volcano cyprids. Comparative transcriptomic analysis identified 9060 differentially expressed genes, with 4383 upregulated in the cement glands. Four cement proteins, named Mvcp113k, Mvcp130k, Mvcp52k and Mvlcp1-122k, were detected in the cement glands. The salivary secretion pathway was significantly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the differentially expressed genes, implying that the secretion of cyprid adhesive might be analogous to that of saliva. Lysyl oxidase had a higher expression level in the cement glands and was speculated to function in the curing of cyprid adhesive. Furthermore, the KEGG enrichment analysis of the 352 proteins identified in the cement gland proteome partially confirmed the comparative transcriptomic results. These results present insights into the molecular mechanisms underlying the synthesis, secretion and curing of barnacle cyprid adhesive and provide potential molecular targets for the development of environmentally friendly antifouling compounds.

scholarly journals OsMGT1 Confers Resistance to Magnesium Deficiency By Enhancing the Import of Mg in Rice

2019 ◽  
Vol 20 (1) ◽  
pp. 207 ◽  
Author(s):  
Ludan Zhang ◽  
Yuyang Peng ◽  
Jian Li ◽  
Xinyue Tian ◽  
Zhichang Chen
Keyword(s):  
Plant Growth ◽  
Molecular Mechanisms ◽  
Magnesium Deficiency ◽  
Expression Patterns ◽  
Tissue Expression ◽  
Mesophyll Cells ◽  
Mg Deficiency ◽  
Biochemical Processes ◽  
Essential Nutrient ◽  
Mg Content

Magnesium (Mg) is an essential nutrient element for plant growth and plays an important role in numerous physiological and biochemical processes. Mg deficiency inhibits plant growth and has become a growing problem for crop productions in agriculture. However, the molecular mechanisms for the resistance to Mg deficiency in plants were not well understood. In this study, we identified a Mg transporter gene OsMGT1 that confers resistance to Mg deficiency in rice (Oryza sativa). The expression of OsMGT1 was highly induced by Mg deficiency in shoots. Investigation of tissue expression patterns revealed that OsMGT1 was mainly expressed in the phloem region; however, Mg deficiency remarkably enhanced its expression in xylem parenchyma and mesophyll cells in shoots. Knockout of OsMGT1 resulted in a significant reduction in Mg content and biomass when grown at Mg-limited conditions. Furthermore, the sensitivity to low-Mg in mutants was intensified by excessive calcium supply. In addition, overexpression of OsMGT1 increased Mg content and biomass under low-Mg supply. In conclusion, our results indicate that OsMGT1 plays an important role in rice Mg import and is required for the resistance to Mg deficiency, which can be utilized for molecular breeding of low-Mg tolerant plants.

scholarly journals Integrated Full-Length Transcriptome and RNA-Seq to Identify Immune System Genes from the Skin of Sperm Whale (Physeter macrocephalus)

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 233
Author(s):  
Daling Wang ◽  
Ying Li ◽  
Reyilamu Aierken ◽  
Qi Kang ◽  
Xianyan Wang ◽  
...  
Keyword(s):  
Immune System ◽  
Molecular Mechanisms ◽  
Gene Annotation ◽  
Average Length ◽  
Enrichment Analysis ◽  
Sperm Whale ◽  
Living Environment ◽  
Full Length ◽  
Physeter Macrocephalus ◽  
Rna Seq

Cetaceans are a group of secondary aquatic mammals whose ancestors returned to the ocean from land, and during evolution, their immune systems adapted to the aquatic environment. Their skin, as the primary barrier to environmental pathogens, supposedly evolved to adapt to a new living environment. However, the immune system in the skin of cetaceans and the associated molecular mechanisms are still largely unknown. To better understand the immune system, we extracted RNA from the sperm whale’s (Physeter macrocephalus) skin and performed PacBio full-length sequencing and RNA-seq sequencing. We obtained a total of 96,350 full-length transcripts with an average length of 1705 bp and detected 5150 genes that were associated with 21 immune-related pathways by gene annotation enrichment analysis. Moreover, we found 89 encoding genes corresponding to 33 proteins were annotated in the NOD-like receptor (NLR)-signaling pathway, including NOD1, NOD2, RIP2, and NF-κB genes, which were discussed in detail and predicted to play essential roles in the immune system of the sperm whale. Furthermore, NOD1 was highly conservative during evolution by the sequence comparison and phylogenetic tree. These results provide new information about the immune system in the skin of cetaceans, as well as the evolution of immune-related genes.

RNA-seq Analysis Reveals Mitochondrial and Cuticular Protein Genes Are Associated with Phosphine Resistance in the Rusty Grain Beetle (Coleoptera:Laemophloeidae)

2020 ◽  
Author(s):  
Er-Hu Chen ◽  
Jin-Yan Duan ◽  
Wei Song ◽  
Dian-Xuan Wang ◽  
Pei-An Tang
Keyword(s):  
Molecular Mechanisms ◽  
Function Analysis ◽  
Resistance Management ◽  
Enrichment Analysis ◽  
Cuticular Protein ◽  
Rna Seq ◽  
Stored Grain ◽  
Phosphine Resistance ◽  
Go Enrichment ◽  
Susceptible Populations

Abstract The rusty grain beetle, Cryptolestes ferrugineus (Stephens), is a serious pest of stored grain, which has developed high levels of resistance to phosphine. In this study, five geographically distant populations of C. ferrugineus had been collected in China, specifically in granaries where phosphine fumigant is used for pest control, and they showed a high resistance ratio up to 1,907 (LC50 = 21.0 mg/liter). Then, a reference transcriptome was constructed to use as a basis for investigating the molecular mechanisms of phosphine resistance in this species, which consisted of 47,006 unigenes with a mean length of 1,090. Subsequently, the RNA-Seq analysis of individuals from the most susceptible and resistant populations led to the identification of 54 genes that are differentially expressed. GO and KEGG analysis demonstrated that genes associated with mitochondrial and respiration functions were significantly enriched. Also, the ‘structural constituent of cuticle’ term was annotated in the GO enrichment analysis and further qRT-PCR confirmed that the expression levels of nine cuticular protein genes were significantly increased in the resistant population. In conclusion, we present here a transcriptome-wide overview of gene expression changes between resistant and susceptible populations of C. ferrugineus, and this in turn documents that mitochondria and cuticular protein genes may play together a crucial role in phosphine resistance. Further gene function analysis should enable the provision of advice to expedite resistance management decisions.

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