scholarly journals Integrated Physiological and Transcriptomic Analyses Responses to Altitude Stress in Oat (Avena sativa L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Yu Jinqiu ◽  
Li Bing ◽  
Song Tingting ◽  
He Jinglei ◽  
KongLing Zelai ◽  
...  
Keyword(s):  
High Altitude ◽  
Avena Sativa ◽  
Molecular Mechanisms ◽  
Rna Seq ◽  
High Altitudes ◽  
Genome Wide ◽  
New Findings ◽  
Polymerase Chain ◽  
Transcriptomic Changes ◽  
Stressful Environments

Oat is an annual gramineous forage grass with the remarkable ability to survive under various stressful environments. However, understanding the effects of high altitude stresses on oats is poor. Therefore, the physiological and the transcriptomic changes were analyzed at two sites with different altitudes, low (ca. 2,080 m) or high (ca. 2,918 m), respectively. Higher levels of antioxidant enzyme activity, reactive oxygen and major reductions in photosynthesis-related markers were suggested for oats at high altitudes. Furthermore, oat yields were severely suppressed at the high altitude. RNA-seq results showed that 11,639 differentially expressed genes were detected at both the low and the high altitudes in which 5,203 up-regulated and 6,436 down-regulated. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment tests were conducted and a group of major high altitude-responsive pigment metabolism genes, photosynthesis, hormone signaling, and cutin, suberine and wax biosynthesis were excavated. Using quantitative real-time polymerase chain response, we also confirmed expression levels of 20 DEGs (qRT-PCR). In summary, our study generated genome-wide transcript profile and may be useful for understanding the molecular mechanisms of Avena sativa L. in response to high altitude stress. These new findings contribute to our deeper relevant researches on high altitude stresses and further exploring new candidategenes for adapting plateau environment oat molecular breeding.

scholarly journals Integrated physiological and transcriptomic analyses responses to altitude stress in oat (Avena sativa L.)

2020 ◽  
Author(s):  
YU Jinqiu ◽  
Li Bing ◽  
Cui Guowen ◽  
Song Tingting ◽  
He Wenhua ◽  
...  
Keyword(s):  
High Altitude ◽  
Differentially Expressed Genes ◽  
Avena Sativa ◽  
Molecular Mechanisms ◽  
Stomatal Density ◽  
Differentially Expressed ◽  
Photochemical Quenching ◽  
Antioxidant Enzyme Activities ◽  
New Findings ◽  
Genes Encoding

Abstract Background The oat is an annual gramineous forage grass with the remarkable ability to survive under various stressful environments. However, understanding the effects of high altitude stresses on oats is poor. Therefore, the physiological and the transcriptomic changes were analyzed at two sites with different altitudes, low (ca. 2,080 m) or high (ca. 2,918 m) respectively.Results It was indicated that oats at high altitude showed higher levels of antioxidant enzyme activities and significant decreases in the non-photochemical quenching coefficient,chlorophyll content and stomatal density. Furthermore, oat yields were severely suppressed at the high altitude. RNA-seq results showed that 11,639 differentially expressed genes were detected at both the low and the high altitudesin which 5,203 up-regulated and 6,436 down-regulated. GO and KEGG annotations suggested that many differentially expressed genes be involved in pathways of cellular processes, metabolic processes and plant-pathogen interactions. Furthermore, 125 differentially expressed genes encoding TFs were involved in signal transductions by regulating the resistance genes in oats at high altitude. Some differentially expressed genes related to pigment metabolisms and photosyntheses were differentially expressed suggesting that these genes probably play responsive and regulatory roles in oats under the high altitude stress. Meanwhile, 273 differentially expressed genes related to hormone signaling pathways were significantly enriched in gibberellin, auxin, jasmonic acid and abscisic acid pathways indicating that these genes participated in the processes of oats responding to high altitude stresses.Conclusion In summary, our study generated genome-wide transcript profile and may be useful for understanding the molecular mechanisms of Avena sativa L. in response to high altitude stresses.These new findings contribute to our deeper relevant researches on altitude stresses and further exploring new candidategenes for adapting plateau environment oat molecular breeding.

scholarly journals Transcriptome analysis of two Pogostemon cablin chemotypes reveals genes related to patchouli alcohol biosynthesis

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12025
Author(s):  
Wuping Yan ◽  
Zhouchen Ye ◽  
Shijia Cao ◽  
Guanglong Yao ◽  
Jing Yu ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Perennial Herb ◽  
Pcr Analysis ◽  
Biosynthetic Pathways ◽  
Rna Seq ◽  
Patchouli Alcohol ◽  
Pogostemon Cablin ◽  
Polymerase Chain ◽  
Distribution Frequency

Pogostemon cablin, a medicinally and economically important perennial herb, is cultivated around the world due to its medicinal and aromatic properties. Different P. cablin cultivars exhibit different morphological traits and patchouli oil components and contents (especially patchouli alcohol (PA) and pogostone (PO)). According to the signature constituent of the leaf, P. cablin was classified into two different chemotypes, including PA-type and PO-type. To better understand the molecular mechanisms of PA biosynthesis, the transcriptomes of Chinese-cultivated P. cablin cv. PA-type “Nanxiang” (NX) and PO-type “Paixiang” (PX) were analyzed and compared with ribonucleic acid sequencing (RNA-Seq) technology. We obtained a total of 36.83 G clean bases from the two chemotypes, compared them with seven databases and revealed 45,394 annotated unigenes. Thirty-six candidate unigenes participating in the biosynthesis of PA were found in the P. cablin transcriptomes. Overall, 8,390 differentially expressed unigenes were identified between the chemotypes, including 2,467 upregulated and 5,923 downregulated unigenes. Furthermore, six and nine differentially expressed genes (DEGs) were mapped to the terpenoid backbone biosynthetic and sesquiterpenoid and triterpenoid biosynthetic pathways, respectively. One key sesquiterpene synthase gene involved in the sesquiterpenoid and triterpenoid biosynthetic pathways, encoding patchoulol synthase variant 1, was significantly upregulated in NX. Additionally, GC-MS analysis of the two chemotypes in this study showed that the content of PA in NX was significantly higher than that of PX, while the content of PO showed the opposite phenotype. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis showed that the DEG expression tendency was consistent with the transcriptome sequencing results. Overall, 23 AP2/ERF, 13 bHLH, 11 MYB, 11 NAC, three Trihelix, 10 WRKY and three bZIP genes that were differentially expressed may act as regulators of terpenoid biosynthesis. Altogether, 8,314 SSRs were recognized within 6,825 unigenes, with a distribution frequency of 18.32%, among which 1,202 unigenes contained more than one SSR. The transcriptomic characteristics of the two P. cablin chemotypes are comprehensively reported in this study, and these results will contribute to a better understanding of the molecular mechanism of PA biosynthesis. Our transcriptome data also provide a valuable genetic resource for further studies on P. cablin.

scholarly journals Genome-wide transcriptome analysis between Small-tail Han sheep and the Surabaya fur sheep using high-throughput RNA sequencing

Reproduction ◽  
2013 ◽  
Vol 145 (6) ◽  
pp. 587-596 ◽  
Author(s):  
Xiangyang Miao ◽  
Qingmiao Luo
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Complex Trait ◽  
Future Research ◽  
Rna Seq ◽  
Molecular Biology Technique ◽  
High Fecundity ◽  
Next Generation Sequencing Technology ◽  
Genome Wide ◽  
Generation Sequencing

The Small-tail Han sheep and the Surabaya fur sheep are two local breeds in North China, which are characterized by high-fecundity and low-prolificacy breed respectively. Significant genetic differences between these two breeds have provided increasing interests in the identification and utilization of major prolificacy genes in these sheep. High prolificacy is a complex trait, and it is difficult to comprehensively identify the candidate genes related to this trait using the single molecular biology technique. To understand the molecular mechanisms of fecundity and provide more information about high prolificacy candidate genes in high- and low-fecundity sheep, we explored the utility of next-generation sequencing technology in this work. A total of 1.8 Gb sequencing reads were obtained and resulted in more than 20 000 contigs that averaged ∼300 bp in length. Ten differentially expressed genes were further verified by quantitative real-time RT-PCR to confirm the reliability of RNA-seq results. Our work will provide a basis for the future research of the sheep reproduction.

scholarly journals Genome-Wide Identification of the LAC Gene Family and Its Expression Analysis Under Stress in Brassica napus

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1985 ◽  
Author(s):  
Xiaoke Ping ◽  
Tengyue Wang ◽  
Na Lin ◽  
Feifei Di ◽  
Yangyang Li ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Vital Role ◽  
Gene Family Evolution ◽  
Rna Seq ◽  
Chain Reaction ◽  
Element Analysis ◽  
Cis Element ◽  
Genome Wide ◽  
Polymerase Chain

Lignin is an important biological polymer in plants that is necessary for plant secondary cell wall ontogenesis. The laccase (LAC) gene family catalyzes lignification and has been suggested to play a vital role in the plant kingdom. In this study, we identified 45 LAC genes from the Brassica napus genome (BnLACs), 25 LAC genes from the Brassica rapa genome (BrLACs) and 8 LAC genes from the Brassica oleracea genome (BoLACs). These LAC genes could be divided into five groups in a cladogram and members in same group had similar structures and conserved motifs. All BnLACs contained hormone- and stress- related elements determined by cis-element analysis. The expression of BnLACs was relatively higher in the root, seed coat and stem than in other tissues. Furthermore, BnLAC4 and its predicted downstream genes showed earlier expression in the silique pericarps of short silique lines than long silique lines. Three miRNAs (miR397a, miR397b and miR6034) target 11 BnLACs were also predicted. The expression changes of BnLACs under series of stresses were further investigated by RNA sequencing (RNA-seq) and quantitative real-time polymerase chain reaction (qRT-PCR). The study will give a deeper understanding of the LAC gene family evolution and functions in B. napus.

scholarly journals Genome-wide methylation and expression analyses reveal the epigenetic landscape of immune-related diseases for tobacco smoking

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Ying Mao ◽  
Peng Huang ◽  
Yan Wang ◽  
Maiqiu Wang ◽  
Ming D. Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cigarette Smoke ◽  
Tobacco Smoking ◽  
Molecular Mechanisms ◽  
Functional Enrichment ◽  
Chronic Obstructive ◽  
Rna Seq ◽  
Immune System Diseases ◽  
Genome Wide ◽  
A Genome

Abstract Background Smoking is a major causal risk factor for lung cancer, chronic obstructive pulmonary disease (COPD), cardiovascular disease (CVD), and is the main preventable cause of deaths in the world. The components of cigarette smoke are involved in immune and inflammatory processes, which may increase the prevalence of cigarette smoke-related diseases. However, the underlying molecular mechanisms linking smoking and diseases have not been well explored. This study was aimed to depict a global map of DNA methylation and gene expression changes induced by tobacco smoking and to explore the molecular mechanisms between smoking and human diseases through whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq). Results We performed WGBS on 72 samples (36 smokers and 36 nonsmokers) and RNA-seq on 75 samples (38 smokers and 37 nonsmokers), and cytokine immunoassay on plasma from 22 males (9 smokers and 13 nonsmokers) who were recruited from the city of Jincheng in China. By comparing the data of the two groups, we discovered a genome-wide methylation landscape of differentially methylated regions (DMRs) associated with smoking. Functional enrichment analyses revealed that both smoking-related hyper-DMR genes (DMGs) and hypo-DMGs were related to synapse-related pathways, whereas the hypo-DMGs were specifically related to cancer and addiction. The differentially expressed genes (DEGs) revealed by RNA-seq analysis were significantly enriched in the “immunosuppression” pathway. Correlation analysis of DMRs with their corresponding gene expression showed that genes affected by tobacco smoking were mostly related to immune system diseases. Finally, by comparing cytokine concentrations between smokers and nonsmokers, we found that vascular endothelial growth factor (VEGF) was significantly upregulated in smokers. Conclusions In sum, we found that smoking-induced DMRs have different distribution patterns in hypermethylated and hypomethylated areas between smokers and nonsmokers. We further identified and verified smoking-related DMGs and DEGs through multi-omics integration analysis of DNA methylome and transcriptome data. These findings provide us a comprehensive genomic map of the molecular changes induced by smoking which would enhance our understanding of the harms of smoking and its relationship with diseases.

scholarly journals Genome-wide RNA sequencing as a method for assessing the effects of synthetic derivatives of melanocortin under normal conditions and under acute stress

2020 ◽  
pp. 101-102
Author(s):  
И.Б. Филиппенков ◽  
В.В. Ставчанский ◽  
Н.Ю. Глазова ◽  
Е.А. Себенцова ◽  
Н.Г. Левицкая ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Acute Stress ◽  
Regulation Of Gene Expression ◽  
Rna Seq ◽  
Structural Analogue ◽  
Specific Effects ◽  
Genome Wide ◽  
Transcriptome Response ◽  
Synthetic Derivatives ◽  
Derivatives Of

В целях исследования молекулярных механизмов действия пептидов меланокортинового ряда был проведен сравнительный анализ действия семакса и его структурного аналога АКТГ(6-9)PGP на транскриптом гиппокампа крыс в норме и условиях острого стресса с помощью метода RNA-Seq. Полученные результаты выявили общие и специфические эффекты пептидов меланокортинового ряда в регулировании экспрессии генов в условиях острого стресса и нормы. Предложена модель формирования ответа транскриптома на введение пептидов, основанная на аллостерическом взаимодействии пептидов с рецепторами. In order to study the molecular mechanisms of action of the peptides of the melanocortin series, a comparative analysis of the effect of Semax and its structural analogue of ACTH(6-9)PGP on transcripts of rat hippocampus under normal and acute stress conditions was performed using the RNA-Seq method. The results revealed common and specific effects of peptides in the regulation of gene expression under acute stress and normal conditions. We proposed a model for the formation of transcriptome response to peptide administration based on allosteric interaction of peptides with receptors.

scholarly journals Comparative Transcriptomics and RNA-Seq-Based Bulked Segregant Analysis Reveals Genomic Basis Underlying Cronartium ribicola vcr2 Virulence

2021 ◽  
Vol 12 ◽  
Author(s):  
Jun-Jun Liu ◽  
Richard A. Sniezko ◽  
Arezoo Zamany ◽  
Holly Williams ◽  
Kangakola Omendja ◽  
...  
Keyword(s):  
Allele Frequency ◽  
Molecular Mechanisms ◽  
Bulked Segregant Analysis ◽  
Diagnostic Tools ◽  
Cronartium Ribicola ◽  
Pinus Monticola ◽  
Rna Seq ◽  
White Pine ◽  
Fungal Virulence ◽  
Genome Wide

Breeding programs of five-needle pines have documented both major gene resistance (MGR) and quantitative disease resistance (QDR) to Cronartium ribicola (Cri), a non-native, invasive fungal pathogen causing white pine blister rust (WPBR). WPBR is one of the most deadly forest diseases in North America. However, Cri virulent pathotypes have evolved and can successfully infect and kill trees carrying resistance (R) genes, including vcr2 that overcomes MGR conferred by the western white pine (WWP, Pinus monticola) R gene (Cr2). In the absence of a reference genome, the present study generated a vcr2 reference transcriptome, consisting of about 20,000 transcripts with 1,014 being predicted to encode secreted proteins (SPs). Comparative profiling of transcriptomes and secretomes revealed vcr2 was significantly enriched for several gene ontology (GO) terms relating to oxidation-reduction processes and detoxification, suggesting that multiple molecular mechanisms contribute to pathogenicity of the vcr2 pathotype for its overcoming Cr2. RNA-seq-based bulked segregant analysis (BSR-Seq) revealed genome-wide DNA variations, including about 65,617 single nucleotide polymorphism (SNP) loci in 7,749 polymorphic genes shared by vcr2 and avirulent (Avcr2) pathotypes. An examination of the distribution of minor allele frequency (MAF) uncovered a high level of genomic divergence between vcr2 and Avcr2 pathotypes. By integration of extreme-phenotypic genome-wide association (XP-GWAS) analysis and allele frequency directional difference (AFDD) mapping, we identified a set of vcr2-associated SNPs within functional genes, involved in fungal virulence and other molecular functions. These included six SPs that were top candidate effectors with putative activities of reticuline oxidase, proteins with common in several fungal extracellular membrane (CFEM) domain or ferritin-like domain, polysaccharide lyase, rds1p-like stress responsive protein, and two Cri-specific proteins without annotation. Candidate effectors and vcr2-associated genes provide valuable resources for further deciphering molecular mechanisms of virulence and pathogenicity by functional analysis and the subsequent development of diagnostic tools for monitoring the virulence landscape in the WPBR pathosystems.

scholarly journals Genome-Wide Transcriptome Analysis Reveals Intermittent Fasting-Induced Metabolic Rewiring in the Liver

Dose-Response ◽  
2019 ◽  
Vol 17 (3) ◽  
pp. 155932581987678 ◽  
Author(s):  
Gavin Yong-Quan Ng ◽  
Sung-Wook Kang ◽  
Joonki Kim ◽  
Asfa Alli-Shaik ◽  
Sang-Ha Baik ◽  
...  
Keyword(s):  
Transcriptome Analysis ◽  
Energy Homeostasis ◽  
Molecular Mechanisms ◽  
Energy Restriction ◽  
Metabolic Changes ◽  
Intermittent Fasting ◽  
Energy Status ◽  
Metabolic Switching ◽  
Genome Wide ◽  
Transcriptomic Changes

Scope: Intermittent fasting (IF) has been extensively reported to promote improved energy homeostasis and metabolic switching. While IF may be a plausible strategy to ameliorate the epidemiological burden of disease in many societies, our understanding of the underlying molecular mechanisms behind such effects is still lacking. The present study has sought to investigate the relationship between IF and changes in gene expression. We focused on the liver, which is highly sensitive to metabolic changes due to energy status. Mice were randomly assigned to ad libitum feeding or IF for 16 hours per day or for 24 hours on alternate days for 3 months, after which genome-wide transcriptome analysis of the liver was performed using RNA sequencing. Our findings revealed that IF caused robust transcriptomic changes in the liver that led to a complex array of metabolic changes. We also observed that the IF regimen produced distinct profiles of transcriptomic changes, highlighting the significance of temporally different periods of energy restriction. Our results suggest that IF can regulate metabolism via transcriptomic mechanisms and provide insight into how genetic interactions within the liver might lead to the numerous metabolic benefits of IF.

scholarly journals Transcriptional profiling in the livers of rats after hypobaric hypoxia exposure

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6499 ◽  
Author(s):  
Zhenguo Xu ◽  
Zhilong Jia ◽  
Jinlong Shi ◽  
Zeyu Zhang ◽  
Xiaojian Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Altitude ◽  
Liver Tissue ◽  
Hypobaric Hypoxia ◽  
Cellular Response ◽  
Molecular Mechanisms ◽  
Receptor Interaction ◽  
Control Group ◽  
Acute Hypobaric Hypoxia ◽  
Genome Wide

Ascent to high altitude feels uncomfortable in part because of a decreased partial pressure of oxygen due to the decrease in barometric pressure. The molecular mechanisms causing injury in liver tissue after exposure to a hypoxic environment are widely unknown. The liver must physiologically and metabolically change to improve tolerance to altitude-induced hypoxia. Since the liver is the largest metabolic organ and regulates many physiological and metabolic processes, it plays an important part in high altitude adaptation. The cellular response to hypoxia results in changes in the gene expression profile. The present study explores these changes in a rat model. To comprehensively investigate the gene expression and physiological changes under hypobaric hypoxia, we used genome-wide transcription profiling. Little is known about the genome-wide transcriptional response to acute and chronic hypobaric hypoxia in the livers of rats. In this study, we carried out RNA-Sequencing (RNA-Seq) of liver tissue from rats in three groups, normal control rats (L), rats exposed to acute hypobaric hypoxia for 2 weeks (W2L) and rats chronically exposed to hypobaric hypoxia for 4 weeks (W4L), to explore the transcriptional profile of acute and chronic mountain sickness in a mammal under a controlled time-course. We identified 497 differentially expressed genes between the three groups. A principal component analysis revealed large differences between the acute and chronic hypobaric hypoxia groups compared with the control group. Several immune-related and metabolic pathways, such as cytokine-cytokine receptor interaction and galactose metabolism, were highly enriched in the KEGG pathway analysis. Similar results were found in the Gene Ontology analysis. Cogena analysis showed that the immune-related pathways were mainly upregulated and enriched in the acute hypobaric hypoxia group.

scholarly journals The Scleraxis Transcription Factor Directly Regulates Multiple Distinct Molecular and Cellular Processes During Early Tendon Cell Differentiation

2021 ◽  
Vol 9 ◽  
Author(s):  
Han Liu ◽  
Jingyue Xu ◽  
Yu Lan ◽  
Hee-Woong Lim ◽  
Rulang Jiang
Keyword(s):  
Transcription Factor ◽  
Cell Differentiation ◽  
Molecular Mechanisms ◽  
Target Genes ◽  
Rna Seq ◽  
Tendon Cell ◽  
Tendon Development ◽  
Genome Wide ◽  
Direct Target ◽  
Embryonic Tendon

Proper development of tendons is crucial for the integration and function of the musculoskeletal system. Currently little is known about the molecular mechanisms controlling tendon development and tendon cell differentiation. The transcription factor Scleraxis (Scx) is expressed throughout tendon development and plays essential roles in both embryonic tendon development and adult tendon healing, but few direct target genes of Scx in tendon development have been reported and genome-wide identification of Scx direct target genes in vivo has been lacking. In this study, we have generated a ScxFlag knockin mouse strain, which produces fully functional endogenous Scx proteins containing a 2xFLAG epitope tag at the carboxy terminus. We mapped the genome-wide Scx binding sites in the developing limb tendon tissues, identifying 12,097 high quality Scx regulatory cis-elements in-around 7,520 genes. Comparative analysis with previously reported embryonic tendon cell RNA-seq data identified 490 candidate Scx direct target genes in early tendon development. Furthermore, we characterized a new Scx gene-knockout mouse line and performed whole transcriptome RNA sequencing analysis of E15.5 forelimb tendon cells from Scx–/– embryos and control littermates, identifying 68 genes whose expression in the developing tendon tissues significantly depended on Scx function. Combined analysis of the ChIP-seq and RNA-seq data yielded 32 direct target genes that required Scx for activation and an additional 17 target genes whose expression was suppressed by Scx during early tendon development. We further analyzed and validated Scx-dependent tendon-specific expression patterns of a subset of the target genes, including Fmod, Kera, Htra3, Ssc5d, Tnmd, and Zfp185, by in situ hybridization and real-time quantitative polymerase chain reaction assays. These results provide novel insights into the molecular mechanisms mediating Scx function in tendon development and homeostasis. The ChIP-seq and RNA-seq data provide a rich resource for aiding design of further studies of the mechanisms regulating tendon cell differentiation and tendon tissue regeneration. The ScxFlag mice provide a valuable new tool for unraveling the molecular mechanisms involving Scx in the protein interaction and gene-regulatory networks underlying many developmental and disease processes.

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