scholarly journals Identification, Classification, and Functional Analysis of AP2/ERF Family Genes in the Desert Moss Bryum argenteum

2018 ◽  
Vol 19 (11) ◽  
pp. 3637 ◽  
Author(s):  
Xiaoshuang Li ◽  
Bei Gao ◽  
Daoyuan Zhang ◽  
Yuqing Liang ◽  
Xiaojie Liu ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Abiotic Stress Tolerance ◽  
Plant Responses ◽  
Rna Seq ◽  
Bryum Argenteum ◽  
Erf Family ◽  
Stress Related Genes ◽  
Rehydration Process

Bryum argenteum is a desert moss which shows tolerance to the desert environment and is emerging as a good plant material for identification of stress-related genes. AP2/ERF transcription factor family plays important roles in plant responses to biotic and abiotic stresses. AP2/ERF genes have been identified and extensively studied in many plants, while they are rarely studied in moss. In the present study, we identified 83 AP2/ERF genes based on the comprehensive dehydrationrehydration transcriptomic atlas of B. argenteum. BaAP2/ERF genes can be classified into five families, including 11 AP2s, 43 DREBs, 26 ERFs, 1 RAV, and 2 Soloists. RNA-seq data showed that 83 BaAP2/ERFs exhibited elevated transcript abundances during dehydration–rehydration process. We used RT-qPCR to validate the expression profiles of 12 representative BaAP2/ERFs and confirmed the expression trends using RNA-seq data. Eight out of 12 BaAP2/ERFs demonstrated transactivation activities. Seven BaAP2/ERFs enhanced salt and osmotic stress tolerances of yeast. This is the first study to provide detailed information on the identification, classification, and functional analysis of the AP2/ERFs in B. argenteum. This study will lay the foundation for the further functional analysis of these genes in plants, as well as provide greater insights into the molecular mechanisms of abiotic stress tolerance of B. argenteum.

scholarly journals Potassium: A Vital Regulator of Plant Responses and Tolerance to Abiotic Stresses

Agronomy ◽  
2018 ◽  
Vol 8 (3) ◽  
pp. 31 ◽  
Author(s):  
Mirza Hasanuzzaman ◽  
M. Bhuyan ◽  
Kamrun Nahar ◽  
Md. Hossain ◽  
Jubayer Mahmud ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Stress Tolerance ◽  
Molecular Mechanisms ◽  
Abiotic Stress Tolerance ◽  
Ion Homeostasis ◽  
Enzyme Activation ◽  
Regulatory Function ◽  
Plant Responses ◽  
Plant Structure ◽  
Physiological Processes

Among the plant nutrients, potassium (K) is one of the vital elements required for plant growth and physiology. Potassium is not only a constituent of the plant structure but it also has a regulatory function in several biochemical processes related to protein synthesis, carbohydrate metabolism, and enzyme activation. Several physiological processes depend on K, such as stomatal regulation and photosynthesis. In recent decades, K was found to provide abiotic stress tolerance. Under salt stress, K helps to maintain ion homeostasis and to regulate the osmotic balance. Under drought stress conditions, K regulates stomatal opening and helps plants adapt to water deficits. Many reports support the notion that K enhances antioxidant defense in plants and therefore protects them from oxidative stress under various environmental adversities. In addition, this element provides some cellular signaling alone or in association with other signaling molecules and phytohormones. Although considerable progress has been made in understanding K-induced abiotic stress tolerance in plants, the exact molecular mechanisms of these protections are still under investigation. In this review, we summarized the recent literature on the biological functions of K, its uptake, its translocation, and its role in plant abiotic stress tolerance.

scholarly journals Comparative RNA-Seq Analyses of Solenopsis japonica (Hymenoptera: Formicidae) Reveal Gene in Response to Cold Stress

Genes ◽  
2021 ◽  
Vol 12 (10) ◽  
pp. 1610
Author(s):  
Mohammad Vatanparast ◽  
Youngjin Park
Keyword(s):  
Gene Expression ◽  
Cold Stress ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Predatory Behavior ◽  
P Value ◽  
Molecular Response ◽  
Rna Seq ◽  
Protein Database ◽  
Brood Chamber

Solenopsis japonica, as a fire ant species, shows some predatory behavior towards earthworms and woodlice, and preys on the larvae of other ant species by tunneling into a neighboring colony’s brood chamber. This study focused on the molecular response process and gene expression profiles of S. japonica to low (9 °C)-temperature stress in comparison with normal temperature (25 °C) conditions. A total of 89,657 unigenes (the clustered non-redundant transcripts that are filtered from the longest assembled contigs) were obtained, of which 32,782 were annotated in the NR (nonredundant protein) database with gene ontology (GO) terms, gene descriptions, and metabolic pathways. The results were 81 GO subgroups and 18 EggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) keywords. Differentially expressed genes (DEGs) with log2fold change (FC) > 1 and log2FC < −1 with p-value ≤ 0.05 were screened for cold stress temperature. We found 215 unigenes up-regulated and 115 unigenes down-regulated. Comparing transcriptome profiles for differential gene expression resulted in various DE proteins and genes, including fatty acid synthases and lipid metabolism, which have previously been reported to be involved in cold resistance. We verified the RNA-seq data by qPCR on 20 up- and down-regulated DEGs. These findings facilitate the basis for the future understanding of the adaptation mechanisms of S. japonica and the molecular mechanisms underlying the response to low temperatures.

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.

scholarly journals Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Xia Tang ◽  
Delong Feng ◽  
Min Li ◽  
Jinxue Zhou ◽  
Xiaoyuan Li ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Rna Seq ◽  
Pairwise Interactions ◽  
Micro Rnas ◽  
Non Coding Rnas ◽  
First Time

Abstract Fully elucidating the molecular mechanisms of non-coding RNAs (ncRNAs), including micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), underlying hepatocarcinogenesis is challenging. We characterized the expression profiles of ncRNAs and constructed a regulatory mRNA-lncRNA-miRNA (MLMI) network based on transcriptome sequencing (RNA-seq) of hepatocellular carcinoma (HCC, n = 9) patients. Of the identified miRNAs (n = 203) and lncRNAs (n = 1,090), we found 16 significantly differentially expressed (DE) miRNAs and three DE lncRNAs. The DE RNAs were highly enriched in 21 functional pathways implicated in HCC (p < 0.05), including p53, MAPK, and NAFLD signaling. Potential pairwise interactions between DE ncRNAs and mRNAs were fully characterized using in silico prediction and experimentally-validated evidence. We for the first time constructed a MLMI network of reciprocal interactions for 16 miRNAs, three lncRNAs, and 253 mRNAs in HCC. The predominant role of MEG3 in the MLMI network was validated by its overexpression in vitro that the expression levels of a proportion of MEG3-targeted miRNAs and mRNAs was changed significantly. Our results suggested that the comprehensive MLMI network synergistically modulated carcinogenesis, and the crosstalk of the network provides a new avenue to accurately describe the molecular mechanisms of hepatocarcinogenesis.

Transcriptome Analysis of Pyrethroid-Resistant Chrysodeixis includens (Lepidoptera: Noctuidae) Reveals Overexpression of Metabolic Detoxification Genes

2020 ◽  
Author(s):  
Clerison R Perini ◽  
Christine A Tabuloc ◽  
Joanna C Chiu ◽  
Frank G Zalom ◽  
Regis F Stacke ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Pyrethroid Resistance ◽  
Expression Profiles ◽  
Laboratory Strain ◽  
Rna Seq ◽  
Glutathione S Transferase ◽  
Metabolic Resistance ◽  
Body Tissues ◽  
Metabolic Detoxification ◽  
Chrysodeixis Includens

Abstract Chrysodeixis includens (Walker, [1858]) is one of the most important defoliator of soybean in Brazil because of its extensive geographical distribution and high tolerance to insecticides compared with other species of caterpillars. Because of this, we conducted bioassays to evaluate the efficacy of pyrethroid λ-cyhalothrin on a C. includens resistant strain (MS) and a susceptible (LAB) laboratory strain. High throughput RNA sequencing (RNA-seq) of larval head and body tissues were performed to identify potential molecular mechanisms underlying pyrethroid resistance. Insecticide bioassays showed that MS larvae exhibit 28.9-fold resistance to pyrethroid λ-cyhalothrin relative to LAB larvae. RNA-seq identified evidence of metabolic resistance in the head and body tissues: 15 cytochrome P450 transcripts of Cyp6, Cyp9, Cyp4, Cyp304, Cyp307, Cyp337, Cyp321 families, 7 glutathione-S-transferase (Gst) genes, 7 α-esterase genes from intracellular and secreted catalytic classes, and 8 UDP-glucuronosyltransferase (Ugt) were overexpressed in MS as compared with LAB larvae. We also identified overexpression of GPCR genes (CiGPCR64-like and CiGPCRMth2) in the head tissue. To validate RNA-seq results, we performed RT-qPCR to assay selected metabolic genes and confirmed their expression profiles. Specifically, CiCYP9a101v1, CiCYP6ae149, CiCYP6ae106v2, CiGSTe13, CiCOE47, and CiUGT33F21 exhibited significant overexpression in resistant MS larvae. In summary, our findings detailed potential mechanisms of metabolic detoxification underlying pyrethroid resistance in C. includens.

scholarly journals Unique transcriptome features of pea (Pisum sativum L.) lines with differing responses to beneficial soil microorganisms

2021 ◽  
Vol 19 (2) ◽  
pp. 131-141
Author(s):  
Alexey M. Afonin ◽  
Emma S. Gribchenko ◽  
Evgeny A. Zorin ◽  
Anton S. Sulima ◽  
Daria A. Romanyuk ◽  
...  
Keyword(s):  
Pisum Sativum ◽  
Mycorrhizal Fungi ◽  
Soil Microorganisms ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Arbuscular Mycorrhizal ◽  
Plant Responses ◽  
Single Nucleotide Variants ◽  
Interaction Efficiency

BACKGROUND: Garden pea (Pisum sativum L.) possesses the ability to form beneficial symbioses with various soil microorganisms. However, different pea cultivars, genotypes, and lines gain more or less benefit from these interactions, so the trait named efficiency of interaction with soil microorganisms (EIBSM) was suggested to describe this phenomenon. The molecular mechanisms underlying the manifestation of the EIBSM trait are not properly studied, and only few works focusing on plant responses to combined microbial preparations have been published to date. METHODS: Eight pea lines previously described as contrasting in manifestation of the EIBSM trait were grown in pots with soil under combined inoculation with nodule bacteria and arbuscular mycorrhizal fungi, and the transcriptome profiles of the whole root systems of the plants were investigated using 3'MACE RNA sequencing. RESULTS: The relatedness of the lines inferred from the analysis of transcripts SNVs (Single Nucleotide Variants) corresponded to the manifestation of the EIBSM trait: three high-EIBSM lines and three low-EIBSM lines formed two distinct clusters. Thus, the gene expression profiles were compared between these two clusters, which enabled identification of transcriptome signatures characteristic for each group. The lines previously described as high-EIBSM have lower symbiotic activity, and the expression levels of pathogen response genes were elevated compared to the lines with low EIBSM. CONCLUSION: This result suggests that the mechanism of high interaction efficiency may be connected to stricter host control of symbionts, allowing such plants to expend less on the symbioses.

scholarly journals Genome-wide investigation of the AP2/ERF gene family in ginger: evolution and expression profiling during development and abiotic stresses

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Haitao Xing ◽  
Yusong Jiang ◽  
Yong Zou ◽  
Xiaoling Long ◽  
Xiaoli Wu ◽  
...  
Keyword(s):  
Gene Structure ◽  
Abiotic Stresses ◽  
Growth And Development ◽  
Expression Profiles ◽  
Rna Seq ◽  
Qrt Pcr ◽  
Genome Wide ◽  
Evolutionary Features ◽  
Erf Family

Abstract Background AP2/ERF transcription factors (TFs) constitute one of the largest TF families in plants, which play crucial roles in plant metabolism, growth, and development as well as biotic and abiotic stresses responses. Although the AP2/ERF family has been thoroughly identified in many plant species and several AP2/ERF TFs have been functionally characterized, little is known about this family in ginger (Zingiber officinale Roscoe), an important affinal drug and diet vegetable. Recent completion of the ginger genome sequencing provides an opportunity to investigate the expression profiles of AP2/ERF genes in ginger on a genome-wide basis. Results A total of 163 AP2/ERF genes were obtained in the Z.officinale genome and renamed according to the chromosomal distribution of the ZoAP2/ERF genes. Phylogenetic analysis divided them into three subfamilies, of which 35 belonged to the AP2 subfamily, 120 to ERF, three to RAV, and five to Sololist, respectively, which is in accordance with the number of conserved domains and gene structure analysis. A total of 10 motifs were detected in ZoAP2/ERF genes, and some of the unique motifs were found to be important for the function of ZoAP2/ERF genes. The chromosomal localization, gene structure, and conserved protein motif analyses, as well as the characterization of gene duplication events provided deep insight into the evolutionary features of these ZoAP2/ERF genes. The expression profiles derived from the RNA-seq data and quantitative reserve transcription (qRT-PCR) analysis of ZoAP2/ERFs during development and responses to abiotic stresses were investigated in ginger. Conclusion A comprehensive analysis of the AP2/ERF gene expression patterns in various tissues by RNA-seq and qRT-PCR showed that they played an important role in the growth and development of ginger, and genes that might regulate rhizome and flower development were preliminary identified. In additionally, the ZoAP2/ERF family genes that responded to abiotic stresses were also identified. This study is the first time to identify the ZoAP2/ERF family, which contributes to research on evolutionary characteristics and better understanding the molecular basis for development and abiotic stress response, as well as further functional characterization of ZoAP2/ERF genes with an aim of ginger crop improvement.

scholarly journals Brain and Pituitary Transcriptome Analyses Reveal the Differential Regulation of Reproduction-Related LncRNAs and mRNAs in Cynoglossus semilaevis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yani Dong ◽  
Likang Lyu ◽  
Haishen Wen ◽  
Bao Shi
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Gene Interaction ◽  
Cynoglossus Semilaevis ◽  
Rna Seq ◽  
Tongue Sole ◽  
Gene Interaction Networks ◽  
Half Smooth Tongue Sole ◽  
The Brain

Long noncoding RNAs (lncRNAs) have been identified to be involved in half-smooth tongue sole (Cynoglossus semilaevis) reproduction. However, studies of their roles in reproduction have focused mainly on the ovary, and their expression patterns and potential roles in the brain and pituitary are unclear. Thus, to explore the mRNAs and lncRNAs that are closely associated with reproduction in the brain and pituitary, we collected tongue sole brain and pituitary tissues at three stages for RNA sequencing (RNA-seq), the 5,135 and 5,630 differentially expressed (DE) mRNAs and 378 and 532 DE lncRNAs were identified in the brain and pituitary, respectively. The RNA-seq results were verified by RT-qPCR. Moreover, enrichment analyses were performed to analyze the functions of DE mRNAs and lncRNAs. Interestingly, their involvement in pathways related to metabolism, signal transduction and endocrine signaling was revealed. LncRNA-target gene interaction networks were constructed based on antisense, cis and trans regulatory mechanisms. Moreover, we constructed competing endogenous RNA (ceRNA) networks. In summary, this study provides mRNA and lncRNA expression profiles in the brain and pituitary to understand the molecular mechanisms regulating tongue sole reproduction.

scholarly journals Comprehensive analysis based on DNA methylation and RNA-seq reveals hypermethylation of the up-regulated WT1 gene with potential mechanisms in PAM50 subtypes of breast cancer

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11377
Author(s):  
Chongyang Ren ◽  
Xiaojiang Tang ◽  
Haitao Lan
Keyword(s):  
Breast Cancer ◽  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Molecular Subtypes ◽  
Wilms Tumor ◽  
Expression Profiles ◽  
Gene Signature ◽  
The Cancer Genome Atlas ◽  
Body Region ◽  
Rna Seq

Background Breast cancer (BC), one of the most widespread cancers worldwide, caused the deaths of more than 600,000 women in 2018, accounting for about 15% of all cancer-associated deaths in women that year. In this study, we aimed to discover potential prognostic biomarkers and explore their molecular mechanisms in different BC subtypes using DNA methylation and RNA-seq. Methods We downloaded the DNA methylation datasets and the RNA expression profiles of primary tissues of the four BC molecular subtypes (luminal A, luminal B, basal-like, and HER2-enriched), as well as the survival information from The Cancer Genome Atlas (TCGA). The highly expressed and hypermethylated genes across all the four subtypes were screened. We examined the methylation sites and the downstream co-expressed genes of the selected genes and validated their prognostic value using a different dataset (GSE20685). For selected transcription factors, the downstream genes were predicted based on the Gene Transcription Regulation Database (GTRD). The tumor microenvironment was also evaluated based on the TCGA dataset. Results We found that Wilms tumor gene 1 (WT1), a transcription factor, was highly expressed and hypermethylated in all the four BC subtypes. All the WT1 methylation sites exhibited hypermethylation. The methylation levels of the TSS200 and 1stExon regions were negatively correlated with WT1 expression in two BC subtypes, while that of the gene body region was positively associated with WT1 expression in three BC subtypes. Patients with low WT1 expression had better overall survival (OS). Five genes including COL11A1, GFAP, FGF5, CD300LG, and IGFL2 were predicted as the downstream genes of WT1. Those five genes were dysregulated in the four BC subtypes. Patients with a favorable 6-gene signature (low expression of WT1 and its five predicted downstream genes) exhibited better OS than that with an unfavorable 6-gene signature. We also found a correlation between WT1 and tamoxifen using STITCH. Higher infiltration rates of CD8 T cells, plasma cells, and monocytes were found in the lower quartile WT1 group and the favorable 6-gene signature group. In conclusion, we demonstrated that WT1 is hypermethylated and up-regulated in the four BC molecular subtypes and a 6-gene signature may predict BC prognosis.

scholarly journals Microstructural Observation and Transcriptome Analysis of Pistil Abortion in ‘Li Guang’ Apricot

2020 ◽  
Author(s):  
Tong Zhao ◽  
Li Cheng ◽  
Cuilian Chen ◽  
De Zhang ◽  
Zhongxing Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Paraffin Section ◽  
Pollen Grains ◽  
Gansu Province ◽  
Signal Molecules ◽  
Rna Seq ◽  
Factors Affecting ◽  
Expression Levels ◽  
Pistil Abortion

Abstract Background: ‘Li Guang’ apricot, a famous local variety, originated in Dunhuang city, Gansu Province,China. It has a long flowering period and a large amount of flowers, but serious pistil abortion has become one of the key factors affecting the fruit set, yield and quality. The distribution and regulation of hormones play an important role in signal molecules of flower abortion. The critical mechanisms of hormone metabolism and the expression levels of genes involved in these processes are, however, poorly understood. Results: To clarify the critical molecular mechanisms of hormone-induced abortion in apricot, normal and abortive flower buds were taken as materials, the pistil abortion of apricot flower was studied by paraffin section, and the RNA seq was used to identify the genes related to flowering regulation. The pistil style was lower than filament. Microstructure showed that the pollen grains of abortive flowers were decreased sharply, the ovaries shrunk and the ovule primordia developed stagnately. Through RNA-Seq, 6647 differentially expressed genes, including 2543 up-regulated and 4104 down-regulated genes, were identified. According to the KEGG Pathway, the pyruvate metabolism, plant hormone signal transduction, spliceosome, RNA transport, protein processing in endoplasmic reticulum and other metabolic pathways were significantly enriched. It revealed that AUX1, AUX / IAA, TIR1, ARF, GH3 and SAUR , vital genes displayed identical differential expression profiles to auxin transduction pathway, and ABF , SnRK2 , PP2C to abscisic acid, JAZ, MYC2 to jasmonic acid. The qRT-PCR assay with independent samples showed that the expression levels of these selected genes were basically consistent with RNA-Seq results. Conclusions : In the whole differentiate stage of flower, pistil abortion represent versatile style . In this process, the changes of hormones play an important role in pistil abortion, especially IAA,GA,and CTK. Related genes involved in hormones synthesis expression regulate the content of hormones and to adapt to the occurrence of pistil abortion under adversity. At the same time, the ethylene response signal factor ERF1/2 (DN70415) was up-regulated in normal flowers, which further indicated that ethylene might be the key regulatory factor affecting the abortion of ‘Liguang’ apricot flowers.

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