Transcriptome profiling of differentially expressed genes of male and female inflorescences in spinach (Spinacia oleracea L.)

Genome ◽  
2021 ◽  
Author(s):  
Zhiyuan Liu ◽  
Haoying Wang ◽  
Zhaosheng Xu ◽  
Helong Zhang ◽  
Guoliang Li ◽  
...  
Keyword(s):  
Sex Determination ◽  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Spinacia Oleracea ◽  
Transcriptome Profiling ◽  
Vital Role ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Male And Female ◽  
Spinacia Oleracea L

Spinach (Spinacia oleracea L.) is commonly considered a dioecious plant with heterogametic (XY) and homogametic (XX) sex chromosomes. The characteristic is also utilized for the production of spinach hybrid seeds. However, the molecular mechanisms of sex determination in spinach are still unclear because of a lack of genomic and transcriptomic information. In this study, RNA-sequencing (RNA-seq) was performed in male and female inflorescences to provide insight into the molecular basis of sex determination in spinach. Comparative transcriptome analyses showed that 2,278 differentially expressed genes (DEGs) were identified between male and female inflorescences. A high correlation between the RNA-Seq and qRT-PCR validation for DEGs was observed. Among these, 182 DEGs were annotated to transcription factors including the MYB family protein, bHLH family, and MADS family, suggesting these factors might play a vital role in sex determination. Moreover, 26 DEGs related to flower development, including nine ABCE class genes, were detected. Expression analyses of hormone pathways showed that brassinosteroids may be key hormones related to sex determination in spinach. Overall, this study provides a large amount of DEGs related to sexual expression and lays a foundation for unraveling the regulatory mechanism of sex determination in spinach.

scholarly journals The identification of differentially expressed genes in male and female gametophytes of simple thalloid liverwort Pellia endiviifolia sp. B using an RNA-seq approach

Planta ◽  
2020 ◽  
Vol 252 (2) ◽  
Author(s):  
Izabela Sierocka ◽  
Sylwia Alaba ◽  
Artur Jarmolowski ◽  
Wojciech M. Karlowski ◽  
Zofia Szweykowska-Kulinska
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Male And Female ◽  
Pellia Endiviifolia

scholarly journals Transcriptome profiling provides new insights into florets number difference of inflorescence in lavandula angustifolia

2020 ◽  
Author(s):  
haiping hao ◽  
xiao pei zhu ◽  
Hui Li ◽  
Jian Gong ◽  
Amjad Farooq ◽  
...  
Keyword(s):  
Essential Oil ◽  
Differentially Expressed Genes ◽  
Transcriptome Profiling ◽  
Extraction Methods ◽  
Essential Oil Composition ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Oil Composition ◽  
Aba Metabolism ◽  
Aba Content

Abstract Background Lavender flowers essential oil had been for a variety of therapeutic and cosmetic purposes, and had been popular for centuries. The previous studies of lavender mainly focused on essential oil composition and extraction methods, ignoring the factors which affected the production of essential oils, such as the floret number. This study aims to get a deeper insight into florets number difference mechanism. Results Hormone profile showed positive correlation between ABA content and the number of florets while IAA was negatively correlated. RNA-Seq results showed that 2848 differentially expressed genes screened by comparing different florets samples in one plant. By analyzing dynamic changes of differentially expressed genes, many potentially interesting genes were identified that encoded putative regulators or key components of ABA metabolism and signaling transduction, such as NCED, PYL, PP2C, SnRK2. These genes were highlighted to reveal their importance in regulation of florets numbers. Conclusions 1. The different ABA concentrations lead to florets difference in the Lavandula angustifolia “JX-2” clusters; 2. ABA may affect the florets number by regulating IAA transport and accumulation. The results will be useful for a better understanding of the molecular mechanism on florets number difference that could be laid the foundation for molecular breeding of muti-flortes varieties.

scholarly journals Molecular Mechanisms Underlying Sugarcane Response to Aluminum Stress by RNA-Seq

2020 ◽  
Author(s):  
Thiago Mateus Rosa-Santos ◽  
Renan Gonçalves da Silva ◽  
Poornasree Kumar ◽  
Pratibha Kottapalli ◽  
Chiquito Crasto ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Aluminum Tolerance ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Aluminum Stress ◽  
Physiological Processes ◽  
Aluminum Ions ◽  
Detoxification Mechanism ◽  
Genomic Studies

Sugarcane is an important sugar-source crop. As any other plant, it can be exposed to several abiotic stress conditions. Though some metals contribute to critical physiological processes in plants, the presence of aluminum ions (Al3+) can be very toxic. In order to develop plants that flourish in acidic soils, it is critical to gain insights into the molecular mechanisms of sugarcane response to aluminum stress. To determine the genes involved in sugarcane response to aluminum stress we generated 372 million paired-end RNA sequencing reads, from roots of CTC-2 and RB855453 two contrasting cultivars. Data normalization resulted in 162,161 contigs and 97,335 trinity genes. After the read cutoff, the differentially expressed genes were 4,858 in CTC-2 and 1,307 in the RB855453, Treatment Vs Control, respectively. The differentially expressed genes were annotated into 34 functional categories. The majority of the genes were upregulated in the CTC-2 (tolerant cultivar) and down regulated in RB855453 (sensitive cultivar). Here, we present the first root-transcriptome of sugarcane under aluminum stress. The results and conclusions of this study provide a valuable resource for future genetic and genomic studies in sugarcane. This transcriptome analysis points out that sugarcane tolerance to aluminum may be explained by an efficient detoxification mechanism combined with the lateral root formation and activation of redox enzymes. Following our results, we present here, a hypothetical model for the aluminum tolerance in CTC-2 cultivar.

scholarly journals BIOM-33. LOW EXPRESSION OF DYNLT3 PREDICTS BETTER PROGNOSIS FOR FEMALE GLIOBLASTOMA PATIENTS

2020 ◽  
Vol 22 (Supplement_2) ◽  
pp. ii8-ii8
Author(s):  
Yuanjun Hu ◽  
Jing Wang ◽  
Zhong-ping Chen
Keyword(s):  
Median Survival ◽  
Molecular Mechanisms ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Rank Test ◽  
Female Group ◽  
Male And Female ◽  
The Central Nervous System ◽  
Lower Expression ◽  
Low Expression

Abstract BACKGROUND Glioblastoma (GBM) is the most malignant tumor in the central nervous system. It has been confirmed that the prognosis of GBM has obvious gender predilection. As female patients have an advantage than males, it is increasingly accepted to take gender into account while treating GBM. Therefore, it is important to figure out molecular mechanisms related to gender predilection. METHODS We first analyzed the protein expression of GBM (Male=24, Female=16) based on the dataset from Clinical Proteomic Tumor Analysis Consortium (CPTAC) of the National Cancer Institute’s（NCI）and mainly focused on those differential expression proteins between males and females on X chromosome. Then the differentially expressed genes from CPTAC was further confirmed in TCGA data and their role in the overall survival of GBM patients were analyzed. RESULTS 18 proteins, differentially expressed between male and female were selected. 12 out of them expressed higher in female while the other 6 were higher in male (P< 0.05). We found one protein, DYNLT3 might be a predictor for GBM patients’ survival through analyzing the transcriptome profiling database of TCGA. The low expression of DYNLT3 was related to a longer survival of female group. The median survival was 556 days (95% CI, 446 to 665) with lower expression level of DYNLT3, compared with 375 days (95% CI, 291 to 459) in higher expression group (P=0.011 by log-rank test) in all cases including both male and female. For female group, the median survival was 653 days (95% CI, 464 to 842) with lower expression of DYNLT3, which was much better than 305 days (95% CI, 379 to 642) (P=0.008) with higher expression of DYNLT3. No significant predicting value of DYNLT3 expression was found in male group. CONCLUSIONS The expression of DYNLT3 might be a positive predictor for survival of GBM patients, especially for female cases.

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.

Geno-transcriptomic dissection of proteinuria in the uninephrectomized rat uncovers a molecular complexity with sexual dimorphism

2010 ◽  
Vol 42A (4) ◽  
pp. 301-316 ◽  
Author(s):  
Yoram Yagil ◽  
Martin Hessner ◽  
Herbert Schulz ◽  
Claudia Gosele ◽  
Larissa Lebedev ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Focal And Segmental Glomerulosclerosis ◽  
Male And Female ◽  
Matrix Deposition ◽  
Males And Females ◽  
Molecular Complexity ◽  
The Difference ◽  
Underlying Mechanisms

Investigation of proteinuria, whose pathophysiology remains incompletely understood, is confounded by differences in the phenotype between males and females. We initiated a sex-specific geno-transcriptomic dissection of proteinuria in uninephrectomized male and female Sabra rats that spontaneously develop focal and segmental glomerulosclerosis, testing the hypothesis that different mechanisms might underlie the pathophysiology of proteinuria between the sexes. In the genomic arm, we scanned the genome of 136 male and 111 female uninephrectomized F2 populations derived from crosses between SBH/y and SBN/y. In males, we identified proteinuria-related quantitative trait loci (QTLs) on RNO2 and 20 and protective QTLs on RNO6 and 9. In females, we detected proteinuria-related QTLs on RNO11, 13, and 20. The only QTL overlap between the sexes was on RNO20. Using consomic strains, we confirmed the functional significance of this QTL in both sexes. In the transcriptomic arm, we searched on a genomewide scale for genes that were differentially expressed in kidneys of SBH/y and SBN/y with and without uninephrectomy. These studies identified within each sex differentially expressed genes of relevance to proteinuria. Integrating genomics with transcriptomics, we identified differentially expressed genes that mapped within the boundaries of the proteinuria-related QTLs, singling out 24 transcripts in males and 30 in females, only 4 of which ( Tubb5, Ubd, Psmb8, and C2) were common to both sexes. Data mining revealed that these transcripts are involved in multiple molecular mechanisms, including immunity, inflammation, apoptosis, matrix deposition, and protease activity, with no single molecular pathway predominating in either sex. These results suggest that the pathophysiology of proteinuria is highly complex and that some of the underlying mechanisms are shared between the sexes, while others are sex specific and may account for the difference in the proteinuric phenotype between males and females.

scholarly journals Comprehensive analysis of differential expression profiles via transcriptome sequencing in SH-SY5Y cells infected with CV-A16

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241174
Author(s):  
Yajie Hu ◽  
Zhen Yang ◽  
Shenglan Wang ◽  
Danxiong Sun ◽  
Mingmei Zhong ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Transcriptome Sequencing ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Transcriptome Profiling ◽  
Differentially Expressed ◽  
Control Group ◽  
Protein Coding ◽  
Qrt Pcr ◽  
Protein Coding Genes

Coxsackievirus A16 (CV-A16) is one of the viruses that is most frequently associated with hand-foot-and-mouth disease (HFMD). Previous studies have shown that CV-A16 infections are mostly self-limiting, but in recent years, it has been gradually found that CV-A16 infections can also induce neurological complications and eventually cause death in children with HFMD. Moreover, no curative drugs or preventative vaccines have been developed for CV-A16 infection. Therefore, it is particularly important to investigate the mechanism of CV-A16 infection-induced neuropathy. In the current study, transcriptome sequencing technology was used to identify changes in the transcriptome of SH-SY5Y cells infected with CV-A16, which might hide the mechanism of CV-A16-induced neuropathology. The transcriptome profiling showed that 82,406,974, 108,652,260 and 97,753,565 clean reads were obtained in the Control, CV-A16-12 h and CV-A16-24 h groups, respectively. And it was further detected that a total of 136 and 161 differentially expressed genes in CV-A16-12 h and CV-A16-24 h groups, respectively, when compared with Control group. Then, to explore the mechanism of CV-A16 infection, we focused on the common differentially expressed genes at different time points of CV-A16 infection and found that there were 34 differentially expressed genes based on which clustering analysis and functional category enrichment analysis were performed. The results indicated that changes in oxidation levels were particularly evident in the GO term analysis, while only the “Gonadotropin-releasing hormone receptor pathway” was enriched in the KEGG pathway analysis, which might be closely related to the neurotoxicity caused by CV-A16 infection. Meanwhile, the ID2 closely related to nervous system has been demonstrated to be increased during CV-A16 infection. Additionally, the data on differentially expressed non-protein-coding genes of different types within the transcriptome sequencing results were analyzed, and it was speculated that these dysregulated non-protein-coding genes played a pivotal role in CV-A16 infection. Ultimately, qRT-PCR was utilized to validate the transcriptome sequencing findings, and the results of qRT-PCR were in agreement with the transcriptome sequencing data. In conclusion, transcriptome profiling was carried out to analyze response of SH-SY5Y cells to CV-A16 infection. And our findings provide important information to elucidate the possible molecular mechanisms which were linked to the neuropathogenesis of CV-A16 infection.

scholarly journals Dysregulated BMP2 in the Placenta May Contribute to Early-Onset Preeclampsia by Regulating Human Trophoblast Expression of Extracellular Matrix and Adhesion Molecules

2021 ◽  
Vol 9 ◽  
Author(s):  
Yuyin Yi ◽  
Hua Zhu ◽  
Christian Klausen ◽  
Hsun-Ming Chang ◽  
Amy M. Inkster ◽  
...  
Keyword(s):  
Extracellular Matrix ◽  
Differentially Expressed Genes ◽  
Early Onset ◽  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Bone Morphogenetic Protein 2 ◽  
Rna Seq ◽  
Placental Development ◽  
Human Trophoblast ◽  
Early Onset Preeclampsia

Many pregnancy disorders, including early-onset preeclampsia (EOPE), are associated with defects in placental trophoblast cell invasion and differentiation during early placental development. Bone morphogenetic protein 2 (BMP2) belongs to the TGF-β superfamily and controls various physiological and developmental processes. However, the expression of BMP2 in the placenta and underlying molecular mechanisms of how BMP2 regulates trophoblast function remain unclear. In this study, we analyzed several publicly available microarray and RNA-seq datasets and revealed differences in expression of TGF-β superfamily members between gestational age-matched non-preeclamptic control and EOPE placentas. Importantly, BMP2 levels were significantly reduced in EOPE placentas compared with controls, and RNAscope in situ hybridization further demonstrated BMP2 expression was disrupted in EOPE placental villi. To explore the molecular mechanisms of BMP2-regulated early trophoblast differentiation, we examined BMP2 expression in first-trimester human placenta and found it to be localized to all subtypes of trophoblasts and the decidua. RNA-seq analysis on control and BMP2-treated primary human trophoblast cells identified 431 differentially expressed genes, including several canonical TGF-β/BMP signaling targets (BAMBI, ID1, INHBA, IGFBP3). Gene ontology annotations revealed that differentially expressed genes were involved in cell adhesion and extracellular matrix organization. Furthermore, we identified adhesion molecule with IgG-like domain 2 (AMIGO2) as a novel target for BMP2 that contributed to BMP2-induced trophoblast invasion and endothelial-like tube formation. Overall, our findings provide insight into the molecular processes controlled by BMP2 during early placental development that may contribute to the pathogenesis of EOPE.

scholarly journals Changes in Ovary Transcriptome and Alternative splicing at estrus from Xiang pigs with Large and Small Litter Size

2019 ◽  
Author(s):  
Fuping Zhang ◽  
Liangting Tang ◽  
Xueqin Ran ◽  
Ning Mao ◽  
Yiqi Ruan ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Candidate Genes ◽  
Differentially Expressed Genes ◽  
Litter Size ◽  
Molecular Mechanisms ◽  
Reproductive Traits ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Small Litter ◽  
Small Litter Size

AbstractBackground/AimsLitter size is one of the most important reproductive traits in pig breeding, which is affected by multiple genes and the environment. Ovaries are the most important reproductive organs and have a profound impact on the reproduction efficiency. Therefore, genetic differences in the ovaries may contribute to the observed differences in litter size. Although QTLs and candidate genes have been reported to affect the litter size in many pig breeds, however, the findings cannot elucidate the marked differences of the reproductive traits between breeds. The aim of present work is to elucidate the mechanisms of the differences for the reproductive traits and identify candidate genes associated with litter size in Xiang pig breed.MethodsThe changes in ovary transcriptome and alternative splicing were investigated at estrus between Xiang pigs with large and small litter size by RNA-seq technology. The RNA-seq results were confirmed by RT-qPCR method.ResultsWe detected 16,219 - 16,285 expressed genes and 12 types of alternative splicing (AS) events in Xiang pig samples. A total of 762 differentially expressed genes were identified by XL (Xiang pig group with larger litter size) vs XS (Xiang pig group with small litter size) sample comparisons. A total of 34 genes were upregulated and 728 genes were downregulated in XL ovary samples compared with the XS samples. Alternative splicing (AS) rates in XL samples were slightly lower than that observed in XS samples. Most of differentially expressed genes were differentially regulated on AS level. Eleven candidate genes were potentially identified to be related to Xiang pig fecundity and litter size, which may be closely related to the gonad development, oocyte maturation or embryo quality.ConclusionThe significant changes in the expression of the protein-coding genes and the level of alternative splicing in estrus ovarian transcriptome between XL and XS groups probably are the molecular mechanisms of phenotypic variation in litter size.

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