scholarly journals Molecular Cloning and Characterization of Genes Expressed during Early Tomato (Lycopersicon esculentum Mill.) Fruit Development by mRNA Differential Display

1996 ◽  
Vol 121 (1) ◽  
pp. 52-56 ◽  
Author(s):  
Denise M. Tieman ◽  
Avtar K. Handa
Keyword(s):  
Differential Display ◽  
Fruit Development ◽  
Cell Expansion ◽  
Tomato Fruit ◽  
Expression Patterns ◽  
Mrna Differential Display ◽  
Differentially Expressed ◽  
Threonine Deaminase ◽  
Primer Sets ◽  
Root Tissues

The growth of tomato fruit is the result of cell division early in development followed by cell expansion until the onset of ripening. We have utilized the mRNA differential display technique to clone genes differentially expressed in 10- and 20-day-old tomato fruit, when most fruit cells are undergoing a transition to growth by cell expansion. Of 1753 total bands observed using 30 independent primer sets, 31 differential display bands were obtained only in either 10-or 20-day - old fruit RNAs. Seven differentially expressed bands from 10-day-old fruit RNAs and six from 20-day-old fruit RNAs were cloned and characterized by sequence analysis and mRNA expression patterns in developing fruit, leaf and root tissues. Two clones had sequence similarities to 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) synthase or threonine deaminase genes, while the remaining clones did not correspond to previously characterized genes. Steady state levels of mRNAs corresponding to seven clones were upregulated between 10 and 20 days of fruit development, while two clones were downregulated during growth and ripening. Most clones also hybridize to mRNA species present in leaf and root tissues. Collectively, these results suggest a transition in gene expression between 10- and 20-day-old fruit development.

Identification of Genes (SPON2 and C20orf2) Differentially Expressed between Cancerous and Noncancerous Lung Cells by mRNA Differential Display

Genomics ◽  
1999 ◽  
Vol 61 (1) ◽  
pp. 5-14 ◽  
Author(s):  
Ryokuhei Manda ◽  
Takashi Kohno ◽  
Yoshihiro Matsuno ◽  
Seiichi Takenoshita ◽  
Hiroyuki Kuwano ◽  
...  
Keyword(s):  
Differential Display ◽  
Mrna Differential Display ◽  
Differentially Expressed ◽  
Lung Cells

scholarly journals Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0256319
Author(s):  
Fernando G. Razo-Mendivil ◽  
Fernando Hernandez-Godínez ◽  
Corina Hayano-Kanashiro ◽  
Octavio Martínez
Keyword(s):  
Secondary Metabolites ◽  
Capsicum Annuum ◽  
Stress Responses ◽  
Tomato Fruit ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
Mature Stage ◽  
Tomato Fruit Ripening

Chili pepper (Capsicum annuum) is one of the most important crops worldwide. Its fruits contain metabolites produced over the maturation process like capsaicinoids and carotenoids. This metabolic process produces internal changes in flavor, color, texture, and aroma in fruits to make them more attractive for seed dispersal organisms. The chiltepin (C. annuum L. var. glabriusculum) is a wild variety of the C. annuum L. species that is considered a source of genetic resources that could be used to improve the current chili crops. In this study, we performed a transcriptomic analysis on two fruit maturation stages: immature stage (green fruit) and mature stage (red fruit) of a wild and a cultivated pepper variety. We found 19,811 genes expressed, and 1,008 genes differentially expressed (DEGs) in at least one of the five contrast used; 730 DEGs were found only in one contrast, and most DEGs in all contrasts were downregulated. GO enrichment analysis showed that the majority of DEGs are related to stress responses. KEGG enrichment analysis detected differences in expression patterns in metabolic pathways related to phenylpropanoid biosynthesis, secondary metabolites, plant hormone signal transduction, carotenoid biosynthesis and sesquiterpenoid and triterpenoid biosynthesis. We selected 105 tomato fruit ripening-related genes, and found 53 pepper homologs differentially expressed related to shape, size, and secondary metabolite biosynthesis. According to the transcriptome analysis, the two peppers showed very similar gene expression patterns; differences in expression patterns of genes related to shape, size, ethylene and secondary metabolites biosynthesis suggest that changes produced by domestication of chilli pepper could be very specific to the expression of genes related to traits desired in commercial fruits.

scholarly journals Identification of Thymus Specific and Developmentally Regulated Genes by an Improved Version of the mRNA Differential Display Technique

1999 ◽  
Vol 7 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Steve Pascolo ◽  
Debbie Tsoukatou ◽  
Clio Mamalaki
Keyword(s):  
Gene Expression ◽  
Differential Display ◽  
Mrna Differential Display ◽  
Differentially Expressed ◽  
Major Drawback ◽  
Hematopoietic Stem ◽  
Adult Mice ◽  
Functional Features ◽  
Display Technique ◽  
Differential Display Technique

During embryogenesis in mouse, the thymus is seeded by waves of hematopoietic stem cells that provide the first peripheral T lymphocytes after birth. It is known that embryo thymocytes and adult thymocytes have different phenotypic and functional features. The identification of genes expressed in the thymus only during embryogenesis would help to understand the molecular basis underlying these characteristics. We used the mRNA differential display technique to compare gene expression between thymus and kidney from embryo (171/2 days) and adult mice. This technique is the method of choice for comparing gene expression because it is able to display rapidly and simultaneously the mRNA complement from several different types of cells. The major drawback of the method is that it leads to the cloning of many false positives and therefore needs a high throughput method to screen for the truly differentially expressed cDNAs. We combined advantages from previously described methods in order to develop a new version of the mRNA differential display technique that is fast, cheap, and reliable. Instead of oligo dT priming, we used random hexameres for the reverse transcription of total RNA and 10-mer primers for the amplification of internal parts of the cDNAs. We obtained reproducible and clean patterns of discrete bands. We were able to easily identify DNAs differentially amplified between embryo and adult tissues (embryo specific; E 58.73), between thymus and kidney (thymus specific; Thy 52.54), or between embryo and adult thymus (embryo thymus specific; E Thy 58.73) cDNA fragments. After reamplification, cloning, and sequencing of these DNA fragments, it appeared that in most cases, one band corresponded to a single DNA sequence. On a northern blot, each of these candidate genes recognized a transcript that is differentially expressed as expected. Thus, we report an optimized, reproducible, and fast mRNA differential display method that overcomes the usual problems met with the originally described technique or its reported modifications.

scholarly journals Screening of Genes Involved in Isooctane Tolerance in Saccharomyces cerevisiae by Using mRNA Differential Display

2000 ◽  
Vol 66 (11) ◽  
pp. 4883-4889 ◽  
Author(s):  
Shigenori Miura ◽  
Wen Zou ◽  
Mitsuyoshi Ueda ◽  
Atsuo Tanaka
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Differential Display ◽  
Northern Blot Analysis ◽  
Single Gene ◽  
Expression Patterns ◽  
Mrna Differential Display ◽  
Yeast Cells ◽  
Critical Determinant ◽  
Wild Type Parent

ABSTRACT A Saccharomyces cerevisiae strain, KK-211, isolated by the long-term bioprocess of stereoselective reduction in isooctane, showed extremely high tolerance to the solvent, which is toxic to yeast cells, but, in comparison with its wild-type parent, DY-1, showed low tolerance to hydrophilic organic solvents, such as dimethyl sulfoxide and ethanol. In order to detect the isooctane tolerance-associated genes, mRNA differential display (DD) was employed using mRNAs isolated from strains DY-1 and KK-211 cultivated without isooctane, and from strain KK-211 cultivated with isooctane. Thirty genes were identified as being differentially expressed in these three types of cells and were classified into three groups according to their expression patterns. These patterns were further confirmed and quantified by Northern blot analysis. On the DD fingerprints, the expression of 14 genes, including MUQ1, PRY2, HAC1,AGT1, GAC1, and ICT1(YLR099c) was induced, while the expression of the remaining 16 genes, including JEN1, PRY1,PRY3, and KRE1, was decreased, in strain KK-211 cultivated with isooctane. The genes represented by HAC1,PRY1, and ICT1 have been reported to be associated with cell stress, and AGT1 and GAC1have been reported to be involved in the uptake of trehalose and the production of glycogen, respectively. MUQ1 andKRE1, encoding proteins associated with cell surface maintenance, were also detected. Based on these results, we concluded that alteration of expression levels of multiple genes, not of a single gene, might be the critical determinant for isooctane tolerance in strain KK-211.

Development of a method for mRNA differential display in filamentous fungi: comparison of mRNA differential display reverse transcription polymerase chain reaction and cDNA amplified fragment length polymorphism in Leptosphaeria maculans

2001 ◽  
Vol 47 (10) ◽  
pp. 955-960 ◽  
Author(s):  
Kevin S Gellatly ◽  
Gavin J Ash ◽  
Janet L Taylor
Keyword(s):  
Gene Expression ◽  
Differential Display ◽  
Fragment Length Polymorphism ◽  
Leptosphaeria Maculans ◽  
Mrna Differential Display ◽  
Differentially Expressed ◽  
Chain Reaction ◽  
Differential Display Reverse Transcription ◽  
Polymerase Chain ◽  
Cdna Fragments

We modified a technique, cDNA-AFLP, for identifying differentially expressed genes in plants to work in the filamentous fungus Leptosphaeria maculans (Desmaz.) Ces. & De Not. The cDNA fragments generated by our method ranged in size from approximately 100 to 400 bps. On average, twice as many cDNA fragments were amplified per primer set with cDNA amplified fragment length polymorphism in comparison with mRNA differential display reverse transcription polymerase chain reaction. The DNA fragments of interest were excised from gels and analyzed by single-stranded conformation polymorphism to eliminate nondifferentially expressed cDNA contamination. The method was used to examine gene expression differences between cultures grown in the presence or absence of an analog of the Brassica phytoalexin brassinin. Eleven of the fourteen fragments examined were determined by reverse Northern blot to be differentially expressed. In examining gene expression differences between young cultures not producing sirodesmins and older cultures that were producing these phytotoxins, we found 17 of 25 fragments were differentially expressed. Northern blots with these fragments confirmed the results.Key words: Phoma lingam, ascomycete, blackleg, Brassica.

scholarly journals Transcriptome analysis of the oriental melon (Cucumis meloL. var.makuwa) during fruit development

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2834 ◽  
Author(s):  
Ah-Young Shin ◽  
Yong-Min Kim ◽  
Namjin Koo ◽  
Su Min Lee ◽  
Seokhyeon Nahm ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Fruit Development ◽  
De Novo ◽  
Expression Patterns ◽  
Soluble Sugars ◽  
Carotenoid Biosynthesis ◽  
Northern China ◽  
Differentially Expressed ◽  
Oriental Melon ◽  
Expression Of Genes

BackgroundThe oriental melon (Cucumis meloL. var.makuwa) is one of the most important cultivated cucurbits grown widely in Korea, Japan, and northern China. It is cultivated because its fruit has a sweet aromatic flavor and is rich in soluble sugars, organic acids, minerals, and vitamins. In order to elucidate the genetic and molecular basis of the developmental changes that determine size, color, and sugar contents of the fruit, we performedde novotranscriptome sequencing to analyze the genes expressed during fruit development.ResultsWe identified a total of 47,666 of representative loci from 100,875 transcripts and functionally annotated 33,963 of the loci based on orthologs inArabidopsis thaliana. Among those loci, we identified 5,173 differentially expressed genes, which were classified into 14 clusters base on the modulation of their expression patterns. The expression patterns suggested that the differentially expressed genes were related to fruit development and maturation through diverse metabolic pathways. Analyses based on gene set enrichment and the pathways described in the Kyoto Encyclopedia of Genes and Genomes suggested that the expression of genes involved in starch and sucrose metabolism and carotenoid biosynthesis were regulated dynamically during fruit development and subsequent maturation.ConclusionOur results provide the gene expression patterns related to different stages of fruit development and maturation in the oriental melon. The expression patterns give clues about important regulatory mechanisms, especially those involving starch, sugar, and carotenoid biosynthesis, in the development of the oriental melon fruit.

Analysis of Differentially Expressed Genes in Prunus persica for the Treatment of Hypoxia Using Generalized Linear Models

2020 ◽  
Vol 17 (9) ◽  
pp. 4183-4189
Author(s):  
Nisha Baid ◽  
Preethi Meghadri ◽  
Vinai G. Biju ◽  
Blessy B. Mathew ◽  
C. M. Prashanth
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Generalized Linear Models ◽  
Prunus Persica ◽  
Linear Models ◽  
Expression Patterns ◽  
High Capacity ◽  
Differentially Expressed ◽  
Root Tissues

The gene structure of organisms gets altered when exposed to an abnormal condition which could adversely affect the growth of the target. RNA sequencing can be deployed to identify diseasecausing mutations in the genes of patients for whom genetic analysis failed to return a diagnosis. One such disease is Hypoxia, a condition in which there is a deficiency in the availability of oxygen in the tissues. RNA sequencing helps in analyzing the global expression patterns of hypoxia and in understanding the cellular alterations of those suffering from it. It gives an understanding of the comprehensive regulation of the gene expression by environmental spur or specific factors which can be used to diagnose and treat hypoxia before it gets fatal. Prunus persica is a plant which has a high capacity for anoxic tolerance, and analyzing the gene expression changes which are associated to hypoxia treatments in the root tissues of two genotypes of the peach plant (Flooding tolerant and Flooding sensitive) can prevent physiological disorders. Further, gene ontology is used to cover three domains-cellular component, molecular function and biological processes related to the differentially expressed genes. We use Generalized Linear Models here, to find the differentially expressed genes in Prunus persica when exposed to the conditions of Hypoxia (Absence of Oxygen) and Normoxia (Excess of Oxygen) and find their Ontologies and genomic pathways to understand and diagnose the Processes that are most affected.

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