Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of the transcriptome of the pulp of a spontaneous late-ripening sweet orange mutant and its wild type improves our understanding of fruit ripening in citrus

ABSTRACT: Fruit ripening is a complex, genetically programmed process that occurs in conjunction with the differentiation of chloroplasts into chromoplasts and involves changes to the organoleptic properties of the fruit. In this study, an integrative analysis of the transcriptome and proteome was performed to identify important regulators and pathways involved in fruit ripening in a spontaneous late-ripening mutant (‘Fengwan’ orange, Citrus sinensis L. Osbeck) and its wild type (‘Fengjie 72-1’). At the transcript level, 628 genes showed a 2-fold or more expression difference between the mutant and wild type as detected by an RNA sequencing approach. At the protein level, 130 proteins differed by 1.5-fold or more in their relative abundance, as indicated by iTRAQ (isobaric tags for relative and absolute quantitation) analysis. A comparison of the transcriptome and proteome data revealed some aspects of the regulation of metabolism during orange fruit ripening. First, a large number of differential genes were found to belong to the plant hormone pathways and cell-wall-related metabolism. Secondly, we noted a correlation between ripening-associated transcripts and sugar metabolites, which suggests the importance of these metabolic pathways during fruit ripening. Thirdly, a number of genes showed inconsistency between the transcript and protein level, which is indicative of posttranscriptional events. These results reveal multiple ripening-associated events during citrus ripening and provide new insights into the molecular mechanisms underlying citrus ripening regulatory networks

ORGANISM(S): Citrus sinensis

PROVIDER: GSE69432 | GEO | 2015/06/02

SECONDARY ACCESSION(S): PRJNA285488

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Uncover miRNAs in citrus fruit ripening

Project description:Fruit ripening in Citrus is not well understood at the molecular level. Knowledge of the regulatory mechanism of citrus fruit ripening at the post-transcriptional level in particular is lacking. Here, we comparatively analyzed the miRNAs and their targeted genes in a spontaneous late-ripening mutant, ?Fengwan? sweet orange (MT) (Citrus sinensis L. Osbeck), and its wild-type counterpart ('Fengjie 72-1', WT). Using high-throughput sequencing of small RNAs and RNA degradome tags, we identified 107 known and 21 novel miRNAs, as well as 225 target genes. A total of 24 miRNAs (16 known miRNAs and 8 novel miRNAs) were shown to be differentially expressed between MT and WT. The expression pattern of several key miRNAs and their target genes during citrus fruit development and ripening stages was examined. Csi-miR156k, csi-miR159 and csi-miR166d suppressed specific transcription factors (GAMYBs, SPLs and ATHBs) that are supposed to be important regulators involved in citrus fruit development and ripening. In the present study, miRNA-mediated silencing of target genes was found under complicated and sensitive regulation in citrus fruit. The identification of miRNAs and their target genes provide new clues for future investigation of mechanisms that regulate citrus fruit ripening.

2017-02-10 | GSE84191 | GEO

Microarray Based Analysis of the Developing Sweet Orange Transcriptome

2008-03-05 | GSE10731 | GEO

Expression data from Senescence Process of citrus

Project description:The postharvest senescence processes of citrus fruits were analyzed transcriptomic. The present study was aimed to: further uncover the rind-flesh communication of hesperidium; characterize the differential storage behaviors of different citrus varieties; reveal the important changes during storing process; and demonstrate the specific non-climacteric characteristics of citrus fruits. We chose four major table fruit varieties of citrus: satsuma mandarin (Citrus unshiu Marc) (M), ponkan (Citrus reticulata Blanco) (K), newhall navel orange (Citrus sinensis L. Osbeck) (O) and shatian pummelo (Citrus grandis Osbeck) (P). They were sampled every 10 days during 50 DAH (days after harvest), almost covering the commercial storage period of loose-skin citrus.

2014-12-03 | E-GEOD-63706 | biostudies-arrayexpress

Global increase in DNA Methylation during ripening of sweet orange [ncRNA-seq]

Project description:Using sRNA-Seq to provide small RNA status in fruit ripening stages in sweet orange DNA methylation is an important epigenetic mark involved in many biological processes. The genome of the climacteric tomato fruit undergoes a global loss of DNA methylation due to active DNA demethylation during the ripening process. It is unclear whether the ripening of other fruits is also associated with global DNA demethylation. We characterized the single-base resolution DNA methylomes of sweet orange fruits. Compared to immature orange fruits, ripe orange fruits gained DNA methylation at over 30,000 genomic regions and lost DNA methylation at about 1,000 genomic regions, suggesting a global increase in DNA methylation during orange fruit ripening. This increase in DNA methylation was correlated with decreased expression of DNA demethylase genes. The application of a DNA methylation inhibitor interfered with ripening, indicating that the DNA hypermethylation is critical for the proper ripening of orange fruits. We found that ripening-associated DNA hypermethylation was associated with the repression of several hundred genes, such as photosynthesis genes, and with the activation of hundreds of genes including genes involved in ABA responses. Our results suggest important roles of DNA methylation in orange fruit ripening.

2018-12-28 | GSE120025 | GEO

High-Spatiotemporal-Resolution Transcriptomes Insights into Fruit Development and Ripening in Citrus sinensis

Project description:To excavate the underlying molecular regulation network that during citrus fruit development and ripening, we used RNA-seq to generate high-resolution profiles of global gene expression in four different fruit tissues at six development stages. Using weighted gene coexpression network analysis, we identified modules of coexpressed genes and hub genes of tissue-specific networks. In general, this study was aimed to uncover the new molecular insights into citrus fruit development and ripening, and to reveal the specific nonclimacteric characteristics of citrus fruit.

2019-06-24 | GSE125726 | GEO

Global increase in DNA Methylation during ripening of sweet orange [RNA-seq]

Project description:Using RNA-Seq to analyse the gene expression pattern in five fruit ripening stages in sweet orange

2018-12-28 | GSE108930 | GEO

Global increase in DNA Methylation during ripening of sweet orange [BS-seq]

Project description:Using BS-Seq to provide single-base resolution of DNA methylation status in five fruit ripening stages in sweet orange

2018-12-28 | GSE108931 | GEO

Microarray Based Analysis of the Developing Sweet Orange Transcriptome

Project description:Using a custom microarray platform, we examined expression of 366 genes in leaf, two peel tissues, juice sac, and whole fruit during various developmental stages of Washington Navel orange fruit (Citrus sinensis L. Osbeck). 366 genes were chosen from Citrus EST libraries by in-silico analysis method. Keywords: time course and tissue comparison Study to compare gene expression between peel layers and over time as fruit matured. Samples taken from leaf tissue, whole fruit at 24 and 38 days after full bloom (DAFB), and from albedo and flavedo layers of the peel at 80 and 165 DAFB, and flavedo from mature fruit at 220 DAFB. In all cases except one, there were three technical replicates hybridized for each Sample simultaneously.

2010-05-26 | E-GEOD-10731 | biostudies-arrayexpress

Genomic and transcriptomic analyses of valencia orange provide insights into its domestication and traits formation

Project description:Valencia orange (Citrus sinensis Osbeck), namely summer orange (SO), is a type of late-ripening sweet oranges, the ripening time of which is 4 to 5 months later than that of the middle-ripening common sweet orange (CO). The mastication of SO fruit pulp is worse than that of CO. To date, how the late-ripening and poor pulp mastication traits were domesticated in SO is unknown. In this study, 13 SO cultivars and 12 CO cultivars were used for whole-genome resequencing. Population genetic diversity analysis divided these 25 samples into SO and CO subgroups, respectively. There were 144 and 141 genes identified by selective sweep analysis to be strongly selected during SO and CO evolutionary processes, respectively. Based on gene functional annotation and pathway enrichment analysis, most of these selected genes in SO were related to resistance and lignin biosynthesis. Simultaneously, we comparatively analyzed the transcriptome profiles of the peel and pulp tissues among three SO cultivars and three CO cultivars, which also revealed the difference of lignin synthesis between SO and CO fruits. Moreover, according to the comparative analysis of the lignin content and the expressions of the genes related to lignin biosynthesis in SO and CO fruits, we suggested that lignin may play an important role in the pulp mastication trait of SO. In addition, a SNP molecular marker was developed to distinguish SO and CO. This study reveals that the mastication trait may be formed in the process of SO domestication, while the late-ripening trait may be formed in a genetic mutation event.

2021-08-26 | GSE164142 | GEO

Comparison of transcriptomes in five varieties of citrus fruit

Project description:To identify genes associated with citrus peel development and manifestation of peel disorders, we analyzed flavedo, albedo and juice sac tissues from five types of citrus fruit including, mandarin orange, navel orange, valencia orange, grapefruit and lemon.

2014-01-01 | GSE50384 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data