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Investigation of the microRNAs in safflower seed, leaf and petal by high-throughput sequencing

ABSTRACT: We report that there are at least 236 known miRNAs expressed in safflower, of which 100 miRNAs with relatively high expression level exhibited evolutionary conservation across multiple plants. Comparison of their expression patterns among different tissues shows that a total of 116, 133 and 128 miRNAs are significantly differentially expressed between safflower seed/leaf, seed/petal and leaf/petal. Meanwhile, interestingly, the majority of the most significantly differentially expressed miRNAs between tissues are tissue-specific miRNAs. In addition, 15 putative novel miRNAs have been identified in safflower. The small RNA transcriptomes obtained in this study provide a basis for further investigation of the physiological roles of identified miRNAs in safflower.

ORGANISM(S): Carthamus tinctorius

PROVIDER: GSE25165 | GEO | 2010/11/06

SECONDARY ACCESSION(S): PRJNA134421

REPOSITORIES: GEO

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Investigation of the microRNAs in safflower seed, leaf and petal by high-throughput sequencing

Project description:We report that there are at least 236 known miRNAs expressed in safflower, of which 100 miRNAs with relatively high expression level exhibited evolutionary conservation across multiple plants. Comparison of their expression patterns among different tissues shows that a total of 116, 133 and 128 miRNAs are significantly differentially expressed between safflower seed/leaf, seed/petal and leaf/petal. Meanwhile, interestingly, the majority of the most significantly differentially expressed miRNAs between tissues are tissue-specific miRNAs. In addition, 15 putative novel miRNAs have been identified in safflower. The small RNA transcriptomes obtained in this study provide a basis for further investigation of the physiological roles of identified miRNAs in safflower. Investigate the small RNA transcriptomes in 3 tissues

2010-11-06 | E-GEOD-25165 | biostudies-arrayexpress

Carthamus tinctorius

Project description:Investigation of the microRNAs in safflower seed, leaf and petal by high-throughput sequencing

| PRJNA134421 | ENA

Proteome and Ubiquitome Changes during Rose Petal Senescence

Project description:Petal senescence involves numerous programmed changes in biological and biochemical processes. Ubiquitination plays a critical role in protein degradation, a hallmark of organ senescence. Therefore, we investigated changes in the proteome and ubiquitome of senescing rose (Rosa hybrida) petals to better understand their involvement in petal senescence. Of 3859 proteins quantified in senescing petals, 1198 were up-regulated and 726 were down-regulated during senescence. We identified 2208 ubiquitinated sites including 384 with increased ubiquitination in 298 proteins and 1035 with decreased ubiquitination in 674 proteins. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that proteins related to peptidases in proteolysis and autophagy pathways were enriched in the proteome, suggesting that protein degradation and autophagy play important roles in petal senescence. In addition, many transporter proteins accumulated in senescing petals, and several transport processes were enriched in the ubiquitome, indicating that transport of substances is associated with petal senescence and regulated by ubiquitination. Moreover, several components of the brassinosteroid (BR) biosynthesis and signaling pathways were significantly altered at the protein and ubiquitination levels, implying that BR plays important roles in petal senescence. Our data provide a comprehensive view of rose petal senescence at the posttranslational level.

2020-05-27 | PXD016490 | Pride

Proteomes and Ubiquitylomes Analysis Reveals the Involvement of Ubiquitination in Protein Degradation in rosa hybrida during petal abscission.

Project description:We employed Non-standard quantitative techniques and quantitative proteomics techniques based on mass spectrometry to perform proteomics analyses for the petal abscission zone of rose petal at stage 3 stage 5. In total, 6595 proteins were detected, we compared differentially expressed proteins (DEPs) between stage 3 and stage 5 (FC>1.5, P-value<0.05). We found that 271 proteins were significantly up-regulated, while 444 proteins were significantly down-regulated.

2023-03-11 | PXD036665 | Pride

affy_petaldvt_lyon_rose: Flower/Petal initiation and development in roses

Project description:affy_petaldvt_lyon_rose. The objective is to identify genes involved in petal development in rose. We aim at identifying genes whose expression correlates with flower opening and scent emission. In this study, we used a microarray approach to compare the transcriptome of a scented rose flower (PF) versus non-scented rose flower (RF). Samples (petal tissues) were collected at the same time early in the afternoon. Total RNA was extracted using the Plant RNA kit (Macherey Nagel), and then used to hybridize Rosa-Affymetrix microarrays. Keywords: scented vs non-scented flowers

2011-09-01 | GSE18357 | GEO

affy_petaldvt_lyon_rose: Flower/Petal initiation and development in roses

2011-08-31 | E-GEOD-18357 | biostudies-arrayexpress

affy_duplicature_lyon_rose. Double flower phenomenon: Control of petal number in roses

Project description:affy_duplicature_lyon_rose. The objective is to identify the genes involved in petal doubling in rose. In this study we are using two rosa gallica genotypes: wild-type (simple flower rose) and Cardinal de Richelieu (double flower rose), and two rosa hybrida genotypes : Souvenir de la Malmaison, which has about 110 petal, and its bud sport cultivar, Souvenir de St Anne’s. In this study, we used a microarray approach to compare the transcriptome of double flower rose (CDR) versus simple flower rose (G). The objective is to identify genes whose expression is associated with the double flower phenotype. These genes are putative candidates involved in the control of petal organ number per flower. Floral buds were dissected under a microscope and pooled in eppendorf tubes. Tissue samples were harvested at the same time during 3 weeks in April 2007. Total RNA was extracted from the pools of flowers using the Plant RNA kit (Macherey Nagel), and then used to hybridize Rosa-Affymetrix microarrays. Keywords: genotype comparison

2011-09-01 | GSE18353 | GEO

Histone H3K4 methyltransferase DcATX1 promotes ethylene induced petal senescence in carnation (Dianthus caryophyllus L.)

Project description:Petal senescence is controlled by a complex regulatory network. Epigenetic regulation like histone modification influences chromatin state and gene expression. However, involvement of histone methylation in regulating petal senescence is still largely unknown. Here, we found that the trimethylation of histone H3 at Lysine 4 (H3K4me3) is increased during the ethylene induced petal senescence in carnation (Dianthus caryophyllus L.). The H3K4me3 levels are positively associated with the expression of transcription factor DcWRKY75, ethylene biosynthetic genes DcACS1 and DcACO1, and senescence associated genes (SAGs) DcSAG12 and DcSAG29. Further, we identified that carnation DcATX1 (ARABIDOPSIS HOMOLOG OF TRITHORAX1) encodes a histone lysine methyltransferase which can methylate H3K4. Knockdown of DcATX1 delays ethylene induced petal senescence in carnation, which is associated with the downregulated expression of DcWRKY75, DcACO1 and DcSAG12. While overexpression of DcATX1 exhibits the opposite effects. DcATX1 promotes the transcription of DcWRKY75, DcACO1 and DcSAG12 by targeting to their promoters to elevate the H3K4me3 levels. Overall, our results demonstrate that DcATX1 is a H3K4 methyltransferase that promotes the expression of DcWRKY75, DcACO1, DcSAG12 and maybe other downstream target genes by regulating H3K4me3 levels, thereby accelerating ethylene induced petal senescence in carnation. This study further indicates that epigenetic regulation is important for plant senescence process.

2023-11-30 | GSE218725 | GEO

affy_duplicature_lyon_rose. Double flower phenomenon: Control of petal number in roses

2011-08-31 | E-GEOD-18353 | biostudies-arrayexpress

Dynamic liposomal and transcriptomic profiling reveal the metabolic network and regulators governing TAGs formation in seeds of safflower

Project description:In this study, depending on quantitative liposome and transcriptomic analyses, we unveiled safflower seed lipidic landscapes at 5 different developmental stages of seeds and revealed a parallel classification of 417 lipid compounds and their co-expressed genes into 7 distinct lipidic metabolites vs gene modules (MM vs GM). An essential transcriptional regulatory network for major lipid compounds changes that occurred throughout the seed growth cycle was constructed via integrative bioinformatics coupled with functional genomic assays. Sixteen transcription factors were identified that regulate the accumulation of triacylglycerols (TAGs) and fatty acids (FAs). Our findings thus shed light on the seeds of safflower metabolic regulatory network involved in the biosynthesis of major lipid compounds and provide a prospective resource for the designed improvement of oilseed quality.

2023-05-20 | GSE232144 | GEO

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