Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1002122 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25516031.fastq.gz | Fastqsanger.gz | |||
| SRR25516032.fastq.gz | Fastqsanger.gz | |||
| SRR25516033.fastq.gz | Fastqsanger.gz | |||
| SRR25516034.fastq.gz | Fastqsanger.gz | |||
| SRR25516035.fastq.gz | Fastqsanger.gz |
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Project description:Petal is not only the target of selection by horticulturalists to enhance the ornamental value of plants but also emerged as a unique model system for plant organogenesis studies. It is known that three major groups of pigments, betalains, carotenoids and anthocyanins, are responsible for the attractive natural display of flower colors. While carotenoids and betalains generally yield yellow or red colors, anthocyanins confer a diverse range of color from orange to red to violet and blue. In this study, we collected 11 species (Erysimum cheiri, Malcolmia maritime, Brassica oleracea, Raphanus sativus, Orychophragmus violaceus, Eruca sativa, Orychophragmus violaceus, Iberis amara, Aubrieta x cultorum, Lobularia maritime, Matthiola incana) belong to different tribe in Brassicaceae family with varied flower color and performed petal transcriptome analysis. de novo transcriptome assembly showed that average length of the contigs varied from 631bp in O. violaceus to 1212bp in Matthiola incana which indicated that the complexity of the genomes are different much. Protein homology between these species and those sequenced species in Brassicaceae family are consistent with the known phylogenetic relationships. However, O. violaceus has closer relationships with Sisymbrium irio than expected Brassica species. Clustering analysis of genes in anthocyanin and carotenoids synthesis pathway indicated that while silence or low expression of CCD4 (Carotenoid Cleavage Dioxygenase 4) leading to the yellow color formation in different species, purple or red color variation might result from different genes expression variation. These results not only provide transcriptome data for petal development study but also provide useful information for Brassica flower improvement for ornamental purpose.
2017-01-24 | GSE93879 | GEO
Project description:The purpose of this study was to explore the mechanism of aerobic decay of whole-plant corn silage and the effect of Neolamarckia cadamba essential oil on aerobic stability of whole-plant corn silage. Firstly, the dynamic changes of temperature, microbial community and metabolite content after aerobic exposure of whole-plant corn silage were determined, and the main microbial species and mechanism leading to aerobic spoilage of whole-plant corn silage were analyzed. The N. cadamba essential oil was extracted from fresh N. cadamba leaves by steam distillation, and the minimal inhibitory concentration, antibacterial stability and bacteriostatic mechanism of N. cadamba essential oil against undesirable microorganisms in whole-plant corn silage were determined. According to the minimum inhibitory concentration of N. cadamba essential oil on undesirable microorganisms in silage, N. cadamba essential oil was added to whole-plant corn silage to explore the effect of N. cadamba essential oil on the aerobic stability of whole-plant corn silage.
2023-09-13 | GSE241081 | GEO
Project description:Oilseed rape is both an important oleaginous crop and agriculture sightseeing crop whereas has relatively scanty flower color. As natural flavonoids, Anthocyanin are responsible for the attractive red, purple, and blue colors of various tissues in higher plants, especially for the ornamental plants flower. One Brassica napus-Orychophragmus violaceus disomic addition line (M4) obtained previously exhibits red petals whichresult from anthocyanin biosynthesis. Transcriptome analysis of M4, B. napus (H3), natural individuals of O. violaceus with purple petals (OvP) and white petals (OvW) revealed that most of structural genes for the anthocyanin synthesis were up-regulated in both M4 and OvP, especially key gene ANS in the last step. Reads assembling and sequence alignment showed that the regulatory DEG PAP2 in M4 was from the transcript of O. violaceus. OvPAP2 was transformed into Arabidopsis thaliana and B. napus driven by the CaMV35S promoter and the rape petal-specific prompter XY355. Transgenic A. thaliana plants showed different levels of purple pigments in most of the organs, including the petals, and transgenic B. napus flowers exhibited restricted accumulation of anthocyanins in stamens when driven by CaMV35S promoter, but generated both red petals and anthers driven by the XY355 promoter. These results provided a platform for expounding the anthocyanin biosynthesis pathway in B. napus petals and give a successful case for flower color modification of the agriculture sightseeing rape.
2017-12-30 | GSE93089 | GEO
Project description:Orychophragmus violaceus cultivar:wuhan ov Genome sequencing and assembly
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Project description:The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal’s feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or hay, each supplemented with a concentrate mixture. Samples were fractionated into ruminal fluid, squeezed solid and solid matter. DNA, proteins and metabolites were analyzed subsequently. DNA extracts were used for Illumina sequencing of the 16S rRNA gene and the metabolomes of rumen fluids were determined by 500MHz-NMR spectroscopy. Tryptic peptides derived from protein extracts were measured by LC-ESI-MS/MS and spectra were processed by a two-step database search for quantitative metaproteome characterization. Protein- and DNA-based datasets revealed significant differences between sample fractions and diets and affirmed similar trends concerning shifts in phylogenetic composition. Ribosomal genes and proteins belonging to the phylum of Proteobacteria, particularly Succinivibrionaceae, exhibited a higher abundance in corn silage-based samples while fiber-degraders of the Lachnospiraceae family emerged in great quantities throughout the solid phase fractions. The analysis of 8163 quantified bacterial proteins revealed the presence of 166 carbohydrate active enzymes in varying abundance. Cellulosome affiliated proteins were less expressed in the grass silage, glycoside hydrolases appeared in slightest numbers in the corn silage. Most expressed glycoside hydrolases belonged to families 57 and 2. Enzymes analogous to ABC transporters for amino acids and monosaccharides were more abundant in the corn silage whereas oligosaccharide transporters showed a higher abundance in the fiber-rich diets. Proteins involved in carbon metabolism were detected in high numbers and identification of metabolites like short-chain fatty acids, methylamines and phenylpropionate by NMR enabled linkage between producers and products. This study forms a solid basis to retrieve deeper insight into the complex network of gut microbial adaptation.
2017-08-15 | PXD006070 | Pride