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DcReyJapo

ABSTRACT: Reynoutria japonica

PROVIDER: PRJEB80042 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR13670025_1.fastq.gz	Fastqsanger.gz
	ERR13670025_2.fastq.gz	Fastqsanger.gz
	ERR13670026_1.fastq.gz	Fastqsanger.gz
	ERR13670026_2.fastq.gz	Fastqsanger.gz
	ERR13670027_1.fastq.gz	Fastqsanger.gz

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Reynoutria japonica

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ChIP-seq of holocentric Chionographis japonica to determine the centromere distribution and genome organization

Project description:To determine the distribution of centromere units in the genome of holocentric Chionographis japonica, we performed CENH3-ChIPseq using the customized species-specific CENH3 antibody. We mixed the chromatins of C. japonica and Secale cereal (inbred line Lo7) to dilute the highly abundant centromeric Chio satellite repeats (16%) in the C. japonica genome before immunoprecipitation. In addition, to determine the large-scale genome organization, we performed ChIPseq by targeting the evolutionarily conserved eu- and heterochromatin-specific histone marks H3K4me2 and H33K9me2

2023-05-08 | GSE228407 | GEO

Identification of microRNAs in response to blue light irridiation by high-throughput sequencing in Saccharina japonica

Project description:Blue light (BL) is an important environmental factor that plays critical role in algae growth and development. Saccharina japonica, as a typical brown alga, showed greatly affected by BL. However, little has been known about the regulation pathway of BL response in algae. microRNAs (miRNAs) participated in great number of life process regulation and may be also involved in the BL response in plants. To identify miRNAs from S. japonica and characterize their probable roles in BL response, we sequenced and compared small RNA libraries under BL irradiation and dark conditions. 20 potential novel miRNAs were identified from S. japonica. Bioinformatics analysis of the miRNAs indicated that their potential targets were involved in various biological processes. Based on differential expression analysis and qRT-PCR experiment, some probable miRNAs related to BL responses were selected for further verification of their function, such as miR398. Our results demonstrated that miRNAs might play vital roles in metabolism of S. japonica, including BL responses.

2017-06-12 | GSE36704 | GEO

Global lysine succinylation analysis unveils post-translational regulation effect on phenylpropanoids metabolism remodeling during Lonicera japonica flowering development

Project description:Lonicera japonica Thunb is a typical Chinese medicinal material with the homology of medicine and food. Post-translational modification (PTM) of proteins can significantly affect protein structure and function, and plays a very important regulatory role in plant development. However, to date, little is known about the functions of PTM in L. japonica. Therefore, the study of lysine succinylation during the floral developmental stages will help to understand the mechanism of the secondary metabolism of L. japonica. In this study, we first analyzed lysine succinylation exist in L. japonica, and found lysine succinylation is highly abundant in juvenile bud stage than gold flowering stage. Then a highly efficient enrichment method for succinylation peptides was used to identify 586 succinylation modification sites in 303 proteins in L. japonica. Our bioinformatics analysis further revealed that the succinylated proteins are involved in many important biological processes including TCA, amino acid metabolism and secondary metabolism. With the development of flowering stage of L. japonica, the succinylation degree of aspartate transaminase was up-regulated while 4-coumarate-CoA ligase was down-regulated, suggesting that succinylation of proteins is important for the bioactive compounds’ biosynthesis process in L. japonica. Protein modification in vitro also verified the impact of succinylation on both 4CL and AT enzyme activity would be changed. As a consequence, current examine provides new insight into the molecular mechanism underlying the accumulation of active ingredients in L. japonica at the post-translational modification level.

2024-05-23 | PXD051484 | Pride

Variations of Metabolites and Proteome from Lonicera japonica Thunb. Buds Blossom to Flowers under UV Radiation

Project description:Lonicera japonica Thunb., known as Jin Yin Hua or Japanese honeysuckle, is an herbal medicine in Asian countries. Its flowers have been used as folk medicine for clinical practice or used as food or making healthy beverage for 1500 years in China. To investigate the molecular developmental processes from L. japonica buds to flowers under UV radiation, comparative proteomics analyses of buds and flowers were performed. Fifty-four differential proteins were identified including 42 increased proteins and 12 decreased proteins. The abundance of proteins related to glycolysis, TCA/organic acid transformation, major carbohydrate metabolism, oxidative pentose phosphate, stress, secondary metabolism, hormone, and mitochondrial electron transport were increased during flower opening process under UV radiation. Six metabolites were identified and relatively quantified by LC-MS/MS in L. japonica buds and flowers. The 1,1-diphenyl-2-picrylhydrazyl assay revealed that antioxidant activity of L. japonica buds was better than that of flowers. These results suggest that UV-B radiation could induce the production of endogenous ethylene in L. japonica buds, which facilitate the buds blossom and activate the antioxidant system. Additionally, the higher content of metabolites and antioxidant capability in L. japonica buds indicates that L. japonica buds stage might be the better harvest time compared to the flower.

2017-01-18 | PXD005324 | Pride

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