Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Metabolome and Transcriptome Analyses Reveal the Regulatory Mechanisms of Photosynthesis in Developing Ginkgo biloba Leaves.

ABSTRACT: Ginkgo (Ginkgo biloba L.) is a deciduous tree species with high timber, medicinal, ecological, ornamental, and scientific values, and is widely cultivated worldwide. However, for such an important tree species, the regulatory mechanisms involved in the photosynthesis of developing leaves remain largely unknown. Here, we observed variations in light response curves (LRCs) and photosynthetic parameters (photosynthetic capacity (P_nmax) and dark respiration rate (R_d)) of leaves across different developmental stages. We found the divergence in the abundance of compounds (such as 3-phospho-d-glyceroyl phosphate, sedoheptulose-1,7-bisphosphate, and malate) involved in photosynthetic carbon metabolism. Additionally, a co-expression network was constructed to reveal 242 correlations between transcription factors (TFs) and photosynthesis-related genes (p < 0.05, |r| > 0.8). We found that the genes involved in the photosynthetic light reaction pathway were regulated by multiple TFs, such as bHLH, WRKY, ARF, IDD, and TFIIIA. Our analysis allowed the identification of candidate genes that most likely regulate photosynthesis, primary carbon metabolism, and plant development and as such, provide a theoretical basis for improving the photosynthetic capacity and yield of ginkgo trees.

SUBMITTER: Guo Y

PROVIDER: S-EPMC7961846 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis of Ginkgo biloba kernels.

Project description:Ginkgo biloba is a dioecious species native to China with medicinally and phylogenetically important characteristics; however, genomic resources for this species are limited. In this study, we performed the first transcriptome sequencing for Ginkgo kernels at five time points using Illumina paired-end sequencing. Approximately 25.08-Gb clean reads were obtained, and 68,547 unigenes with an average length of 870 bp were generated by de novo assembly. Of these unigenes, 29,987 (43.74%) were annotated in publicly available plant protein database. A total of 3,869 genes were identified as significantly differentially expressed, and enrichment analysis was conducted at different time points. Furthermore, metabolic pathway analysis revealed that 66 unigenes were responsible for terpenoid backbone biosynthesis, with up to 12 up-regulated unigenes involved in the biosynthesis of ginkgolide and bilobalide. Differential gene expression analysis together with real-time PCR experiments indicated that the synthesis of bilobalide may have interfered with the ginkgolide synthesis process in the kernel. These data can remarkably expand the existing transcriptome resources of Ginkgo, and provide a valuable platform to reveal more on developmental and metabolic mechanisms of this species.

| S-EPMC4593864 | biostudies-literature

Multifeature analyses of vascular cambial cells reveal longevity mechanisms in old Ginkgo biloba trees.

Project description:Aging is a universal property of multicellular organisms. Although some tree species can live for centuries or millennia, the molecular and metabolic mechanisms underlying their longevity are unclear. To address this, we investigated age-related changes in the vascular cambium from 15- to 667-y-old Ginkgo biloba trees. The ring width decreased sharply during the first 100 to 200 y, with only a slight change after 200 y of age, accompanied by decreasing numbers of cambial cell layers. In contrast, average basal area increment (BAI) continuously increased with aging, showing that the lateral meristem can retain indeterminacy in old trees. The indole-3-acetic acid (IAA) concentration in cambial cells decreased with age, whereas the content of abscisic acid (ABA) increased significantly. In addition, cell division-, cell expansion-, and differentiation-related genes exhibited significantly lower expression in old trees, especially miR166 and HD-ZIP III interaction networks involved in cambial activity. Disease resistance-associated genes retained high expression in old trees, along with genes associated with synthesis of preformed protective secondary metabolites. Comprehensive evaluation of the expression of genes related to autophagy, senescence, and age-related miRNAs, together with analysis of leaf photosynthetic efficiencies and seed germination rates, demonstrated that the old trees are still in a healthy, mature state, and senescence is not manifested at the whole-plant level. Taken together, our results reveal that long-lived trees have evolved compensatory mechanisms to maintain a balance between growth and aging processes. This involves continued cambial divisions, high expression of resistance-associated genes, and continued synthetic capacity of preformed protective secondary metabolites.

| S-EPMC6995005 | biostudies-literature

Temporospatial Flavonoids Metabolism Variation in <i>Ginkgo biloba</i> Leaves.

Project description:Ginkgo (Ginkgo biloba L.) is a high-value medicinal tree species characterized by its flavonoids beneficial effects that are abundant in leaves. We performed a temporospatial comprehensive transcriptome and metabolome dynamics analyses of clonally propagated Ginkgo plants at four developmental stages (time: May to August) across three different environments (space) to unravel leaves flavonoids biosynthesis variation. Principal component analysis revealed clear gene expression separation across samples from different environments and leaf-developmental stages. We found that flavonoid-related metabolism was more active in the early stage of leaf development, and the content of total flavonoid glycosides and the expression of some genes in flavonoid biosynthesis pathway peaked in May. We also constructed a co-expression regulation network and identified eight GbMYBs and combining with other TF genes (3 GbERFs, 1 GbbHLH, and 1 GbTrihelix) positively regulated the expression of multiple structural genes in the flavonoid biosynthesis pathway. We found that part of these GbTFs (Gb_11316, Gb_32143, and Gb_00128) expressions was negatively correlated with mean minimum temperature and mean relative humidity, while positively correlated with sunshine duration. This study increased our understanding of the molecular mechanisms of flavonoids biosynthesis in Ginkgo leaves and provided insight into the proper production and management of Ginkgo commercial plantations.

| S-EPMC7728922 | biostudies-literature

Long-chain betulaprenol-type polyprenols from the leaves of Ginkgo biloba.

Project description:A long-chain betulaprenol-type polyprenol mixture was isolated from the leaves of Ginkgo biloba mainly as acetate. The structure was determined by mass spectroscopy, 1H-n.m.r. spectroscopy and 13C-n.m.r. spectroscopy. The mixture contained polyprenols-14-22, predominantly polyprenols-17, -18 and -19, and consisted of the dimethylallyl terminal unit (omega-terminal), two trans-isoprene residues, a sequence of 11-19 cis-isoprene residues and a terminal hydroxylated isoprene unit (alpha-terminal) aligned in that order. The concentration of these polyprenols in leaves increased from 0.04 to 2.0% of dry wt. with maturing of the leaves, though the content of total lipids was constant. The distribution of chain length in these polyprenols showed little variation throughout the whole life of the leaves.

| S-EPMC1152129 | biostudies-other

Metabolomic and transcriptomic analyses of mutant yellow leaves provide insights into pigment synthesis and metabolism in Ginkgo biloba.

Project description:BackgroundGinkgo (Ginkgo biloba L.) is an excellent landscape species. Its yellow-green leaf mutants are ideal materials for research on pigment synthesis, but the regulatory mechanism of leaf coloration in these ginkgo mutants remains unclear.ResultsWe compared the metabolomes and transcriptomes of green and mutant yellow leaves of ginkgo over the same period in this study. The results showed that the chlorophyll content of normal green leaves was significantly higher than that of mutant yellow leaves of ginkgo. We obtained 931.52M clean reads from different color leaves of ginkgo. A total of 283 substances in the metabolic profiles were finally detected, including 50 significantly differentially expressed metabolites (DEMs). We identified these DEMs and 1361 differentially expressed genes (DEGs), with 37, 4, 3 and 13 DEGs involved in the photosynthesis, chlorophyll, carotenoid, and flavonoid biosynthesis pathways, respectively. Moreover, integrative analysis of the metabolomes and transcriptomes revealed that the flavonoid pathway contained the upregulated DEM (-)-epicatechin. Fourteen DEGs from the photosynthesis pathway were positively or negatively correlated with the DEMs.ConclusionsOur findings suggest a complex metabolic network in mutant yellow leaves. This study will provide a basis for studies of leaf color variation and regulation.

| S-EPMC7709416 | biostudies-literature

UV-B promotes flavonoids synthesis in Ginkgo biloba leaves

Project description:We conducted RNA-seq from the Ginkgo leaves after UV-B treatment,and constructed the molecular regulatory network of flavonoids synthesis under UV-B radiation in G. biloba.

2019-12-13 | GSE141890 | GEO

Rejuvenation improves the flavonoid accumulation in Ginkgo biloba leaves

Project description:We sequenced mRNA of G. biloba leaves from truncation treatment and control using the Illumina HiSeq4000 platform. We identified the transcriptome changes in leaves between truncation group and control group, which provided valuable information for uncovering the molecular mechanisms of flavonoid accumulation in G. biloba under rejuvenation.

2020-06-15 | GSE149736 | GEO

Advances in the Studies of Ginkgo Biloba Leaves Extract on Aging-Related Diseases.

Project description:The prevalence of degenerative disorders in public health has promoted in-depth investigations of the underlying pathogenesis and the development of new treatment drugs. Ginkgo biloba leaves extract (EGb) is obtained from Ginkgo biloba leaves and has been used for thousands of years. In recent decades, both basic and clinical studies have established the effects of EGb. It is widely used in various degenerative diseases such as cerebrovascular disease, Alzheimer's disease, macroangiopathy and more. Here, we reviewed several pharmacological mechanisms of EGb, including its antioxidant properties, prevention of mitochondrial dysfunctions, and effect on apoptosis. We also described some clinical applications of EGb, such as its effect on neuro and cardiovascular protection, and anticancer properties. The above biological functions of EGb are mainly focused on aging-related disorders, but its effect on other diseases remains unclear. Thus, through this review, we aim to encourage further studies on EGb and discover more potential applications.

| S-EPMC5758353 | biostudies-literature

Transcriptome Profile Analysis from Different Sex Types of Ginkgo biloba L.

Project description:In plants, sex determination is a comprehensive process of correlated events, which involves genes that are differentially and/or specifically expressed in distinct developmental phases. Exploring gene expression profiles from different sex types will contribute to fully understanding sex determination in plants. In this study, we conducted RNA-sequencing of female and male buds (FB and MB) as well as ovulate strobilus and staminate strobilus (OS and SS) of Ginkgo biloba to gain insights into the genes potentially related to sex determination in this species. Approximately 60 Gb of clean reads were obtained from eight cDNA libraries. De novo assembly of the clean reads generated 108,307 unigenes with an average length of 796 bp. Among these unigenes, 51,953 (47.97%) had at least one significant match with a gene sequence in the public databases searched. A total of 4709 and 9802 differentially expressed genes (DEGs) were identified in MB vs. FB and SS vs. OS, respectively. Genes involved in plant hormone signal and transduction as well as those encoding DNA methyltransferase were found to be differentially expressed between different sex types. Their potential roles in sex determination of G. biloba were discussed. Pistil-related genes were expressed in male buds while anther-specific genes were identified in female buds, suggesting that dioecism in G. biloba was resulted from the selective arrest of reproductive primordia. High correlation of expression level was found between the RNA-Seq and quantitative real-time PCR results. The transcriptome resources that we generated allowed us to characterize gene expression profiles and examine differential expression profiles, which provided foundations for identifying functional genes associated with sex determination in G. biloba.

| S-EPMC4910463 | biostudies-literature

Identification and characterization of microRNA expression in Ginkgo biloba L. leaves

Project description:High-throughput small RNA sequencing were performed to identify a large number of miRNAs and their targets in mature female and male G. biloba leaves for the first time. We ascertained that the regulatory networks of the miRNAs are involved in many different primary biological processes based on potential target designations. Our study is the first to provide useful information for uncovering the regulatory networks of miRNAs in basal gymnosperm G. biloba leaves.

2015-07-13 | GSE65229 | 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