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ABSTRACT:
PROVIDER: PRJNA1110555 | ENA |
REPOSITORIES: ENA
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Project description:Very little is known about the mechanism controlling petiole rigidity in sacred lotus (Nelumbo nucifera Gaertn.). To investigate the mechanism controlling the lotus petiole rigidity, morphological and proteomic analyses were performed. Anatomically, there is a great variation between the petioles of floating and vertical leaves. The number of vascular bundles, ligneous cells and thickness of cell wall were higher in the initial vertical leaf petiole (IVP) compared to the initial floating leaf petiole (IFP). A total of 4855 proteins were quantified through comparative proteomic analysis, among which 421 proteins expressed 1.5 folds higher in IFP and 483 proteins expressed 1.5 folds higher in IVP. Protein function categories indicated hundreds of proteins involved in cell wall organization and biosynthesis, and cell wall assembly. Functional enrichment analysis for the differentially abundant proteins indicated the enrichment of 105 proteins in 6 different pathways, while 43 out the total proteins were enriched in lignin biosynthesis pathway. In consistent with genes and proteins expressions in lignin biosynthesis, the contents of lignin monomers precursors were significantly different in IFP and IVP. These findings support the involvement of lignin in lotus petioles rigidity.
2021-07-29 | PXD009136 | Pride
Project description:Lotus (Nelumbo nucifera Gaertn) belongs to the family Nymphaeaceae, and is a popular aquatic vegetable that is rich in nutrients. It is widely cultivated in China, and many varieties of lotus are used for different purposes, suited to different climates, and consumed in different ways. Lotus is commonly produced by asexual propagation, so mutation through hybridization and variation fixed by asexual propagation are the main ways to create new varieties. Therefore, the formation of adventitious roots (ARs) in lotus, which does not have a well-developed principal root, is an important part of growth and development. It would be very useful to control ARs formation for lotus production and breeding.
2022-02-23 | PXD006883 | Pride
Project description:To reveal the molecular mechanism during de novo root regeneration from Arabidopsis leaf explants cultured on B5 medium without exogenous hormones, we carried out an RNA-seq experiment using detached leaf explants with partial petiole before culture (i.e. time 0) and 2 d after culturing (DAC) from12-d-old Col-0 seedlings. Gene expression of the wounded region (including the partial petiole and some surrounding tissues), which comprises regeneration-competent cells, was analyzed.
2019-10-22 | GSE139165 | GEO
Project description:Nelumbo, a perennial aquatic herbage that belongs to the family of Nelumbonaceae, comprises two extant species: N. nucifera Gaertn. and N. lutea (Wild.) Pers. Based on a previous study, N. nucifera is distributed in over Asia and Northern Australia while N. lutea is found in North America and northern of South America (1). N. nucifera can be divided into two cultivars including temperate lotus and tropical lotus based on its rhizome phenotype. The temperate lotus rhizome is expanded at the end of growth while tropical lotus root is of no significant enlargement during development (2). Normally, the temperate lotus root buds germinate in April, thereafter it takes several days from sowing to long roots and leaves. In mid-to-late may, vertical leaves rise out of the water, following July and August are the blooming period. Secondarily the first half of September is the final flowering period. The fruit ripening period is from late July to mid September, which is also the period of stem expansion and enrichment. After mid-October, it’s the dormant period, which is the lotus storage organ’s substance accumulation period. Thus the storage organ, mainly lotus rhizome, provides the energy for the lifecycle (Fig.1). Lotus rhizome, which is called metamorphic storage organ, is a kind of modified subterraneous stem, like potato (Solanum tuberosum) tuber and onion (Allium cepa L.) bulb (3). Most parts of lotus like rhizome, leaf, lotus seed and germ are used for traditional medicine (4). Rhizome especially is a kind of popular vegetable in Asia for its richness in nutrients including starch, proteins, vitamins (5). Nowadays it is a worldwide product in the form of the processed and semi-finished form like tea and vegetables. In general, the development of lotus rhizome can be classified into four stages: stolon stage, initial swelling, middle swelling, and later swelling stage (6, 7). The first three stages mainly focus on cell division and synthesis of some important carbohydrates, like starch, which play a critical part in the quantity and quality of rhizome, while accumulation of starch greatly increases at the last stage. Numerous studies have done in lotus to shed light on the environmental factors and morphometric indexes relevant to rhizome formation (8, 9). Short day light and low temperature promote tuber formation (10, 11). Also genes and proteins related to hormone, photoperiod (12, 13), starch synthesis (14, 15) and flowering time locus family genes were involved in the lotus rhizome formation (16). Previous studies include transcriptomics (6), genomics (17) and certain physiological researches, revealing numerous genes involved in photoperiod pathway, starch metabolism and hormone signal transduction, trying to make lotus a model plant of rhizome growth, while there is a lack of protein-level dynamic analysis and protein phosphorylation information, which is a strong proof for the dynamic processes in lotus rhizome. Proteomics is an indispensable method in storage organs research findings (18, 19), 2-DE and MALDI-TOF-TOF was employed to find some different protein profiles in fresh-cut lotus tuber before and after browning (20). And comparative proteomic was employed to analyze the Horsetail (Equisetum hyemale) underground stem to throw light upon the related proteins of developing rhizomes in ancient vascular plant Equisetum hyemale and different monocot species (21). Proteomics can also assist us in getting the changes of proteins in differently treated samples of potato tuber by using a LC-MS spectral-counting proteomics strategy (1), and shed light on the molecular basis of tuberization in potato to monitor differentially expressed proteins at different development stages (22). But the proteomic study of lotus rhizome enlargement hasn’t been reported now. Here, we employed comparative proteomics and phosphoproteomics to get proteins and its phosphorylation changes in the course of different rhizome development stages. Our data highlights some pathways, proteins and phosphorylated proteins during the development, and the difference between proteome and phosphoproteome in rhizome formation process.
2019-11-12 | PXD010388 | Pride
Project description:Flower-lotus with many attractive floral characteristics has been studied and discussed the most. These characteristics are used as the standards of the classification in most cases, and always attracted the attention of lotus breeders on improvement program because of associating with ornamental and economic values of lotus. However, molecular mechanisms underlying the formation of these attractive floral features still remain largely unknown. Transcriptome sequencing technique has been established as an efficient approach for gene discovery and expression pattern identification. For some plants, a lot of important genes involved in plant critical metabolisms have been successfully identified by this technique. In the study, mass sequence data obtained from the deep sequencing of a mixed flower-bud cDNA pool from three individuals of N. nucifera provide a platform to comprehensively understand the processes of flower formation and development at the molecular level, and will greatly facilitate the genetic improvement of ornamental characteristics and the directive molecular breeding for lotus in the future.
2014-12-08 | GSE57601 | GEO
Project description:Background: The growth and development of leaf and petiole have an important influence on the photosynthesis of plants. The research on molecular mechanism of leaf and petiole development is of great significance, whether it is to improve plant photosynthetic efficiency, cultivate varieties with high photosynthetic efficiency, or improve the yield of crops using leaves as food organs. In this study, we aimed to identify the mRNAs, long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) related to leaf and petiole development in Chinese cabbage (Brassica campestris L. ssp. pekinensis). These data were then used to construct competitive endogenous RNA (ceRNA) networks, which can provide valuable information for better understanding the mechanism of leaf and petiole development. Results: In this study, the leaf and petiole of the baby Chinese cabbage inbred line ‘PHL’ were used as research materials for whole-transcriptome sequencing. A total of 10646 differentially expressed (DE) mRNAs, 303 DE lncRNAs, 7 DE circRNAs, and 195 DE miRNAs were identified between the leaf and petiole. Some transcription factors or proteins that play important roles in leaf and petiole development were identified, such as xyloglucan endotransglucosylase/hydrolase (XTH) protein, expansion protein, TCP15 transcription factor, bHLH transcription factor, LOB domain protein, cellulose synthase (CESA), MOR1-like protein, and plant hormone biosynthesis related genes. Additionally, we constructed a leaf and petiole development-related ceRNA regulatory network, and obtained 85 pairs of ceRNA relationships, including 71 DEmiRNA-DEmRNA, 12 DEmiRNA-DElncRNA and 2 DEmiRNA-DEcircRNA. Three LSH genes (BrLSH1, BrLSH2 and BrLSH3) with significant differential expression between leaf and petiole of baby Chinese cabbage were screened from transcriptome data for subcellular localization analysis and overexpression transgenic verification. The results showed that BrLSH1, BrLSH2 and BrLSH3 were nucleoprotein and BrLSH2 has an obvious inhibitory effect on the growth and development of Arabidopsis thaliana. Conclusions: Our results revealed the potential mRNAs and non-coding RNAs (ncRNAs) involved in leaf and petiole development, which laid a foundation for further research on the molecular mechanism of leaf and petiole development in Chinese cabbage.
2022-12-29 | GSE218959 | GEO