RNA-Seq and BiFC joint analysis revealed that NtCISZOG regulates the expression of NtChlH and positively regulates chlorophyll content in tobacco
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ABSTRACT:
ORGANISM(S): Nicotiana tabacum
PROVIDER: GSE295211 | GEO | 2026/04/18
REPOSITORIES: GEO
Similar Datasets
Project description:RNA-Seq and BiFC joint analysis revealed that NtCISZOG regulates the expression of NtChlH and positively regulates chlorophyll content in tobacco
| PRJNA1253710 | ENA
Project description:The degree of yellowing in tobacco leaves is an important indicator for determining the maturity and harvesting time of tobacco leaves. Reduction in chlorophyll is of utility for promoting the concentrated maturation of tobacco leaves and achieving mechanised harvesting and mining, and utilising tobacco yellow leaf regulatory genes is of great significance for the selection and breeding of tobacco varieties suitable for mechanised harvesting and the resolution of the molecular mechanisms controlling leaf colouration. In this study, the phenotypes of the yellow-leaf K326 and K326 varieties were analysed, and it was observed that the yellow-leaf K326 variety exhibited a distinct yellow leaf phenotype with a significant reduction in chlorophyll content. Subsequently, using a combination of BSA-seq, transcriptomic sequencing (RNA-seq), and proteomic sequencing approaches, we identified the candidate gene Nitab4.5_0008674g0010 that encodes dihydroneopterin aldolase as a factor associated with tobacco leaf yellowing. Finally, by measuring the folate content in K326 and Huangye K326, the folate content in Huangye K326 was observed to be significantly lower than that in K326, thus indicating that folate synthesis plays a crucial role in phenotypic changes in tobacco yellow leaves. This study is the first to use BSA-seq combined with RNA-seq and proteomic sequencing to identify candidate genes in tobacco yellow leaves. The results provide a theoretical basis for the analysis of the mechanism of tobacco yellow leaf mutations.
2024-10-23 | GSE270039 | GEO
Project description:For decades the tobacco plant has served as a model organism in plant biology to answer fundamental biological questions in the areas of plant development, physiology, and genetics. Due to the lack of sufficient coverage of genomic sequences, however, none of the expressed sequence tag (EST)-based chips developed to date cover gene expression from the whole genome. The availability of Tobacco Genome Initiative (TGI) sequences provides a useful resource to build a whole genome exon array, even if the assembled sequences are highly fragmented. Here, the design of a Tobacco Exon Array is reported and an application to improve the understanding of genes regulated by cadmium (Cd) in tobacco is described. From the analysis and annotation of the 1,271,256 Nicotiana tabacum fasta and quality files from methyl filtered genomic survey sequences (GSS) obtained from the TGI and ~56,000 ESTs available in public databases, an exon array with 272,342 probesets was designed (four probes per exon) and tested on two selected tobacco varieties. Two tobacco varieties out of 45 accumulating low and high cadmium in leaf were identified based on the GGE biplot analysis, which is analysis of the genotype main effect (G) plus analysis of the genotype by environment interaction (GE) of eight field trials (four fields over two years) showing reproducibility across the trials. The selected varieties were grown under greenhouse conditions in two different soils and subjected to exon array analyses using root and leaf tissue to understand the genetic make-up of the Cd accumulation. An Affymetrix Exon Array was developed to cover a large (~90%) proportion of the tobacco gene space. The Tobacco Exon Array will be available for research use through the Affymetrix array catalogue. As a proof of the exon array usability, we have demonstrated that the Tobacco Exon Array is a valuable tool for studying Cd accumulation in tobacco leaves. Data from field and greenhouse experiments supported by gene expression studies strongly suggested that the difference in leaf Cd accumulation between the two specific tobacco cultivars is dependent solely on genetic factors and genetic variability rather than on the environment.
2012-11-16 | GSE42319 | GEO
Project description:Decreasing antenna size is regarded as a potential strategy to improve photosynthesis for higher yield potential. Reducing chlorophyll content has been used as a strategy to decrease antenna size. One of the commonly cited benefits of this strategy has been its ability to improve crop nitrogen use efficiency; however, field evidence for this so far is limited. Here we used a mutant, p35s-Ami-YGL1, which has a lower chlorophyll content and also lower antenna size, to study the impacts of modifying leaf chlorophyll content on tissue nitrogen content and nitrogen use efficiency of plants. We show that the nitrogen contents for different tissues, including the seed tissue, on a weight basis were increased in p35s-Ami-YGL1, together with a decrease in C: N. Concurrently, we found that tissue carbon content decreased, while the content of chlorophyll precursors increased. These results suggest that the observed increase in tissue nitrogen content in Ami-YGL1 does not reflect an increase in plant nitrogen absorption or use efficiency, rather it is a result of stunted carbon fixation capacity of plants. The observed increase in seed nitrogen content in Ami-YGL1 suggests a potential strategy to increase seed nitrogen content in crops.
2025-01-01 | GSE252714 | GEO
Project description:Chlorophyll degradation by aerobic marine bacterium
| PRJEB15523 | ENA
Project description:For decades the tobacco plant has served as a model organism in plant biology to answer fundamental biological questions in the areas of plant development, physiology, and genetics. Due to the lack of sufficient coverage of genomic sequences, however, none of the expressed sequence tag (EST)-based chips developed to date cover gene expression from the whole genome. The availability of Tobacco Genome Initiative (TGI) sequences provides a useful resource to build a whole genome exon array, even if the assembled sequences are highly fragmented. Here, the design of a Tobacco Exon Array is reported and an application to improve the understanding of genes regulated by cadmium (Cd) in tobacco is described. From the analysis and annotation of the 1,271,256 Nicotiana tabacum fasta and quality files from methyl filtered genomic survey sequences (GSS) obtained from the TGI and ~56,000 ESTs available in public databases, an exon array with 272,342 probesets was designed (four probes per exon) and tested on two selected tobacco varieties. Two tobacco varieties out of 45 accumulating low and high cadmium in leaf were identified based on the GGE biplot analysis, which is analysis of the genotype main effect (G) plus analysis of the genotype by environment interaction (GE) of eight field trials (four fields over two years) showing reproducibility across the trials. The selected varieties were grown under greenhouse conditions in two different soils and subjected to exon array analyses using root and leaf tissue to understand the genetic make-up of the Cd accumulation. An Affymetrix Exon Array was developed to cover a large (~90%) proportion of the tobacco gene space. The Tobacco Exon Array will be available for research use through the Affymetrix array catalogue. As a proof of the exon array usability, we have demonstrated that the Tobacco Exon Array is a valuable tool for studying Cd accumulation in tobacco leaves. Data from field and greenhouse experiments supported by gene expression studies strongly suggested that the difference in leaf Cd accumulation between the two specific tobacco cultivars is dependent solely on genetic factors and genetic variability rather than on the environment. 22 samples were used with 3 different experimental factors: [1] 2 different tissues (leaves and roots/lateral), [2] 2 different mutations (V5 and V21), and [3] 2 different stimuli (Soil 1 and Soil 2). 2-3 biological replicates were used. One sample did not pass QC and is not included in this submission.
2012-11-16 | E-GEOD-42319 | biostudies-arrayexpress
Project description:To identify the regulatory steps that control chlorophyll accumulation, we compared gene expression in petals and leaves of chrysanthemum cultivars with different chlorophyll levels. Microarray analyses showed that the expression levels of chlorophyll biosynthesis genes encoding glutamyl-tRNA reductase, Mg-protoporphyrin IX chelatase, Mg-protoporphyrin IX monomethylester cyclase, and protochlorophyllorophyllide oxidoreductase were well associated with chlorophyll content: their expression levels were lower in white petals than in green petals, and were highest in leaves. Among chlorophyll catabolic genes, expression of STAY-GREEN, encoding Mg-dechelatase, which is a key enzyme controlling chlorophyll degradation, was considerably higher in white and green petals than in leaves. We searched for transcription factor genes whose expression was well related to chlorophyll level in petals and leaves and found several such genes.
2017-08-19 | GSE102752 | GEO
Project description:Purpose: Analyze changes in the transcriptome of Arabidopsis thaliana in response to sublethal concentrations of silver nanoparticles in order to gain insight into phytotoxicity caused by these nanomaterials. Methods: mRNA was extracted from non-treated and silver nanoparticle-treated 14-day old Arabidopsis thaliana seedlings using the RNAeasy extraction kit (Qiagen). RNA-seq libraries (3 rep/treatment and 3 reps/control) constructed with the TruSeq Stranded mRNA Sample Preparation kit (Illumina) were single-end sequenced (100-nt read length) on an Illumina HiSeq2500 system. Reads were mapped to the A. thaliana TAIR10 reference genome sequence and transcript levels were analyzed using the softare CLC Genomics Workbench (version 7.0.40, Qiagen). Results: Chronic exposure of A. thaliana plants to silver nanoparticles caused a change in abundance of transcripts involved in cell wall synhtesis and response to oxidative and biotic stress-related genes. Conclusions: While exposure to silver nanoparticle lead to gene expression changes, the reduction in chlorophyll concentration and carbon assimilation rate measured in exposed plants cannot be attributed to a shift in photosynthesis-related gene regulation.
2020-12-22 | GSE163583 | GEO
Project description:Plastid pigment metabolism is an important group of biological processes in senescent leaves. In addition, the pigments provide variegated color and serve as precursors for important flavor compounds. However, the molecular mechanisms of their metabolism and color regulation in postharvest tobacco leaves during the yellowing stage remain elusive. In this study, proteomic analyses involved in carotenoid and chlorophyll metabolism and color regulation were performed.
2020-01-06 | PXD016942 |
Project description:Comparative analysis of tobacco leaves transcriptomes unveils carotenoid pathway potentially determined the characteristics of aroma compounds in different environmental regions. Tobacco (Nicotiana tabacum) is a sensitive crop to environmental changes, and a tobacco with unique volatile aroma fractions always formed in specific ecological conditions. In order to investigate the differential expressed genes caused by environmental changes and reveal the formation mechanism of characteristics of tobacco in three different aroma tobacco regions of Guizhou Province, Agilent tobacco microarray was adapted for transcriptome comparison of tobacco leaves in medium aroma tobacco region Kaiyang and light aroma tobacco regions Weining and Tianzhu. Results showed that there was big difference among the gene expression profiles of tobacco leaves in different environmental conditions. A total of 517 differential expressed genes (DEGs) between Weining and Tianzhu were identified, while 733 and 1,005 genes differentially expressed between Longgang and another two tobacco regions Weining and Tianzhu, respectively. Compared with Longgang, up-regulated genes in Weining and Tianzhu were likely involved in secondary metabolism pathways, especially carotenoid pathway, including PHYTOENE SYNTHASE, PHYTOENE DEHYDROGENASE, LYCOPENE ε-CYCLASE, CAROTENOID β-HYDROXYLASE and CAROTENOID CLEAVAGE DIOXYGENASE 1 genes, while most down-regulated genes played important roles in response to temperature and light radiation, such as heat shock proteins. Gene Ontology and MapMan analyses demonstrated that the DEGs among different environmental regions were significantly enriched in light reaction of photosystem II, response of stimulus and secondary metabolism, suggesting they played crucial roles in environmental adaptation and accumulation of aroma compounds in tobacco plants. Through comprehensive transcriptome comparison, we not only identified several stress response genes in tobacco leaves from different environmental regions but also highlighted the importance of carotenoid pathway genes for characteristics of aroma compounds in specific growing regions. Our study primarily laid the foundation for further understanding the molecular mechanism of environmental adaptation of tobacco plants and molecular regulation of aroma substances in tobacco leaves.
2012-02-23 | GSE36008 | GEO