Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Novel resources to investigate leaf plasmodesmata formation in C3 and C4 monocots

ABSTRACT: Novel resources to investigate leaf plasmodesmata formation in C3 and C4 monocots

PROVIDER: PRJNA1083800 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28225600_1.fastq.gz	Fastqsanger.gz
	SRR28225600_2.fastq.gz	Fastqsanger.gz
	SRR28225601_1.fastq.gz	Fastqsanger.gz
	SRR28225601_2.fastq.gz	Fastqsanger.gz
	SRR28225602_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 76

Similar Datasets

Novel resources to investigate leaf plasmodesmata formation in C3 and C4 monocots

Project description:Plasmodesmata (PD) are nanochannels that facilitate cell-to-cell transport in plants. More productive and photosynthetically efficient C4 plants form more PD at the mesophyll (M)-bundle sheath (BS) interface in their leaves than their less efficient C3 relatives. In C4 leaves, PD play an essential role in facilitating the rapid metabolite exchange between the M and BS cells to operate a biochemical CO2 concentrating mechanism, which increases the CO2 partial pressure at the site of Rubisco in the BS cells and hence photosynthetic efficiency. The genetic mechanism controlling PD formation in C3 and C4 leaves is largely unknown, especially in monocot crops, due to the technical challenge of quantifying these nanostructures with electron microscopy. To address this issue, we have generated stably transformed lines of Oryza sativa (rice, C3) and Setaria viridis (setaria, C4) with fluorescent protein-tagged PD to build the first spatiotemporal atlas of leaf pit field (cluster of PD) density in monocots without the need for electron microscopy. Across leaf development, setaria had consistently more PD connections at the M-BS wall interface than rice while the difference in M-M pit field density varied. While light was a critical trigger of PD formation, cell type and function determined leaf pit field density. Complementary temporal mRNA sequencing and gene co-expression network analysis revealed that the pattern of pit field density correlated with differentially expressed PD-associated genes and photosynthesis-related genes. PD-associated genes identified from our co-expression network analysis are related to cell wall expansion, translation and chloroplast signalling.

2024-11-21 | GSE260855 | GEO

Gene expression in the development of C3 and C4 Atriplex and C3 Atriplex prostrata x C4 Atriplex rosea F1 hybrids

Project description:Elucidating the genetic control of development of C3 and C4 photosynthesis. Atriplex rosea (C4) and Atriplex prostrata (C3) were studied along a leaf developmental gradient to compare development between C3 and C4. C3 Atriplex prostrata x C4 Atriplex rosea F1 hybrid were studied along the same developmental gradient and will aid in identifying regulatory elements involved in C3 and C4 leaf development.

2023-01-01 | GSE89920 | GEO

Photosynthesis in C3-C4 intermediate Moricandia species

Project description:Analysis of the metabolism in mature leaves of Moricandia species with C3 and C3-C4 intermediate photosynthesis

2016-10-01 | GSE87343 | GEO

Gene expression in C3 and C4 Atriplex leaves, roots, and stem, and C3xC4 F1 and F3 hybrid

Project description:Elucidating the genetic control of C3 and C4 photosynthesis. Atriplex rosea (C4) and Atriplex prostrata (C3) were at maturity to compare expression between C3 and C4 in leaves, stems, and roots. Their F1 hybrid leaf was studied at maturity and will aid in identifying regulatory elements involved in C3 and C4 leaf development. Two C3 Atriplex prostrata x C4 Atriplex rosea F3 hybrids (F3003 and F3036) were sequenced at a mature leaf stage.

2023-01-01 | GSE90100 | GEO

Exploring the mechanism of C4 photosynthetic differentiation through a unified comparative analysis of maize and rice leaf transcriptomes

Project description:Maize and rice are the two most economically important grass crops and utilize distinct forms of photosynthesis to fix carbon: C4 and C3 respectively. Relative to C3 photosynthesis, C4 photosynthesis reduces photorespiration and affords higher water and nitrogen use efficiencies under hot arid conditions. To define key innovations in C4 photosynthesis, we profiled metabolites and gene expression along a developing leaf gradient. A novel statistical method was implemented to compare transcriptomes from these two species along a unified leaf developmental gradient and define candidate cis-regulatory elements and transcription factors driving photosynthetic gene expression. We also present comparative primary and secondary metabolic profiles along the gradients that provide new insight into nitrogen and carbon metabolism in C3 and C4 grasses. These resources, including community viewers to access and mine these datasets, will enable the elucidation and engineering of C4 photosynthetic networks to improve the photosynthetic capacity of C3 and C4 grasses.

2014-10-12 | GSE54274 | GEO

C3 and C4 plants

Project description:C3 and C4 plants Genome sequencing and assembly

| PRJNA1158447 | ENA

Exploring the mechanism of C4 photosynthetic differentiation through a unified comparative analysis of maize and rice leaf transcriptomes

2014-10-12 | E-GEOD-54274 | biostudies-arrayexpress

Guard and Mesophyll cells transcriptomes in mature leaves of Gynandropsis gynandra (C4) and Tareneya hassleriana (C3).

Project description:We isolated and compared transcriptomes of GC and M from C3 T. hassleriana and C4 G. gynandra. This was achieved using laser-capture microdissection of each cell type from fixed paradermal sections. At least 2,500 cells were isolated for each replicate. RNA was extracted, amplified and subjected to RNAseq.

2016-01-10 | E-MTAB-3379 | biostudies-arrayexpress

Photosynthesis in C3-C4 intermediate Moricandia species

Project description:Photosynthesis in C3-C4 intermediate Moricandia species

| PRJNA344463 | ENA

The evolution of TF-regulatory network of core C4 metabolic pathway genes in the genus of Flaveria [ABA]

Project description:C4 photosynthesis was evolved from ancestral C3 photosynthesis by recruited pre-existed genes to perform new functions. Enzymes and transporters required for C4 metabolic pathway has been well documented, however, transcriptional factors (TFs) that regulate those C4 metabolic genes is poorly understood, in particular, how the TF regulatory network of C4 metabolic genes was re-wired, and the involved metabolic functions of those TFs along the evolution of C4 photosynthesis remained unknown. Here, by using RNA-Seq data from growth condition that reported to have effect on C4 photosynthesis, we constructed the TF regulatory network for four evolutionarily closely related species in the genus Flaveria, which represent different stages of the evolution of C4 photosynthesis, namely, C3, type I C3-C4, type II C3-C4 and C4. Our results show that four TFs are conserved along the evolution whose function either relate to stress response or light response. TFs regulating C4 core genes in C3 species involved in functions belong to RNA regulation and nitrogen metabolism, and that in both intermediate species and C4 species involved in photosynthesis and light responsiveness. Moreover, the TF-network of C4 core metabolic genes has the highest network density in type I C3-C4 species and C4 species when consider the fragment of TF-regulatory network that up-regulated under low CO2, suggesting that TFs regulating C4 genes were recruited to photosynthesis at type I C3-C4 both in involved functions and network density. Our results provide a valuable resource for studying molecular regulatory mechanisms underlying C4 metabolic process.

2020-07-28 | GSE137938 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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