C3 C4 grasses
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1062455 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
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
Project description:Analysis of the metabolism in mature leaves of Moricandia species with C3 and C3-C4 intermediate photosynthesis
2016-10-01 | GSE87343 | GEO
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. [Maize] Nine day old third leaves of maize were cut into fifteen 1 cm segments; samples were pooled from an average of seven plants per biological replicate and six biological replicates in total were collected on different dates. [Rice] 14 day old third leaves of rice were cut into eleven 2 cm segments, samples were pooled from an average of 15 plants per biological replicate and four replicates in total were collected.
2014-10-12 | E-GEOD-54274 | biostudies-arrayexpress
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
Project description:In multicellular systems changes to the patterning of gene expression drive modifications in cell function and trait evolution. One striking example is found in more than sixty plant lineages where compartmentation of photosynthesis between cell types allowed evolution of the efficient C4 pathway from the ancestral C3 state. The molecular events enabling this transition are unclear. We used single nuclei sequencing to generate a cell level expression atlas for C3 rice and C4 sorghum during photomorphogenesis. In both species a conserved cistrome was identified for each cell type and initiation of photosynthesis gene expression was conditioned by cell identity. Photosynthesis genes switching expression from mesophyll in rice to bundle sheath in sorghum acquire hallmarks of bundle sheath identity. The sorghum bundle sheath has also acquired gene networks associated with C3 guard cells. We conclude C4 photosynthesis is based on rewiring in cis that exapts cell identity networks of C3 plants.
2023-12-05 | GSE248919 | GEO
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
Project description:Photosynthesis in C3-C4 intermediate Moricandia species
| PRJNA344463 | ENA
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 | GSE146365 | GEO
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 | GSE145981 | GEO