Ontology highlight
ABSTRACT:
PROVIDER: PRJNA915757 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22892300_1.fastq.gz | Fastqsanger.gz | |||
| SRR22892300_2.fastq.gz | Fastqsanger.gz | |||
| SRR22892301_1.fastq.gz | Fastqsanger.gz | |||
| SRR22892301_2.fastq.gz | Fastqsanger.gz | |||
| SRR22892302_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 15 |
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Project description:Crassulacean acid metabolism (CAM) is a water-use efficient adaptation of photosynthesis that has evolved independently many times in diverse lineages of flowering plants. We hypothesize that convergent evolution of protein sequence and temporal gene expression underpins the independent emergences of CAM from C3 photosynthesis. To test this hypothesis, we generated a de novo genome assembly and genome-wide transcript expression data for Kalanchoe fedtschenkoi, an obligate CAM species within the core eudicots with a relatively small genome (~260 Mb). Our comparative analyses identified signatures of convergence in protein sequence and re-scheduling of diel transcript expression of genes involved in nocturnal CO2 fixation, stomatal movement, heat tolerance, circadian clock and carbohydrate metabolism in K. fedtschenkoi and other CAM species in comparison with non-CAM species. These findings provide new insights into molecular convergence and building blocks of CAM and will facilitate CAM-into-C3 photosynthesis engineering to enhance water-use efficiency in crops.
2018-01-09 | MTBLS519 | MetaboLights
Project description:Kalanchoe blossfeldiana cultivar:Kalanchoe blossfeldiana Poelln Genome sequencing and assembly
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Project description:More than 200 years ago, Alexander von Humboldt documented his first observations of a peculiar phenomenon in Clusia rosea (Clusiaceae), the first tree known to perform crassulacean acid metabolism (CAM). Since then, the photosynthetic and ecophysiological plasticity of Clusia species have captivated the minds of plant scientists worldwide. CAM is a physiological adaptation to low water availability. While stomata are closed during the day, RuBisCO is supplied with CO2 via decarboxylation of organic acids that have been stored and synthesized during the night by phosphoenolpyruvate carboxylases (PEPC). How the physiological reprogramming necessary for CAM evolved remains enigmatic. Photosynthetic physiotypes of CAM, including weak CAM, inducible CAM, and CAM-cycling have additionally fueled a debate on the evolutionary constraints of CAM and the prospects of engineering CAM into C3 crops. Here, we de novo sequenced the genomes of three Clusia species to capture genetic snapshots along an evo-ecophysiological continuum from weak over inducible to strong CAM. Through a combination of chromosome level assembly and annotation, comparative multiomics, and physiological phenotyping, we identify a strong association between diploidization of polyploids and the physiotype diversity of CAM. We illustrate that Clusia major, a plant that seems to exhibits a C3-type mode of photosynthesis, retained almost all hallmarks of CAM. Transposon-mediated genic diploidization, however, acted upon homoeologs in CAM-related gene families, particularly those involved in phosphoenolpyruvate (PEP) recycling via phosphorolytic leaf starch metabolization. In effect, this rendered a plant capable of C3+CAM with open stomata during the day by shifting carbohydrate supply (PEP) to viable soluble sugars. Our findings indicate that polyploidization during genus evolution and subsequent diploidization shaped the emergence of extant physiotypes in Clusia.
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Project description:<p>225 years ago, Alexander von Humboldt observed the first crassulacean acid metabolism (CAM) tree, Clusia rosea (Clusiaceae). Since then, the photosynthetic and ecophysiological plasticity of Clusia</p><p>species have captivated the minds of plant scientists worldwide. CAM is a physiological adaptation to low water availability. While stomata are closed during the day, RuBisCO is supplied with CO2 via</p><p>decarboxylation of organic acids that have been stored and synthesized during the night by phosphoenolpyruvate carboxylases (PEPC). How the physiological reprogramming necessary for CAM</p><p>evolved remains enigmatic. Photosynthetic physiotypes of CAM, including weak CAM, inducible CAM, and CAM-cycling have additionally fueled a debate on the evolutionary constraints of CAM and the prospects of engineering CAM into C3 crops. Here, we de novo sequenced the genomes of three Clusia species to capture genetic snapshots along an evo-ecophysiological continuum from weak over inducible to strong CAM. Through a combination of phased chromosome level assembly and annotation, comparative multiomics, and physiological experiments, we demonstrate that diploidization of polyploids explains the physiotype diversity of CAM. We illustrate that Clusia major, a plant that exhibits a C3-type mode of photosynthesis, retained almost all hallmarks of CAM. Transposon-mediated genic diploidization, however, acted upon homoeologs in CAM-related gene families, preferentially those involved in phosphoenolpyruvate (PEP) recycling via phosphorolytic leaf starch metabolization. In effect this rendered a plant capable of constitutive C3+CAM with open stomata during the day by shifting carbohydrate supply (PEP) to viable soluble sugars. Our findings indicate that polyploidization during genus evolution and subsequent diploidization shaped the emergence of extant C3+CAM physiotypes in Clusia. This study of evolutionary intermediates provides crucial insights into the convergent evolution of physiotype diversity and plasticity of CAM.</p>
2026-03-23 | MTBLS14075 | MetaboLights
Project description:225 years ago, Alexander von Humboldt documented his first observations of a peculiar phenomenon in Clusia rosea (Clusiaceae), the first tree known to perform crassulacean acid metabolism (CAM). Since then, the photosynthetic and ecophysiological plasticity of Clusia species have captivated the minds of plant scientists worldwide. CAM is a physiological adaptation to low water availability. While stomata are closed during the day, RuBisCO is supplied with CO2 via decarboxylation of organic acids that have been stored and synthesized during the night by phosphoenolpyruvate carboxylases (PEPC). How the physiological reprogramming necessary for CAM evolved remains enigmatic. Photosynthetic physiotypes of CAM, including weak CAM, inducible CAM, and CAM-cycling have additionally fueled a debate on the evolutionary constraints of CAM and the prospects of engineering CAM into C3 crops. Here, we de novo sequenced the genomes of three Clusia species to capture genetic snapshots along an evo-ecophysiological continuum from weak over inducible to strong CAM. Through a combination of phased chromosome level assembly and annotation, comparative multiomics, and physiological experiments, we demonstrate that diploidization of polyploids explains the physiotype diversity of CAM. We illustrate that Clusia major, a plant that exhibits a C3-type mode of photosynthesis, retained almost all hallmarks of CAM. Transposon-mediated genic diploidization, however, acted upon homoeologs in CAM-related gene families, preferentially those involved in phosphoenolpyruvate (PEP) recycling via phosphorolytic leaf starch metabolization. In effect this rendered a plant capable of constitutive C3+CAM with open stomata during the day by shifting carbohydrate supply (PEP) to viable soluble sugars. Our findings indicate that polyploidization during genus evolution and subsequent diploidization shaped the emergence of extant C3+CAM physiotypes in Clusia. This study of evolutionary intermediates provides crucial insights into the convergent evolution of physiotype diversity and plasticity of CAM.
2026-03-12 | PXD061385 | Pride
Project description:Already a proven mechanism for drought sustainability, crassulacean acid metabolism (CAM) is a specialized type of photosynthesis that maximizes water-use efficiency (WUE) via an inverse (compared to C3 and C4 photosynthesis-performing species) day/night pattern of stomatal closure/opening to shift CO2 uptake to the nighttime, when evapotranspiration rates are low. A systems-level understanding spanning temporal molecular and metabolic controls is needed to define the cellular behavior that confers advantages in water-limited conditions. Here, we report high-resolution temporal behaviors of transcript, protein, and metabolite abundances across a CAM diel cycle and, where applicable, compare those observations to the well-established C3 model plant, Arabidopsis thaliana. A mechanistic finding that emerged is that CAM operates with a shifted altered redox poise relative to Arabidopsis thaliana. Moreover, we identify widespread rescheduled expression for genes associated with signal transduction mechanisms that are presented in guard cells to regulate stomatal opening/closing. Controlled production and degradation of transcript and proteins is a timing mechanism by which to regulate cellular function, yet knowledge of how this molecular timekeeping regulates CAM physiology is unknown. Here, we provide new insight into complex, post-transcriptional and -translational hierarchies that govern CAM in Agave. These data sets together provide a resource that could inform efforts to engineer traits of the more efficient CAM plant into economically valuable C3 crops.
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Project description:Transcriptomes from Yucca species using C3 and CAM photosynthesis
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Project description:Total protein data for the salt-induced C3 to CAM transition in ice plants.
2025-05-31 | MSV000098059 | MassIVE