Leafy liverwort genomes shed light on the evolution of ericoid symbiosis
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ABSTRACT:
PROVIDER: PRJEB86056 | ENA |
REPOSITORIES: ENA
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Project description:The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago. This symbiosis is still widely found across major land plant lineages, including bryophytes. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. Here, we demonstrate that a broad AM genetic programme is conserved amongst land plants. In this study, we characterised the dynamic response of the liverwort Marchantia paleacea to Rhizophagus irregularis colonization by time-resolved transcriptomics across three stages of symbiosis. Comparative analysis of transcriptional responses to symbiosis in the liverwort M. paleacea and the legume Medicago truncatula further revealed evolutionarily conserved expression patterns for genes underpinning pre-symbiotic signalling, intracellular colonization and nutrient exchange. This study demonstrates that the genetic machinery regulating key aspects of symbiosis in plant hosts is largely conserved and coregulated across land plants.
2024-08-08 | GSE245702 | GEO
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: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.
2026-03-13 | GSE290226 | GEO
Project description:Root nodule symbiosis (RNS) represents a significant phenotypic adaptation in plants to thrive in nitrogen-deficient environments. Recent findings propose a single gain of RNS at the crown of the nitrogen-fixing clade (NF clade). However, the genetic mechanisms underlying the origin and subsequent evolution of RNS remain largely unexplored. Here, we newly sequenced and assembled eleven genomes from the NF clade and studied genetic change along the evolution of RNS. Our results elucidated three key evolutionary stages leading to the formation of stable RNS between plants and symbiotic nitrogen-fixing bacteria.
2025-12-23 | GSE264605 | GEO
Project description:Root nodule symbiosis (RNS) represents a significant phenotypic adaptation in plants to thrive in nitrogen-deficient environments. Recent findings propose a single gain of RNS at the crown of the nitrogen-fixing clade (NF clade). However, the genetic mechanisms underlying the origin and subsequent evolution of RNS remain largely unexplored. Here, we newly sequenced and assembled eleven genomes from the NF clade and studied genetic change along the evolution of RNS. Our results elucidated three key evolutionary stages leading to the formation of stable RNS between plants and symbiotic nitrogen-fixing bacteria.
2025-12-23 | GSE264604 | GEO
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