PXD061385-1

PXD061385 is an original dataset announced via ProteomeXchange.

Title	Clusia genomes shed light on the evolution and diversity of CAM physiotypes
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.
HostingRepository	PRIDE
AnnounceDate	2026-03-12
AnnouncementXML	Submission_2026-03-12_13:33:59.445.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Hannes Kramml
SpeciesList	scientific name: Clusia rosea; NCBI TaxID: NEWT:156476; scientific name: Clusia major; NCBI TaxID: NEWT:180923; scientific name: Clusia minor; NCBI TaxID: NEWT:156471;
ModificationList	acetylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2025-03-03 02:34:26	ID requested
⏵ 1	2026-03-12 13:33:59	announced

Dataset with its publication pending

submitter keyword: diploidization,CAM plant evolution, Clusia, polyploidy

Wolfram Weckwerth
contact affiliation	Molecular Systems Biology (MoSys), Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
contact email	wolfram.weckwerth@univie.ac.at
lab head
Hannes Kramml
contact affiliation	Molecular Systems Biology (MoSys), Department of Functional and Evolutionary Ecology, University of Vienna
contact email	hannes.kramml@univie.ac.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD061385
     1. Label: PRIDE project
     2. Name: Clusia genomes shed light on the evolution and diversity of CAM physiotypes