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C4 photosynthesis has been uncovered in both terrestrial and aquatic plants. However, the extent to which C4 photosynthesis serves as an adaptation to submerged environments in aquatic plants remains elusive. Here, we studied the heterophyllous aquatic plant Nuphar pumila, which has phenotypically distinct leaves depending on the level of submergence. By applying 13C labeling experiments, submersed leaves of N. pumila were shown to exhibit both C4 and C3 photosynthesis, whereas floating leaves are limited to C3 photosynthesis. Leaf-specific single-cell trajectories of epidermal and bundle sheath cells show that, in contrast to terrestrial C4 plants, CO2 fixation in C4 photosynthesis in submersed leaves primarily occurs in the epidermal cells rather than in the mesophyll cells, allowing the leaves to cope with limited inorganic carbon in water. The combined presence of C3 and C4 photosynthesis, along with tissue-specific adaptations in the heterophyllous aquatic plant N. pumila, demonstrates how C4 photosynthesis in aquatic environments likely evolved as an adaptive trait from C3 photosynthesis.<\/jats:p>","DOI":"10.1093\/plphys\/kiag635","type":"journal-article","created":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T12:43:34Z","timestamp":1787921014000},"source":"Crossref","is-referenced-by-count":0,"title":["Single-cell transcriptomics unveils photosynthetic adaptation in submersed leaves of heterophyllous\n                    <i>Nuphar pumila<\/i>"],"prefix":"10.1093","volume":"202","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2674-0341","authenticated-orcid":false,"given":"Yue","family":"Zhang","sequence":"first","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074 ,","place":["China"]},{"name":"Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074 ,","place":["China"]},{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052 ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2397-8269","authenticated-orcid":false,"given":"Marie","family":"Van Hecke","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052 ,","place":["Belgium"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jingru","family":"Che","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5840-007X","authenticated-orcid":false,"given":"Hongsheng","family":"Jiang","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1907-3552","authenticated-orcid":false,"given":"Tao","family":"Shi","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6743-2639","authenticated-orcid":false,"given":"Jun","family":"Ding","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074 ,","place":["China"]},{"name":"Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4310-2544","authenticated-orcid":false,"given":"Wei","family":"Li","sequence":"additional","affiliation":[{"name":"Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qingfeng","family":"Wang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences , Wuhan 430074 ,","place":["China"]},{"name":"Sino-African Joint Research Center, Chinese Academy of Sciences , Wuhan 430074 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yves","family":"Van de Peer","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052 ,","place":["Belgium"]},{"name":"VIB-UGent Center for Plant Systems Biology , Ghent 9052 ,","place":["Belgium"]},{"name":"Department of Biochemistry, Genetics and Microbiology, University of Pretoria , Pretoria 0028 ,","place":["South Africa"]},{"name":"College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University , Nanjing 210095 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2169-4588","authenticated-orcid":false,"given":"Kathleen","family":"Marchal","sequence":"additional","affiliation":[{"name":"Department of Plant Biotechnology and Bioinformatics, Ghent University , Ghent 9052 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