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Oishi et al. report that the synthesis of a betaine lipid, diacylglyceryl-N,N,N-trimethylhomoserine (DGTS) in a green alga Chlorella kessleri replaces phosphatidylcholine and phosphatidylethanolamine, the two most abundant phospholipids, during phosphate deprivation. This study provides insights into the understanding of the phosphorus-deficiency acclimation strategies via lipid remodeling in lower green plants.