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Abstract: Structure and properties of pyrenoid and stroma starch were compared in Chlorella. To obtain pyrenoid starch- and stroma starch-enriched samples of high purity, we investigated the effects of the CO2 concentration and growth phase on the intracellular amount and localization of starch. In cells grown with air containing 3% CO2 (high-CO2 cells) at the log phase, starch was accumulated primarily as stroma starch. When these high-CO2 cells were transferred to low-CO2 conditions (air level, 0.04% CO2), pyrenoid and pyrenoid starch started to develop within several hours. After 12h, the amount of starch per cell had increased to about 2.5-fold of that in the high-CO2 cells, the size of starch granules drastically increased (about 2.5-fold in diameter), and the morphology changed from discoidal to cup-shaped, suggesting that the cells predominantly contained pyrenoid starch. The starch composition and chain-length distribution profile did not change so much within 12h. However, analysis of the starch with a differential scanning calorimeter demonstrated that the peak temperature of gelatinization was significantly decreased as compared with that in the high-CO2 cells. These findings suggest that pyrenoid and stroma starch have distinctive physicochemical properties that are caused by the difference in the water absorption and swelling ratio of starch granules mainly due to the difference in the morphology. [Copyright &y& Elsevier]