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SINGAPORE—Chinese e-commerce company Pinduoduo Inc.’s founder and chairman, Colin Huang, stepped down from the company on Wednesday, even as the five-year-old company overtook Alibaba Group Holding Ltd. to become the country’s largest e-commerce company by annual active buyers.

Mr. Huang, 41 years old, is resigning as China’s powerful internet sector comes under growing government scrutiny. His resignation follows another departure from a major company in the sector: Financial-tech giant Ant Group Co.’s Chief Executive Simon Hustepped down earlier this month.

In a letter to shareholders, Mr. Huang said he was stepping down to pursue personal interests in life sciences. He is in talks with Chinese universities to set up research labs on biotechnology, a person familiar with the matter said. For his next step, he will study biotechnology at these labs, the person said.

Mr. Huang said that the board approved his resignation as the chairman on Wednesday. Chief Executive Officer Chen Lei will take on the additional role of chairman of the Nasdaq-listed company.

Shares of Pinduoduo dropped after the announcement. They were down around 11% midmorning Wednesday.