Pearls are the only 'gems' produced by a living organism. Their formation process (either by natural means or through human intervention) is a response to an injury in an oyster's 'mantle' tissue, such as an intrusion by a foreign body, e.g. a sand grain etc.

The exact mechanisms for the glossy pearl formation are unclear.

Nature's ability to generate so amazingly complex structures like a pearl is impressive and still partially unknown.

[…] Such a challenge will strongly encourage the community to continue to develop approaches and knowledge to decipher the biophysical and molecular details of biomineralization processes.

[…] our fundamental understanding of nacre formation remains limited. Few studies are available that explain the pearl mineralization process as well as the formation of defects […]"

Source : Yes, it turns: experimental evidence of pearl rotation during its formation Royal Society, Open Science

The 2105 study from Université de la Polynésie Française experimentally demonstrated, for the first time, that pearls rotate inside the oyster during their formation - perhaps contributing to their rounded form.

Note: As the quote above explains, the formation of nacre - the material which forms not only pearls but also the shells of marine molluscs in general - has not been fully explained.