Hello @alaahamo,
A pure SPI communication based on Commands, Responses and Events is used to connect with host controller for configuration, NFC data exchange and high-level NFC protocol implementation. More information on this can be found in PN5190 instruction layer.
Key handling will depend on your setup/hardware; for example, you could consider using a MIFARE SAM. These devices offer secure storage and strong protection of highly sensitive keys.
If you are looking for information about DESFire devices, as some of the information and software supporting DESFire is under NDA (Non-Disclosure Agreement), the information is not public, and it is secured under Secure Files. Please consult the Non-Disclosure Agreement FAQs and Secure Access Rights | NXP Semiconductors for more information.
Regards,
Eduardo.