The Arduberry connects the Raspberry Pi with Arduino shields. The Arduberry uses the GPIO headers on the Raspberry Pi to communicate with the Atmega 328 (it does not use USB). It does have the same pinout as the Arduino Uno, and it uses the same chip.
The Arduberry is connected to the Raspberry Pi over Serial, I2C, and SPI. Firmware is loaded to the Arduberry chip using the SPI lines.
Also as a bonus, the Arduberry works with the Raspberry Pi models B, B+ 2, 3, A, and Zero.
There is extensive documentation for the Arduberry on the Dexter Industries website, as well as extensive examples, hardware design files, and information on how to use the Arduberry on Github here.