Hey Angel,
most of the 25-pin I/O port connector pins are directly connected to the AVR (ATXMEGA192A3U (datasheet)) on the AVR board, so are 3.3 V. Regarding pins 13 and 14 for the Modbus serial communication interface, there is a ISL83485 RS-485 Transceiver running with 3.3 V supply that can deliver -8V to +12.5V, with a Bourns SRF2012A-121YA common mode inductor on these two pins.