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I'm still not clear of what you are asking, is it a USB bootloader similar to arduino or are you asking for the actual arduino bootloader
If thew question is about arduino you can find all relevant info https://www.arduino.cc/
if not check https://www.obdev.at/products/vusb/usbasploader.html but note that you will need a programmer to program the bootloader to the AVR in both cases
did you mean that you are gonna communicated your microcontroller w/ PC? if the case like that its plenty ways i.e. you can use usb to ttl(simple one) or ou can use rs232 interfaced with db9.. how it works? just google it CMIIW