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They come from the USB PHY. Microchip USB3320. You should read through that datasheet to ensure you understand the part and if there is anything special you would need to do in the case of what you are doing / not doing with it.
As for the GTRs, you can see in Table 4-2 of UG583 UltraScale Architecture PCB Design User Guide (page 192) will provide proper instruction for the GTRs: