It does depend on motherboard, PCI-E and PCI-E NVMe support varies.
If your MB fully supports PCI-E drives, it's going to be much faster than SATA drives, though, a single PCI-Ex4 NVMe drive can be as fast as dual SATA drives in a RAID configuration!
Unless you're doing serious work that demands the fastest possible storage access and throughput it's not really worth the expense of swapping a motherboard to get the extra performance, though, for most of even a stock SATA 6Gb/s drive is fast enough.