AMD
Advanced Micro Devices, Inc. (AMD) is an American multinational corporation and fabless semiconductor company that designs, develops and sells computer processors and related technologies for business and consumer markets.
AMD's main products include microprocessors, motherboard chipsets, embedded processors, and graphics processors for servers, workstations, personal computers, and embedded system applications. The company has also expanded into new markets, such as the data center, gaming, and high-performance computing markets. AMD's processors are used in a wide range of computing devices, including personal computers, servers, laptops, and gaming consoles.
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The version is no issue for compatibility, correct. The only effect it may have is bottlenecking. PCIe is a very 'dumb' protocol: it doesn't affect any kind of features because the feature set is all handled in either the chipset or the expansion card. The only thing that ever gets an upgrade in PCIe standards is the bandwidth and all kinds of stability improvements that you really won't notice unless you are a power user.
If you want, you can put Nvidia's new 5090 in a PCIe 2.0 x16 slot and it'll function properly. You can also put a PCIe 4.0 SSD in a PCIe 6.0 slot and it'll work fine. Really the only thing you have to worry about is whether the lanes provide enough bandwidth for the expansion card to use all of its power.