If you file separately, you will each have two separate accounts with the IRS for that year. If you file Married Filing Jointly, then you will have one combined account.
If your spouse is a resident alien, as KarenJ2 says above, it should not be an issue filing jointly. She will need an ITIN or Social Security number. You can see more about getting an ITIN or Social Security number here.
Filing jointly means that all her worldwide income is taxable in the US. There are credits for foreign taxes paid on income taxes.
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