Eukaryotic introns, gene mapping, RNA-Seq

Hi! Forgive me if this information is already accessible somewhere. I’ve searched around and haven’t been able to find an answer to this question. The ChocoPhlAn 3 database contains eukaryotic species. Do the eukaryotic marker genes that MetaPhlAn maps to contain introns in their sequences? If so, what happens when running RNA-Seq reads through MetaPhlAn? If not, what happens when running DNA-Seq reads? How does the presences of introns in eukaryotic sequences affect DNA-Seq vs. RNA-Seq read processing through HUMAnN? Thanks!