What exactlly do you mean by gene mapping? Like looking for new genes?

The differences probably come from differences in DNA structure 😉 Like operons × exons/introns

Let me see…
Well there’s difference in sequences of promoters:-35 and -10 regions in Bacteria and TATA box (-30) in eukaryotes.So you could scan on computer the whole genome..also search for ORF(open reading frames).Also eukaryotic genes are composed of coding AND noncoding regions(introns that start with GU and finish with AG).Introns are later spliced.Bacterial genes order can be roughly determined by measuring gradient of transfer in conjugation(first gene present in 100% cases,second in for example 70% etc).You could in both cases use probes for orientation if you need to fragment genome and clone parts.
Anyway first search for conserved domains..and use cDNA (you get from mRNA) whenever possible as a probe.
Cheers! 🙂