While in RNAseq an enrichment of sequences is associated with increased gene expression, what is the interpretation of an enrichment of sequences in whole genome sequences?

In particular, what does it mean if one does not get whole genomes but only a few genes?

It looks to me that there is a fragmentation of genomes. Does this mean that there are more cells or micro-organisms containing these genes (then why there is no the whole genome?) or is it just an artifact?

Thank you