What best explains why some eukaryotes with simplistic appearances have larger genomes?

The presence of tremendous amounts of noncoding DNA offers a compelling explanation for why some eukaryotes with simplistic appearances have larger genomes. Noncoding DNA consists of sequences that do not code for proteins but can serve various functions, such as regulatory roles in gene expression, structural roles in chromosomes, and potential evolutionary reservoirs for new genes. This noncoding DNA can accumulate over time, contributing significantly to genome size without necessarily correlating with the organism's complexity or the number of coding genes it possesses.

While the other factors may play a role in genome evolution, they do not directly account for the large amount of noncoding DNA that is often seen in simpler organisms. For instance, while the presence of numerous coding genes would generally correlate with genome size, this does not apply to organisms that may have large genomes yet fewer coding genes compared to more complex organisms. Higher mutation rates could increase genomic variability but would not inherently explain larger genome sizes. Similarly, increased genetic regulation complexity is more about how genes are expressed rather than the sheer size of the genome itself. Thus, the prominence of noncoding DNA is key to understanding this phenomenon.