Some genomes are particularly challenging for scientists to piece back together using just short, overlapping DNA sequences. In particular, genomes from some organisms have an unusual amount of repetitive sequences, stemming from gene, chromosome, and even whole genome duplication events. Plants are often challenging in this way, and cotton—with two complete genomes that are very similar—presents an even greater challenge.
To solve challenging genomes, researchers can make what are called “physical maps.” These low-resolution maps don't have sequence-level detail, but they do have information about the spacing between specific, short segments of DNA. Physical maps serve as sort of a rough scaffold on top of which the sequence-level information can be assembled.