Many bands appear in a gel agarose containing chloroplast DNA because the chloroplast genome is complex and contains many different types of DNA molecules. These molecules include the large double-stranded circular DNA molecule that contains the chloroplast genes, a single-stranded circular DNA molecule containing the small ribosomal RNA (rRNA) genes, and several linear DNA molecules that contain the transfer RNAs (tRNA) genes. Each of these molecules has a different size and structure, so they form distinct bands when separated by electrophoresis.