Polytene chromosomes, also known as giant chromosomes, are unusual chromosomes. They were discovered to be located in the nuclei of cells in the salivary gland, in third instar larvae, of two-winged (dipteran) flies and other specific tissues in Diptera. These special chromosomes are found in the two-winged (dipteran) fruit fly (Drosophila melonagaster).
Polytene chromosomes are formed by the repeated replication of homologous chromosomes, in which the replicated individual sister chromatid strands do not separate. Polytene chromosomes have approximately 1000 identical DNA molecules, which are all perfectly aligned laterally within the structure. Found to be formed in the "terminal cells" of the larva, these Polytene structures are abnormal chromosomes. These terminal cells are removed when the dipteran move into the next stage of their life cycle: the formation of the pupa. The terminal cells cannot divide and hence, they are eliminated.
The polytene chromosomes have been proven very useful in developing cytological maps. These cytological maps are in-depth and very detailed. They are produced when the chromosomes are stained and viewed under a light microscope, making visible alternating dark bands and light interbands. The dark bands are due to the side-by-side arrangement of tightly folded regions of chromatin strands. These are often seen in miotic and meiotic chromosomes as chromomeres. The light bands are known as the interbands and more DNA is found within the bands rather than in the interbands.