Polytene Chromosomes, also known as giant chromosomes, are unusual chromosomes. They where 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. An example of a two- winged (dipteran) fly that these special chromosomes are found in is the fruitfly (Drosophila melonagaster). Polytene chromosomes are formed by the repeated replication of homologous chromosomes , in which the replicated individual chromatid strands do not separate. Polytene chromosomes have approxiamtely 1000 identical DNA molecules, which are all perfectly aligned laterally within the polytene structure. These polytene structures are abnormal chromosomes which are found to be formed in the "terminal cells" of the larva. 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 this is why they are eliminated.
The polytene chromsomes have been proven very useful in developing cytological maps. These cytologoical 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 arrnagement of tightly folded regions of chromatin strands . These are often seen in miotic and meiotic chromosomes as chromomeres. The light bands are known a the interband and more DNA is found within the bands rather than in the interbands.