Balbiani (1881) discovered Polytene chromosome in the salivary glands of insect larva. Polytene chromosomes are a type of Giant chromosomes, which are formed due to replication of chromosomes without cell divisions called endomitosis. The strands of DNA are held together due to synapsis and forms structure which are bigger than normal chromosomes. The centromeres of all chromosomes form a highly condensed structure called chromocentre making arms of the chromosomes holding together as in case of Drosophila. In certain species of insects like mosquitoes, the chromocenter is not highly condensed and each arm is separated during the cytological preparations. A polytene chromosome occurs in tissues of salivary glands, malpighian tubules, and intestine of Dipteran insects. Polytene chromosomes are observed in Insects, Mammals and also in Plants.

Polytene chromosomes occur in cells which have to express more gene products. The cells having polytene chromosomes are polyploidy in nature. The number of strands in polytene chromosome varies and they are around 1024 strands in Drosophila due to 9 rounds of replications of each chromosome. Polytene chromosomes has specialized structures called puffs, which is an active gene expressing region. Puffs are dynamic in nature and depending on the different stages of organism and environmental stress, the size and position changes. Larger puffs are called Balbiani rings. The Chromosome synapsis is observed only in meiosis and in mitosis, chromosome synapsis is seen only in polytene chromosome, where homologues chromosomes are held together during process of polytinization. Polytene chromosomes express more gene products that are required for development and morphogenesis of the organisms. Usually the polytene chromosomes are present in insect's last larval stage where more proteins are required in pupal development. Polytinization helps the organism to conserve the energy during the development where the cells only increases the DNA content and cell division phase is eliminated, there by conserving the energy and time that is required in cell division as the development phase is shorter in insects.

The Drosophila polytene chromosome consists of 5 arms with one chromocenter. The diploid number of chromosomes in Drosophila is 2n=8. The first pair is allosome and the rest three are autosomes. The fourth chromosome is a short acrocentric chromosome and X chromosome is also an acrocentric and Y is heterochromatic sub meta centric and 2nd and 3rd autosomes are meta centric. During the process of polytinaization, all the centromeres of 4 chromosomes are fused to form chromocenter. The 5 arms of polytene chromosome in Drosophila are designated as 2L, 2R, 3L, 3R and X. Since the short arm of X chromosome is highly heterochromatin, it becomes part of chromocenter. The 4th chromosome has less euchromatin, hence this also becomes part of chromocenter. In males, the Y chromosome is also highly heterochromatin and become part of chromocenter. Therefore polytene chromosome of Drosphila has 5 arms from 8 chromosomes.

Polytene chromosomes have wide application in the field of cytology, gene expression, evolution and speciation. Due the size of the polytene chromosomes, chromosomal aberrations such as inversions, duplications, and deletions can be easily identified. The polytene chromosome arms when stained with dye have specific patterns called bands. The bands are developed due to euchromatin and heterchromatin nature of DNA. The light bands are the regions of euchromatin and dark bands are the region of heterochromatin. These bands are characteristic of each chromosome arms and also specific to individual species. Based on the banding pattern of polytene chromosome, the chromosomes are identified and due to its specific banding pattern species are identified.

The sub species identification is a major challenge in taxonomy, the banding pattern in the polytene chromosome helps in sub species identification as banding patterns of the chromosome arms are unique to each sub species. Further the bands helps in detecting chromosomal aberrations such as deletions and duplications. It is interesting to observe the chromosomal aberrations type inversions, where certain portion of DNA in one of the homologues chromosome is inverted and during mitotic synapsis in polytene chromosome, the inverted region form a loop which can be easily detected in microscopic observations. Further study of inversions has great importance in arthropods as the inversions are sometimes associated with speciation and insecticide resistance development. As the polytene chromosomes are large in size, gene identification with hybridization technique is much easier to view in microscope.

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