Transposable elements comprise more than 50% of the human genome and for many ye

Question

Transposable elements comprise more than 50% of the human genome and for many years were referred to as "junk DNA". a. Explain a recent prevailing hypothesis for why genomes like ours (and also plants, for example) might tolerate such large amounts of "junk". b. Provide two compelling reasons why these transposable element sequences might have a major impact on genome function (and thus might be functionally important). c. How might an abundance of TEs in eukaryotic genomes have contributed to the phenotypic complexity and diversity in higher eukaryotes, such as vertebrates. Specifically, give 2 examples. d. Briefly explain how an abundance of recently active Transposable Elements (TEs) can complicate assembly of short reads available from 2^nd generation sequencing technologies. Describe a method, using 2^nd generation sequencing technology, by which is designed to significantly combat these issues and ensure more accurate assembly of recent TEs (even large ones), and describe why this should improve genome assembly.

Explanation / Answer

A. According to a recent prevailing hypothesis about TE, they are no longer considered as junk. The TE are the mobile elements which can have a profound effect on the evolution of genome and the regulation of gene expression. Therefore the genomes tolerate such a high level of TE.

B. These mobile elements - TE when inserted at a new site in the genome may cause a genomic change.This position shift effects the gene function in following two ways:

C. The phenotypic diversity between the individuals and various species of higher eukaryotic animals such as the vertebrates, are due to the differences in

Both of these are affected by TE. Since, the genetic makeup of an organism affects the phenotype, the TE which regulate the gene expression are indirectly the cause of the phenotypic diversity. This can be evident from the following examples regarding the higher eukaryotes:

D. The second generation sequencing needs a reference genome. If the organism from which the genome is read, has a lot of TE, then it affects the ultimate result of assembly of short reads available from the 2nd generation sequencing by complicating the reference to be read. To overcome these issues the 2nd generation sequencing reverses the telomere repeats and the also uses the 454 sequencing method to ensure accurate assembly of TE. It uses a methods in which instead of using dye, the flashing nucleotides are used which offer uncomplicated and error free sequencing. When the DNA pol adds a new nucleotide during the 2nd generation 454 method of sequencing, they automatically get flashed which make it convenient to read. When the sequencing is error free it automatically improves the genome assembly.

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