c. How might an abundance of TEs in eukaryotic genomes have contributed to the p
ID: 214185 • Letter: C
Question
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 (e.g., 100bp) reads available from 2nd generation sequencing technologies. Describe a method, using 2nd generation sequencing technology designed to combat these issues and ensure more accurate assembly of genomes that include many transposable elements (even large ones), and describe why this should improve genome assembly.
Explanation / Answer
Eukaryotic species show enormous variation in the amount of TEs occupying their genomes. DNA transposons may also contribute substantially to genome expansion. An estimated 65% of the genome of the single-celled eukaryote Trichomonas vaginalis, which was recently sequenced, is made of repetitive DNA. Tremendous variation also exists among species in the relative abundance of DNA transposons and retrotransposons, regardless of their sheer numbers. Yet DNA transposons are common in filamentous fungi and occur occasionally in other yeasts, such as Candida albicans (36). Thus, two independent extinction events of DNA transposons occurred in the lineages leading to Saccharomyces cerevisiae and Schizosaccharomyces pombe. With a haploid genome size of ~2,000 Mb, M. lucifigus is one of the smallest mammalian genomes, but it harbors a surprisingly diverse collection of DNA transposons that is also distinct from other mammalian genomes examined.
The Second generation sequencing techniques are very slow and as the transposable elements keep on moving they hinder the process of DNA assembly. Illumina sequencing is a second generation tech, and it has many disadvantages. Firstly, because it takes so long to produce a single base pair, and because the different molecules in the cluster can get out of sync, it is impossible to sequence long bits of DNA. Mostly, the read length is under 100bp, much less than the 500-1000bp that you can get from Sanger sequencing.
454 sequencing is another second generation sequencing method that gets around this: instead of using dyes they use nucleotides that flash when the polymerase adds them to the DNA; they can get read lengths of greater than 500bp, getting close to Sanger sequencing. However, while 454 has a) longer read lengths b) a cooler name and c) a cooler sequencing method, it cannot rival Illumina for sheer amount of DNA sequenced per unit time.
Secondly, because it is very easy for the polymerase enzyme to add in the wrong RT-base, Illumina sequencing has a relatively high error rate (1-2% per base).
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