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Home > History and Archaeology > History > Strategy for Prokaryotic Genome Sequencing: (English)
Strategy for Prokaryotic Genome Sequencing: (English)

Strategy for Prokaryotic Genome Sequencing: (English)

          
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About the Book

This dissertation, "Strategy for Prokaryotic Genome Sequencing" by Jingwei, Jiang, 江经纬, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. Abstract: Prokaryotes are single-cell microorganisms. These creatures can be further classified to bacteria and archaea. Their DNA genetic meterials are spread around the cytoplasm rather than residing in the nucleus. Unlike eukaryotes, a high percentage of prokaryotic genome is composed of genes. The evolution of prokaryotes is different from that of the eukaryotes. Prokaryotes are found almost everywhere including the harshest environments on Earth. Understanding the whole pictures of their genomes will benefit us a lot in terms of new enzyme discovery, decoding drug resistance, biofuel development, etc.  High-throughput sequencing technology is becoming increasingly popular in various sequencing projects. With different platforms, scientists are able to achieve millions billions of sequences within days. In the last two years, there are a lot of prokaryotic genomes being sequenced under these platforms. However, there are only 1,542 complete chromosomes available in NCBI GenBank (September 2011) since the first complete genome of Bacillus subtilis was published in 1997. The most difficult step in finishing a complete genome is closing all gaps among different contigs. In this thesis, a series of comprehensive simulation studies based on 1,542 complete chromosomes have been performed in search of a cost-effective way to achieve complete prokaryotic genomes. Solutions to both draft and complete genome sequencing were provided by computer simulation. Moreover, classification studies have been performed to identify special prokaryotic phyla/orders (if any) dissatisfying our proposed strategies.  Our results indicate that: 1) low coverage (6x-10x) pyrosequencing with long reads (400 bp) is sufficient to produce highly continuous and complete assemblies, presenting a tiny proportion of false gene duplication/loss. High quality draft genomes could be generated by this strategy; 2) Long repeats to some extent influence the assembly quality, especially for the genome coverage and contig number. The number of contigs and genome coverage rate are significantly correlated with the total size of repeat regions; 3) With a combination of one run of single-end reads (10x, 400bp read length) and one run of paired end reads (10x, 8kb library, 400bp read length), 90% of chromosome assemblies are less than 10 scaffolds and 95% of chromosome assemblies are less than 150 contigs. Most of the chromosomes can be assembled into high quality draft chromosomes (370kb contig N50 size, >99.99% single base accuracy and A comprehensive computer simulation study based on 1,542 chromosomes (all availabe prokaryotic complete chromosomes, September 2011) has been performed in this thesis. The sequencing strategies for both prokaryotic draft and complete genome proposed by the simulation study could facilitate the ongoing prokaryotic complete genome


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Product Details
  • ISBN-13: 9781361275825
  • Publisher: Open Dissertation Press
  • Publisher Imprint: Open Dissertation Press
  • Height: 279 mm
  • No of Pages: 284
  • Spine Width: 15 mm
  • Width: 216 mm
  • ISBN-10: 1361275820
  • Publisher Date: 26 Jan 2017
  • Binding: Paperback
  • Language: English
  • Series Title: English
  • Weight: 662 gr

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