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Genome-Wide Variation Analysis of Yersinia pestis

  • Chao Yang
  • Yujun Cui
Protocol
Part of the Springer Protocols Handbooks book series (SPH)

Abstract

Compared with traditional molecular techniques that target limited numbers of loci, a genome-wide analysis can provide the greatest resolution of genetic variation. Therefore, it has promoted advances in many fields, including population genetics, evolution, and molecular epidemiology. With the rapid development of the next-generation sequencing technology, the cost, manpower, and time required for whole-genome analyses have been reduced, and these analyses are now affordable to regular biological and medical laboratories. Therefore, a wider range of applications of genome-wide analyses is expected, and greater output should be generated in coming years. Here, we introduce the basic protocol for a genome-wide variation analysis of Yersinia pestis, the plague pathogen, which has a genome of 4.6 Mb, based on sequencing data generated with a high-throughput short-read sequencing platform. The protocol only involves the in silico processes, including genome assembly and annotation, variation detection, and phylogeny reconstruction.

Key words

Yersinia pestis Genome-wide analysis Sequencing Phylogenetic analysis 

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Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Chao Yang
    • 1
  • Yujun Cui
    • 1
  1. 1.Beijing Institute of Microbiology and EpidemiologyBeijingChina

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