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Received Dec 13, 2017; Revised Feb 25, 2018; Accepted Mar 28, 2018
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1. Introduction
Tuberculosis (TB) is caused by Mycobacterium tuberculosis that most often affect the lungs. Today, TB is still an unsolved problem. According to the WHO, in Oct, 2017, fact sheet pointed out that the TB is one of the top 10 causes of death worldwide [1]. It spreads from person to person through the air. One person may be infected by TB when only inhaling a few of TB germs. So, many scientists studied the characteristics including codon usage pattern [2], promoter architecture of toxin-antitoxin systems [3], drug-resistance [4], molecular epidemiology [5], protein function and immunogenicity [6], and drugs for the treatment [7] of TB. Typically, Sheen et al. studied the multiple genomes of Mycobacterium tuberculosis and found out some specific novel genes and mutations associated with pyrazinamide resistance [8]. Sun et al. and Khrustalev et al. characterize the mutations in streptomycin-resistant Mycobacterium tuberculosis [9, 10]. Recently, bioinformatics tools are widely used for analyzing the TB [11].
One amino acid is often encoded by more than one codon because the genetic code is redundant. This phenomenon is also known as synonymous codon usage. Many factors may affect the codon usage in Mycobacterium tuberculosis, such as mutation pressure [12], gene length [13], and natural selection [14]. Most previous studies deal with the relatively smaller set of Mycobacterium tuberculosis isolates [15, 16] or the isolates from one area [17, 18]. In this paper, genetic diversity of Mycobacterium tuberculosis from 12 areas is compared and analyzed. So, the objectives of this study aim to deal with the following issues: