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Abstract：
BACKGROUND: Pseudomonas aeruginosa is a common bacterium which is recognized for its association with hospital-acquired infections and its advanced antibiotic resistance mechanisms. Tuberculosis, one of the major causes of mortality, is initiated by the deposition of Mycobacterium tuberculosis. Accessory sequences shared by a subset of strains of a species play an important role in a species\' evolution, antibiotic resistance and infectious potential.
RESULTS: Here, with a multiple sequence aligner, we segmented 25 P. aeruginosa genomes and 28 M. tuberculosis genomes into core blocks (include sequences shared by all the input genomes) and dispensable blocks (include sequences shared by a subset of the input genomes), respectively. For each input genome, we then constructed a scaffold consisting of its core and dispensable blocks sorted by blocks\' locations on the chromosomes. Consecutive dispensable blocks on these scaffold formed instable regions. After a comprehensive study of these instable regions, three characteristics of instable regions are summarized: instable regions were short, site specific and varied in different strains. Three DNA elements (directed repeats (DRs), transposons and integrons) were then studied to see whether these DNA elements are associated with the variation of instable regions. A pipeline was developed to search for DR pairs on the flank of every instable sequence. 27 DR pairs in P. aeruginosa strains and 6 pairs in M. tuberculosis strains were found to exist in the instable regions. On the average, 14% and 12% of instable regions in P. aeruginosa strains covered transposase genes and integrase genes, respectively. In M. tuberculosis strains, an average of 43% and 8% of instable regions contain transposase genes and integrase genes, respectively.
CONCLUSIONS: Instable regions were short, site specific and varied in different strains for both P. aeruginosa and M. tuberculosis. Our experimental results showed that DRs, transposons and integrons may be associated with variation of instable regions.
RESULTS: Here, with a multiple sequence aligner, we segmented 25 P. aeruginosa genomes and 28 M. tuberculosis genomes into core blocks (include sequences shared by all the input genomes) and dispensable blocks (include sequences shared by a subset of the input genomes), respectively. For each input genome, we then constructed a scaffold consisting of its core and dispensable blocks sorted by blocks\' locations on the chromosomes. Consecutive dispensable blocks on these scaffold formed instable regions. After a comprehensive study of these instable regions, three characteristics of instable regions are summarized: instable regions were short, site specific and varied in different strains. Three DNA elements (directed repeats (DRs), transposons and integrons) were then studied to see whether these DNA elements are associated with the variation of instable regions. A pipeline was developed to search for DR pairs on the flank of every instable sequence. 27 DR pairs in P. aeruginosa strains and 6 pairs in M. tuberculosis strains were found to exist in the instable regions. On the average, 14% and 12% of instable regions in P. aeruginosa strains covered transposase genes and integrase genes, respectively. In M. tuberculosis strains, an average of 43% and 8% of instable regions contain transposase genes and integrase genes, respectively.
CONCLUSIONS: Instable regions were short, site specific and varied in different strains for both P. aeruginosa and M. tuberculosis. Our experimental results showed that DRs, transposons and integrons may be associated with variation of instable regions.
摘要：
背景：铜绿假单胞菌是一种常见细菌，因其与医院获得性感染及其先进的抗生素耐药机制相关而被公认。结核病,死亡的主要原因之一，是由结核分枝杆菌的沉积引发的。一个物种的菌株的子集共有的附属序列在物种进化中起着重要的作用，抗生素耐药性和感染潜力。
结果：这里，使用多序列比对器，我们将25个铜绿假单胞菌基因组和28个结核分枝杆菌基因组分为核心区块（包括所有输入基因组共享的序列）和非必需区块（包括输入基因组子集共享的序列），分别。对于每个输入基因组，然后，我们构建了一个支架，该支架由其核心和可有可无的块组成，这些块按染色体上的块位置排序。这些支架上的连续可分配块形成不稳定区域。在对这些不稳定区域进行全面研究后，总结了不稳定区域的三个特征:不稳定区域短，不同菌株的位点特异性和多样性。三个DNA元件（定向重复（DR），转座子和整合子）然后进行研究，以查看这些DNA元素是否与不稳定区域的变异有关。开发了一个管道来搜索每个不稳定序列侧翼的DR对。发现铜绿假单胞菌菌株中存在27对DR对，结核分枝杆菌菌株中存在6对DR。平均而言,14％和12％的铜绿假单胞菌菌株的不稳定区域覆盖转座酶基因和整合酶基因，分别。在结核分枝杆菌菌株中，平均43%和8%的不稳定区域含有转座酶基因和整合酶基因，分别。
结论：不稳定区域短，铜绿假单胞菌和结核分枝杆菌的位点特异性和不同菌株。我们的实验结果表明，DR，转座子和整合子可能与不稳定区域的变化有关。
结果：这里，使用多序列比对器，我们将25个铜绿假单胞菌基因组和28个结核分枝杆菌基因组分为核心区块（包括所有输入基因组共享的序列）和非必需区块（包括输入基因组子集共享的序列），分别。对于每个输入基因组，然后，我们构建了一个支架，该支架由其核心和可有可无的块组成，这些块按染色体上的块位置排序。这些支架上的连续可分配块形成不稳定区域。在对这些不稳定区域进行全面研究后，总结了不稳定区域的三个特征:不稳定区域短，不同菌株的位点特异性和多样性。三个DNA元件（定向重复（DR），转座子和整合子）然后进行研究，以查看这些DNA元素是否与不稳定区域的变异有关。开发了一个管道来搜索每个不稳定序列侧翼的DR对。发现铜绿假单胞菌菌株中存在27对DR对，结核分枝杆菌菌株中存在6对DR。平均而言,14％和12％的铜绿假单胞菌菌株的不稳定区域覆盖转座酶基因和整合酶基因，分别。在结核分枝杆菌菌株中，平均43%和8%的不稳定区域含有转座酶基因和整合酶基因，分别。
结论：不稳定区域短，铜绿假单胞菌和结核分枝杆菌的位点特异性和不同菌株。我们的实验结果表明，DR，转座子和整合子可能与不稳定区域的变化有关。
