Comprehensive study of instable regions in pseudomonas aeruginosa

doi:10.1007/978-3-319-56154-7_4

科研成果详情

题名	Comprehensive study of instable regions in pseudomonas aeruginosa
作者	Wang，Dan; Li，Jingyu; Wang，Lusheng
发表日期	2017
会议录名称	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
ISSN	0302-9743
卷号	10209 LNCS
页码	30-40
摘要	Pseudomonas aeruginosa is recognized for its intrinsically advanced antibiotic resistance mechanisms. Dispensable genome which includes sequences shared by a subset of strains in a species is important to the study of a species’ evolution, antibiotic resistance and infectious potential. In this paper, by using a multiple sequence aligner, we segmented the genomes of 25 Pseudomonas aeruginosa strains into core blocks (shared by all the 25 genomes) and dispensable blocks (shared by a subset of the 25 genomes). In this paper, we use the term instable blocks to refer to dispensable blocks since blocks shared by a subset of the 25 genomes may be vitally important. We then built 25 scaffolds which consisted of core and instable blocks sorted by blocks’ starting positions in the chromosomes for each of the 25 strains. In these scaffolds, consecutive instable blocks formed instable regions. We conducted a comprehensive study on these instable regions and found three characteristics of instable regions: instable regions were short, site specific and varied in different strains. We then studied three DNA elements which may contribute to the variation of instable regions: directed repeats (DRs), transposons and integrons. Past studies have shown that sequences flanked by a pair of DRs can be deleted from their host chromosomes or be inserted into new host chromosomes. We developed a pipeline to search for DR pairs on the flank of every instable sequence and found 27 pairs of DRs existing in the instable regions between 21 distinct pairs of core blocks. We also found that in the average, 14% and 12% of instable regions in the 25 scaffolds covered transposase genes and integrase genes, respectively. Our pipeline is at: https://github.com/shever/repeat finding. Supplemental Tables available at: https://github.com/shever/repeat finding/blob/master/Supplemental Tables.xlsx.
关键词	Deletion Directed repeats Dispensable genome Homologous recombination Insertion Integrase Pan-genome Pseudomonas aeruginosa Transposase
DOI	10.1007/978-3-319-56154-7_4
URL	查看来源
语种	英语English
Scopus入藏号	2-s2.0-85018664839
引用统计
文献类型	会议论文
条目标识符	https://repository.uic.edu.cn/handle/39GCC9TT/13129
专题	个人在本单位外知识产出
通讯作者	Wang，Lusheng
作者单位	Department of Computer Science,City University of Hong Kong,Hong Kong
推荐引用方式 GB/T 7714	Wang，Dan,Li，Jingyu,Wang，Lusheng. Comprehensive study of instable regions in pseudomonas aeruginosa[C], 2017: 30-40.