Quirke A M, Reen F Jerry, Claesson Marcus J, Boyd E Fidelma
Department of Microbiology, University College Cork, National University of Ireland, Cork, Ireland.
Bioinformatics. 2006 Apr 15;22(8):905-10. doi: 10.1093/bioinformatics/btl015. Epub 2006 Jan 27.
Genomic islands (GIs) are large chromosomal regions present in a subset of bacterial strains that increase the fitness of the organism under specific conditions. We compared the complete genome sequences of two Vibrio vulnificus strains YJ016 and CMCP6 and identified 14 regions (ranging in size from 14 to 117 kb), which had the characteristics of GIs. Bioinformatic analysis of these 14 GI regions identified the presence of phage-like integrase genes, aberrant GC content and genome signature (dinucleotide frequency) within each GI compared with the core genome indicating that these regions were acquired from an anomalous source. We examined the distribution of the nine GIs from strain YJ016 among 27 V. vulnificus isolates and found that most GIs were absent from the majority of these isolates. The chromosomal insertion sites of three GIs were adjacent to tRNA sites, which contained novel horizontally acquired DNA in all six available sequenced Vibrionaceae genomes.
Supplementary data are available at Bioinformatics online.
基因组岛（GIs）是存在于一部分细菌菌株中的大型染色体区域，可在特定条件下提高生物体的适应性。我们比较了两株创伤弧菌YJ016和CMCP6的全基因组序列，鉴定出14个区域（大小从14 kb到117 kb不等），这些区域具有基因组岛的特征。对这14个基因组岛区域的生物信息学分析表明，与核心基因组相比，每个基因组岛内存在噬菌体样整合酶基因、异常的GC含量和基因组特征（二核苷酸频率），表明这些区域是从异常来源获得的。我们检测了来自菌株YJ016的9个基因组岛在27株创伤弧菌分离株中的分布，发现大多数分离株中不存在大多数基因组岛。三个基因组岛的染色体插入位点与tRNA位点相邻，在所有六个可用的已测序弧菌科基因组中均含有新的水平获得的DNA。
补充数据可在《生物信息学》在线获取。
