A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I
A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I
复制标题
DOI：
10.1093/bioinformatics/btg453
复制
发表时间：
2004-03-22
期刊：
影响因子：
5.8
通讯作者：
Zhang, CT
中科院分区：
文献类型：
--
作者：
Zhang, R;Zhang, CT
动机：一些基因组岛包含水平转移的基因，这些基因在改变生物体的基因型和表型中起着关键作用，水平基因转移已被认为是细菌进化过程中的普遍事件。提出了一种显示基因组GC含量分布的无窗口方法，即累积GC谱，用于识别基因组中具有完整基因组序列的基因组岛。提出了两个新的指标来评估基因组岛的密码子使用偏差和氨基酸使用偏差。结果：在谷氨酸棒状杆菌基因组中鉴定出一个211 kb的基因组岛（CGGI-1），在创伤弧菌CMCP6 1号染色体基因组中鉴定出三个长度分别为167、40和33 kb的基因组岛VVGI-1、VVGI-2和VVGI-3。CGGI-1两侧有两个类似于500 bp的直接重复序列，并利用一个缬氨酸trna作为整合位点。对于VVGI-1和VVGI-2，每个在5′连接处都有一个整合酶基因。与其他基因组相比，所有已鉴定的基因组岛都显示出不同寻常的GC含量、密码子使用和氨基酸使用。此外，研究发现基因组岛在GC含量变化方面具有相当的同质性。提出了一个量化基因组岛GC含量均匀性的指标h，结果表明，在所分析的所有基因组岛中，h都小于0.1。累积GC谱，以及评估密码子使用偏倚、氨基酸使用偏倚和基因组岛均匀性的各种指标，将对其他基因组的分析有用。
Motivation: Some genomic islands contain horizontally transferred genes, which play critical roles in altering the genotypes and phenotypes of organisms, and horizontal gene transfer has been recognized as a universal event throughout bacterial evolution. A windowless method to display the distribution of genomic GC content, the cumulative GC profile, is proposed to identify genomic islands in genomes whose complete genome sequences are available. Two new indices are proposed to assess the codon usage bias and amino acid usage bias in genomic islands.Results: A 211 kb genomic island (CGGI-1) has been identified in the genome of Corynebacterium glutamicum, and three genomic islands VVGI-1, VVGI-2 and VVGI-3, with lengths 167, 40 and 33 kb, respectively, have been identified in the genome of Vibrio vulnificus CMCP6 chromosome I. The CGGI-1 is flanked by two similar to500 bp direct repeats, and utilizes a Val-tRNA as the integration site. For the VVGI-1 and VVGI-2, each has an integrase gene at 5' junction. All the identified genomic islands show unusual GC content, codon usage and amino acid usage, compared with the rest of the genomes. In addition, it is found that genomic islands are fairly homogenous in terms of GC content variation. An index, h, to quantify the homogeneity of GC content for genomic islands is proposed, and it is shown that h is less than 0.1 for all the genomic islands analyzed. The cumulative GC profile, as well as various indices to assess the codon usage bias, amino acid usage bias and homogeneity of the genomic islands, will be useful in the analysis of other genomes.