Identification of Horizontally-transferred Genomic Islands and Genome Segmentation Points by Using the GC Profile Method

Abstract

The nucleotide composition of genomes undergoes dramatic variations among all three kingdoms of life. GC content, an important characteristic for a genome, is related to many important functions, and therefore GC content and its distribution are routinely reported for sequenced genomes. Traditionally, GC content distribution is assessed by computing GC contents in windows that slide along the genome. Disadvantages of this routinely used window-based method include low resolution and low sensitivity. Additionally, different window sizes result in different GC content distribution patterns within the same genome. We proposed a windowless method, the GC profile, for displaying GC content variations across the genome. Compared to the window-based method, the GC profile has the following advantages: 1) higher sensitivity, because of variation-amplifying procedures; 2) higher resolution, because boundaries between domains can be determined at one single base pair; 3) uniqueness, because the GC profile is unique for a given genome and 4) the capacity to show both global and regional GC content distributions. These characteristics are useful in identifying horizontally-transferred genomic islands and homogenous GC-content domains. Here, we review the applications of the GC profile in identifying genomic islands and genome segmentation points, and in serving as a platform to integrate with other algorithms for genome analysis. A web server generating GC profiles and implementing relevant genome segmentation algorithms is available at: www.zcurve.net.

Keywords: GC profile; Genome segmentation.; Genomic island.

Fig. (1)

Identification of horizontally-transferred genomic islands by using GC profiles. A) GC profiles and B) the GC content distribution based on 20Kb sliding windows for the genome of Rhodopseudomonas palustris. GC profiles of C) Corynebacterium efficiens, D) Corynebacterium glutamicum and E) Vibrio vulnificus CMCP6. F) A typical structure of the genomic island. The schematic representation of CGGI-1, a genomic island in C. glutamicum. Figure not drawn to scale. Segments of GC profiles for genomic island are shown in red, and those for host gnomes are shown in green.

Fig. (2)

Isochore structures revealed by GC profiles. GC profiles (upper panel) and GC content distribution based on 100 Kb sliding windows (lower panel) for A) human chromosome 7, B) dog chromosome 22, C) horse chromosome 2 and D) finch chromosome 14.

Fig. (3)

GC profiles for genomes of the Klebsiella pneumoniae strains A) HS11286, B) NTUH-K2044 and C) KCTC 2242. The GC profile is integrated into MobilomeFINDER, which was used to identify horizontally-transferred genes (red). The tRNA /tmRNA genes are identified as insertion sites (blue stars).

Fig. (4)

Comparative analysis of GC profiles for chromosomes 21, 22, and 31 for human, chimpanzee and dog, respectively. GC profiles for A) human chromosome 21, B) chimpanzee chromosome 22, C) dog chromosome 31. GC content distributions for human chromosome 21 based on sliding windows of D) 1 Kb, E) 20 Kb and F) 200 Kb. GC content changes are masked by high degree of variations when the window size is small, and GC content changes are averaged when the window size is large.