inGeno--an integrated genome and ortholog viewer for improved genome to genome comparisons

Abstract

Background: Systematic genome comparisons are an important tool to reveal gene functions, pathogenic features, metabolic pathways and genome evolution in the era of post-genomics. Furthermore, such comparisons provide important clues for vaccines and drug development. Existing genome comparison software often lacks accurate information on orthologs, the function of similar genes identified and genome-wide reports and lists on specific functions. All these features and further analyses are provided here in the context of a modular software tool "inGeno" written in Java with Biojava subroutines.

Results: InGeno provides a user-friendly interactive visualization platform for sequence comparisons (comprehensive reciprocal protein--protein comparisons) between complete genome sequences and all associated annotations and features. The comparison data can be acquired from several different sequence analysis programs in flexible formats. Automatic dot-plot analysis includes output reduction, filtering, ortholog testing and linear regression, followed by smart clustering (local collinear blocks; LCBs) to reveal similar genome regions. Further, the system provides genome alignment and visualization editor, collinear relationships and strain-specific islands. Specific annotations and functions are parsed, recognized, clustered, logically concatenated and visualized and summarized in reports.

Conclusion: As shown in this study, inGeno can be applied to study and compare in particular prokaryotic genomes against each other (gram positive and negative as well as close and more distantly related species) and has been proven to be sensitive and accurate. This modular software is user-friendly and easily accommodates new routines to meet specific user-defined requirements.

Figure 1

Interactive graphical user interface for genome alignment. Genomes of Listeria monocytogenes (lower genome in the figure) and Listeria innocua (upper genome) are compared using inGeno. Orthologous genes in both genomes are colored with the same color. Linkage lines connect locus collinear blocks and indicate the degree of rearrangement between the genomes. The threshold can be adjusted by a slider in the lower-right corner of the control panel. Red blocks in each genome distinguish genes which are potential strain-specific and determined by a user-given threshold. In this comparison several strain-specific genome islands are detected, e.g., in the figure a red island beginning with lmo0200 is being investigated. It is part of the Lipi1 pathogenicity island. Clusters of green lines indicate genome rearrangement events, these can be caused e.g. by transposons. A large number of transposase genes are found and visualized in the L. monocytogenes genome.

Figure 2

Genome comparison between closely related strains. The comparison between two closely related E. coli K-12 strains (W3110 and MG1655) indicates these are only slightly different, except for a highlighted large inversion. The upper genome is W3110 [24], whereas the lower genome is MG1655 [23-25]. Using inGeno, a couple of strain-specific genes are readily seen, such as TnaB (annotated as low affinity tryptophan permease; b3709 in figure) and other genes (DcuC: b0621, GatA: b2094, RcsC: b2218), which lead to different metabolic capabilities, e.g., the utilization of tryptophan as carbon source may be impaired in W3110.

Figure 3

Strain-specific island – investigation of pathogenicity and metabolism. The top genome is E. coli O157 [25], the lower is E. coli K-12 strain MG1655 [23-25]. The selected region (ECs1272-1296 and ECs1299-1409) is one of the strain-specific islands that are potentially related to bacterial pathogenicity. ECs1282 and ECs1283 are identified by inGeno as hemagglutinin/hemolysin-like protein and hemolysin activator-related protein, respectively. An operon-like structure follows these two genes. InGeno reports these encode for a holo acyl-carrier protein, an oxoacyl-(acyl-carrier protein) reductase, a hydroxydecanoyl-(acyl-carrier protein) dehydratase, an acyl-carrier protein, an aminomethyl transferase and an oxoacyl-(acyl-carrier protein)-synthase. These enzymes and proteins add to the fatty acid metabolism, additional lipids or lipoproteins may be produced by O157 in contrast to MG1655. Moreover, a series of continuous genes encoding urease components are shown for 0157 (ECs1321-1327: UreA-G). The detailed information on these proteins is summarized in Table 1.