Comparative genomics study the evolution of gene organization, which in the past years was by the fast growing number of full genome sequences available in public repositories. Most of the available bioinformatics tools for visualization and comparison of genomes are restricted to two or three genomes at a time, which is a significant limitation in the field of comparative genomics. Recently (this month) a new phylogenetic software was announced – Genomicus. It provides functionality of a synteny browser, which can represent and compare unlimited numbers of genomes in a broad phylogenetic view. The tool provides reconstructed ancestral gene organization, in a way that facilitates the interpretation of the analysis data.
The comparative genomics aims to:
- to identify conserved functional regions
- to document differences among these functional sequences as a first step to understand broader biological differences (metabolic, developmental, etc.) between organisms
- to outline the evolutionary events that have interrupted the gene colinearity between the genomes of two species since their closest common ancestry dna.
Data integrated in Genomicus
Genomicus is based on already integrated and publicly available from the Ensembl (Ensembl Phylogenetic Trees). Genomicus utilize just two main types of information from Ensembl:
- gene positions in the respective genomes
- phylogenetic relationships (orthology, paralogy) between genes.
Genomicus then edits Ensembl phylogenetic trees in the following steps:
- Selection of duplication nodes below a defined threshold, that is optimized to increase the synteny between extant genomes.
- Integration of information from Boreoeutheria, Euarchontoglires and Atlantogenata ancestral nodes in existing trees of placental mammals
- Addition of genomic information from some extant species that are not currently referenced in Ensembl (Branchiostoma floridae, Nematostella vectensis and Oikopleura dioica), together with their respective ancestral nodes.
For each of the integrated genomes, best reciprocal protein BLAST comparisons are performed.
Functionality
Genomicus offers two types of data visualization
- PhyloView – a phylogenetic tree visualization, which shows the chosen reference gene in the centre of the display with 15 neighbouring genes on both side. It displays information about as well as orthologs and paralogs of the query gene in their own respective genomic regions. If these neighbouring genes are orthologs or paralogs of genes in the reference species, they are displayed with matching colours. When an analog of the reference gene is duplicated (shown as a red square), the originating specie may appear twice in the screen.
- AlignView – provides an alignments between the genes contained within the genomic region of the reference gene and all their respective orthologs in other species.
In both views, the phylogenetic tree can be edited (expanding, collapsing, hiding, showing chosen nodes) to clarify the view.
Genomicus also displays orthologous conserved non-coding elements at three levels of conservation. In a ddition a link-out functionality to other browsers like Ensembl, UCSC and NCBI is provided.
System Implementation
Genomicus is a web based application, developed with Perl scripts and modules, executed with mod_perl on an Apache2 server. The data is persisted in a MySQL database. The visualization is based on embed inline-SVG drawings in XHTML, in which the JavaScript usage is limited to an information panel retrieved with AJAX calls. The browsers are required to support the Google Chrome Frame extension.
Availability
Genomicus is freely available for online use at http://www.dyogen.ens.fr/genomicus.
The data can be downloaded at ftp://ftp.biologie.ens.fr/pub/dyogen/genomicus.
