Genomicus: Fast and Intuitive Comparative Genomics in Plant and Animal Genome

Translational and fundamental research both use comparative genomics as a powerful strategy to better understand genome function in an evolutionary context. Genomicus (http://www.genomicus.biologie.ens.fr/genomicus) is a database and a web server that integrates and synthetize comparative genome data in a fast and intuitive way while taking into account the maximum breadth of information available. Four main interfaces (“views”) are available: (i) PhyloView combines phylogenetic trees with comparisons of genomic loci across any number of genomes (ii) AlignView aligns of locus of interest against all other genomes to visualise its topological conservation (iii) MatrixView compares two genomes in a classical dotplot representation (iv) Karyoview visualise chromosome karyotypes “painted” with colours of another genome of interest. All four views are interconnected and benefit from many customizable features. More than 150 eukaryote genomes can be analysed, broken down in five groups following Ensembl and Ensembl Genomes: Vertebrates, Plants, Metazoa, Fungi, Protists. For the vertebrate and plant groups, ancestral gene orders provide a long-term chronological view of gene order evolution. In this tutorial we will show how to navigate in genome data (e.g. visualise and compare orthologous and paralogous genome segments), and how whole genome duplications, gene duplications, gain and loss, chromosomal rearrangements, synteny conservation at all scales and over any phylogenetic distances can be studied. Genomicus makes it easier to observe new patterns by exploring genomic data, and to answer questions by removing a large burden of data processing and transformation usually associated with comparative genomics.