Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics.

Alexandra Louis,Nga Thi Thuy Nguyen,Hugues Roest Crollius,Matthieu Muffato

doi:10.1093/nar/gku1112

Abstract

The Genomicus web server (http://www.genomicus.biologie.ens.fr/genomicus) is a visualization tool allowing comparative genomics in four different phyla (Vertebrate, Fungi, Metazoan and Plants). It provides access to genomic information from extant species, as well as ancestral gene content and gene order for vertebrates and flowering plants. Here we present the new features available for vertebrate genome with a focus on new graphical tools. The interface to enter the database has been improved, two pairwise genome comparison tools are now available (KaryoView and MatrixView) and the multiple genome comparison tools (PhyloView and AlignView) propose three new kinds of representation and a more intuitive menu. These new developments have been implemented for Genomicus portal dedicated to vertebrates. This allows the analysis of 68 extant animal genomes, as well as 58 ancestral reconstructed genomes. The Genomicus server also provides access to ancestral gene orders, to facilitate evolutionary and comparative genomics studies, as well as computationally predicted regulatory interactions, thanks to the representation of conserved non-coding elements with their putative gene targets.

Highlights

The rise of high-throughput DNA sequencing has revolutionized the field of genomics by creating an abundance of genome information in all domains of life
This volume and diversity of data enables ever more powerful evolutionary studies aimed at understanding past genomic events, and generally, to reconstruct the History of life, including the genomic characteristics of the common ancestors of extant species
Conserved non-coding elements (CNEs) and their potential target genes are available in Genomicus

Summary

Introduction

The rise of high-throughput DNA sequencing has revolutionized the field of genomics by creating an abundance of genome information in all domains of life. The inference of the ancestral gene order is deduced from pairwise genome comparisons of all the pairs of extant genomes whose evolutionary path includes the ancestor. The human-dog comparison is used by AGORA to reconstruct the gene order of their last common ancestor (Boreoeutheria), and other ancestral species on the evolutionary path such as Primates, Hominidae, Carnivora and Canidae.

Results

Conclusion