Paul Higgs - Research Topics

Evolution of Mitochondrial Genomes

The OGRe Database for comparative analysis of Mitochondrial Genomes

OGRe stands for Organelle Genome Retrieval. It is principally the work of Wenli Jia and Bin Tang at McMaster and Daniel Jameson at the University of Manchester. You can access the database online here: ogre.mcmaster.ca

OGRe is a relational database that contains over 1000 completely sequenced metazoan mitochondrial genome sequences. Using the database you can:

Download sequences for any combination of selected species and selected genes. Species are classified according to a hierarchical taxonomy to aid in selection of groups of interest.
Download codon usage information for genes on mitochondrial genomes.
Produce gene order diagrams for any combination of species and visualize changes in gene order between pairs of species.

If you use information from OGRe, please cite:

Jameson, D., Gibson, A.P., Hudelot, C. & Higgs, P.G. (2003) OGRe: a relational database for comparative analysis of mitochondrial genomes. Nucl. Acids. Res. 31, 202-206.

The database now forms a resource for research on the evolution of codon usage, context-dependent mutation and genome rearrangements on mitochondrial genomes. See:

Jia WL, Higgs PG (2007) Codon usage in mitochondrial genomes: distinguishing context-depenedent mutation from tranlsational selection. Mol. Biol. Evol. (in press).

Xu, W., Jameson, D., Tang, B., Higgs, P.G. (2006) The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes. J. Mol. Evol. 63, 375-392.

Urbina, D., Tang, B. & Higgs, P.G. (2006) The response of amino acid frequencies to directional mutational pressure in mitochondrial genome sequences is related to the physical properties of the amino acids and to the structure of the genetic code. J. Mol. Evol. 62, 340-361.

Pictures Generated using OGRe

Comparison of human, sea urchin and nematode mitochondrial genomes. Protein genes are in green, rRNA genes in blue and tRNA genes in red. Boxes below the line represent genes on the forward strand (left to right) and boxes above the line represent genes on the reverse strand (right to left). All genes are on the same strand in the nematode. With the exception of the ATP8 gene, which is missing in the nematode, all three species have the same set of genes. The order differs greatly between the species, however.

An example of a pairwise genome comparison produced by OGRe where tRNA genes are included. The blocks of genes coloured red and yellow have exchanged positions between human and chicken but all genes remain on the same strand.

An example of a pairwise genome comparison produced by OGRe where tRNA genes are excluded. There are apparently three separate inversions of blocks of genes between human and locust (shown in red, yellow and blue). The grey and green gene blocks are unchanged.