Gene synteny among cacao and other plants

Clusters of conserved gene order among genomes can be viewed as evidence of their shared evolutionary history and is often indicative of important functional roles for those genes.  Of particular interest are gene orders comprised of single-copy genes, due to their importance in phylogenetic and comparative analysis.

We compare T. cacao gene order with that of arabidopsis, grape, peach and others, using data from a sequence similarity -based definition of orthology between the genes in each species. By assigning the same label to each gene that is part of a homology group (connected component in a graph with edges between sequence-similar genes) we are able to extract clusters of genes with the same label set in T. cacao and in a second species. These localized clusters have the same composition of gene labels, but not necessarily in the same order. A combinatorial approach is employed to compute the statistical significance of the observed cluster configurations between two species.