Single-Copy Gene Clusters Co-Occurring in Cacao and Other Plant Genomes Suggest Mechanism of Gene Reduction after Genome Duplication

Genome duplication has been documented for all plants and yet there is a significant number of single-copy genes in plants with fully sequenced genomes. By looking at conserved clusters of genes across a number of species, we investigate possible mechanisms for gene reduction to generate single copy genes.

We employ a pattern discovery framework to locate conserved gene clusters occurring in the Theobroma cacao Matina 1-6 genome and in several other plant genomes (Arabidopsis thaliana, Glycine max, Populus trichocarpa, Prunus persica, Utricularia gibba, and Vitis vinifera). With the recent availability of these whole genome sequences and gene models, we are able to focus on conserved clusters containing some single-copy genes, or only single-copy genes. We present examples of these clusters and discuss the potential targeted reduction of certain genes to single-copy status following whole genome duplications.

For the mathematical model and references for the pattern discovery framework, see http://researcher.ibm.com/project/2344