Rearrangement phylogeny of genomes in contig form

There has been a trend in increasing the phylogenetic scope of genome sequencing while decreasing the quality of the published sequence for each genome. With reduced finishing effort, there is an increasing number of genomes being published in contig form. Rearrangement algorithms, including gene order-based phylogenetic tools, require whole genome data on gene order, segment order, or some other marker order. Items whose chromosomal location is unknown cannot be part of the input. The question we address here is, for gene order-based phylogenetic analysis, how can we use rearrangement algorithms to handle genomes available in contig form only? Our suggestion is to use the contigs directly in the rearrangement algorithms as if they were chromosomes, while making a number of corrections, e.g., we correct for the number of extra fusion/fission operations required to make contigs comparable to full assemblies. We model the relationship between contig number and genomic distance, and estimate the parameters of this model using insect genome data. With this model, we use distance matrix methods to reconstruct the phylogeny based on genomic distance and numbers of contigs. We compare this with methods to reconstruct ancestral gene orders using uncorrected contig data.