Rearrangement Phylogeny of Genomes in Contig Form

Abstract

There has been a trend in increasing phylogenetic coverage for genome sequencing while decreasing the sequencing coverage for each genome. With lower coverage, 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 can then reconstruct the phylogeny based on genomic distance and numbers of contigs.