Abstract
BackgroundThe increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies—a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence alignment in reasonable time.ResultsWe present a new whole-genome based approach to infer phylogenies that is alignment- and reference-free. In contrast to other methods, it does not rely on pairwise comparisons to determine distances to infer edges in a tree. Instead, a colored de Bruijn graph is constructed, and information on common subsequences is extracted to infer phylogenetic splits.ConclusionsThe introduced new methodology for large-scale phylogenomics shows high potential. Application to different datasets confirms robustness of the approach. A comparison to other state-of-the-art whole-genome based methods indicates comparable or higher accuracy and efficiency.
Highlights
A common task in comparative genomics is the reconstruction of the evolutionary relationships of species or other taxonomic entities, their phylogeny
We proposed a new k-mer based method for phylogenetic inference that neither relies on alignments to a reference sequence nor on pairwise or multiple alignments to infer markers
Prevailing whole-genome approaches perform pairwise comparisons to determine a quadratic number of distances to infer a linear number of tree edges
Summary
A common task in comparative genomics is the reconstruction of the evolutionary relationships of species or other taxonomic entities, their phylogeny. The sheer number of genomes to be analyzed is still posing limits in large-scale scenarios as almost all whole-genome approaches are based on a pairwise comparison of some characteristics of the genomes (e.g. occurrences or frequencies of k-mers or other patterns) to define distances which are used to reconstruct a tree (e.g. by using neighbor joining [7]). This means, for n genomes, O(n2) comparisons are performed in order to infer O(n) edges. If either A or B is of cardinality one, a split is called trivial
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