Homology-Aware Phylogenomics at Gigabase Scales

Research output: Contribution to journalArticlepeer-review

7 Scopus citations


Obstacles to inferring species trees from whole genome data sets range from algorithmic and data management challenges to the wholesale discordance in evolutionary history found in different parts of a genome. Recent work that builds trees directly from genomes by parsing them into sets of small k-mer strings holds promise to streamline and simplify these efforts, but existing approaches do not account well for gene tree discordance. We describe a "seed and extend" protocol that finds nearly exact matching sets of orthologous k-mers and extends them to construct data sets that can properly account for genomic heterogeneity. Exploiting an efficient suffix array data structure, sets of whole genomes can be parsed and converted into phylogenetic data matrices rapidly, with contiguous blocks of k-mers from the same chromosome, gene, or scaffold concatenated as needed. Phylogenetic trees constructed from highly curated rice genome data and a diverse set of six other eukaryotic whole genome, transcriptome, and organellar genome data sets recovered trees nearly identical to published phylogenomic analyses, in a small fraction of the time, and requiring many fewer parameter choices. Our method's ability to retain local homology information was demonstrated by using it to characterize gene tree discordance across the rice genome, and by its robustness to the high rate of interchromosomal gene transfer found in several rice species.

Original languageEnglish (US)
Pages (from-to)590-603
Number of pages14
JournalSystematic biology
Issue number4
StatePublished - Jul 1 2017


  • Oryza
  • k-mer
  • lineage sorting
  • phylogenomics
  • suffix array

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


Dive into the research topics of 'Homology-Aware Phylogenomics at Gigabase Scales'. Together they form a unique fingerprint.

Cite this