Phylogeny and Comparative Genomics: The Shifting Landscape in the Genomics Era

Abstract

In light of the age of genomics, a compilation of small-subunit rRNA-encoding genes (16S rRNA genes) from Rickettsiales is provided, with a phylogeny estimated from a subset of the sequences that spans the diversity of Rickettsiales. Robust phylogeny estimation based on whole-genome sequences supports the close relationship of Bartonellaceae with another lineage of facultative intracellular bacteria, Brucellaceae. The first genome sequence from the Anaplasmataceae also reveals reductive genome evolution, with a genome size of 1.3 Mb and 1,195 predicted open reading frames (ORFs). Significant reclassification of the species within the Anaplasmataceae was proposed based on data. Subsequent reevaluation of the trace file archives determined that the Wolbachia sequences discovered in D. mojavensis were an artifact; however, 2,291 novel Wolbachia sequences were found in another fly genome, Drosophila willistoni. This work underscores the utility of eukaryotic genomes for discovering Rickettsiales endosymbionts and potentially assembling partial to complete bacterial genomes from the eukaryotic reads. A robust phylogeny based on whole-genome sequences supports the current taxonomic delineations within the Anaplasmataceae and Rickettsiaceae, with monophyly of each of the six genera strongly supported. The differences between RefSeq and Pathosystems Resource Integration Center (PATRIC) annotation undoubtedly result in discrepancies in protein family clustering between this work and previous studies. Two mitochondrial small-subunit rRNA gene sequences were included in the phylogeny estimation, and this lineage branched after the Holosporaceae, but basal to the derived Rickettsiales. The diversity of the Rickettsiales highlighted in this chapter presents an exciting challenge for rickettsiology.