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Phylogenetic tree inference from local gene content

Galina Glazko, Michael Gensheimer, Arcady Mushegian
doi: https://doi.org/10.1101/017699
Galina Glazko
1Stowers Institute for Medical Research, 1000 E 50th St., Kansas City MO 64110
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Michael Gensheimer
1Stowers Institute for Medical Research, 1000 E 50th St., Kansas City MO 64110
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Arcady Mushegian
1Stowers Institute for Medical Research, 1000 E 50th St., Kansas City MO 64110
2Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS 66160, USA
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  • For correspondence: mushegian2@gmail.com
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Abstract

Background Complete genome sequences provide many new characters suitable for studying phylogenetic relationships. The limitations of the single sequence-based phylogenetic reconstruction prompted the efforts to build trees based on genome-wide properties, such as the fraction of shared orthologous genes or conservation of adjoining gene pairs. Gene content-based phylogenies, however, have their own biases: most notably, differential losses and horizontal transfers of genes interfere with phylogenetic signal, each in their own way, and special measures need to be taken to eliminate these types of noise.

Results We expand the repertoire of genome-wide traits available for phylogeny building, by developing a practical approach for measuring local gene conservation in two genomes. We counted the number of orthologous genes shared by chromosomal neighborhoods (“bins”), and built the phylogeny of 63 prokaryotic genomes on this basis. The tree correctly resolved all well-established clades, and also suggested the monophily of firmicutes, which tend to be split in other genome-based trees.

Conclusions Our measure of local gene order conservation extracts strong phylogenetic signal. This new measure appears to be substantially resistant to the observed instances of gene loss and horizontal transfer, two evolutionary forces which can cause systematic biases in the genome-based phylogenies.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 08, 2015.
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Phylogenetic tree inference from local gene content
Galina Glazko, Michael Gensheimer, Arcady Mushegian
bioRxiv 017699; doi: https://doi.org/10.1101/017699
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Phylogenetic tree inference from local gene content
Galina Glazko, Michael Gensheimer, Arcady Mushegian
bioRxiv 017699; doi: https://doi.org/10.1101/017699

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